"DNA Res"[Journal] - Search Results

Year	Number of Results
1994	37
1995	41
1996	53
1997	55
1998	50
1999	54
2000	47
2001	31
2002	29
2003	28
2004	38
2005	37
2006	24
2007	26
2008	38
2009	32
2010	35
2011	49
2012	46
2013	68
2014	66
2015	50
2016	51
2017	58
2018	56
2019	42
2020	26
2021	32
2022	41
2023	37
2024	43
2025	33
2026	8

1

AlleleMiner: a long-read pipeline for gene-wise de novo allele phasing and variant detection in diploid citrus cultivars.

Kiryu Y, Kawahara Y, Endo T, Horiike T, Shirasawa K, Isobe S, Shimada T, Fujii H. Kiryu Y, et al. DNA Res. 2026 Mar 3;33(2):dsag004. doi: 10.1093/dnares/dsag004. DNA Res. 2026. PMID: 41773350 Free PMC article.

2

Silver chimaera genome highlights lineage-specific sex chromosome and opsin gene evolution in holocephalans.

Teramura A, Kadota M, Hirase S, Kuraku S, Kikuchi K. Teramura A, et al. DNA Res. 2026 Mar 3;33(2):dsag003. doi: 10.1093/dnares/dsag003. DNA Res. 2026. PMID: 41684233 Free PMC article.

3

Chromosome-level genome assembly of the Gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies.

Aoyagi YB, Shimada R, Hirakawa H, Toyoda A, Toh H, Isobe S, Tajima N, Shirasawa K, Horiike T, Fujii H, Fujiwara T, Bamba M, Nakatsuka T, Tominaga A. Aoyagi YB, et al. DNA Res. 2026 Jan 9;33(1):dsag002. doi: 10.1093/dnares/dsag002. DNA Res. 2026. PMID: 41640233 Free PMC article.

4

Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies.

Shirasawa K, Yoshitake K, Kondo H, Kikuchi S, Koiwai K, Fujii S. Shirasawa K, et al. DNA Res. 2026 Jan 9;33(1):dsag001. doi: 10.1093/dnares/dsag001. DNA Res. 2026. PMID: 41508794 Free PMC article.

5

Giant linear plasmids in Mycobacterium avium harbour a tRNA array unit.

Yano H, Arikawa K, Ikeda H, Nonoyama S, Maruyama F, Kitada S, Kida H, Ato M, Iwamoto T, Nishiuchi Y. Yano H, et al. DNA Res. 2026 Jan 9;33(1):dsaf039. doi: 10.1093/dnares/dsaf039. DNA Res. 2026. PMID: 41482713 Free PMC article.

6

Whole genome analysis of toxic Papilionidae butterflies utilizing aristolochic acid, Pachliopta aristolochiae, and Byasa alcinous.

Komata S, Kajitani R, Yamabe T, Kitamura T, Toyoda A, Kojima T, Itoh T, Fujiwara H. Komata S, et al. DNA Res. 2026 Jan 9;33(1):dsaf038. doi: 10.1093/dnares/dsaf038. DNA Res. 2026. PMID: 41424036 Free PMC article.

7

The genome of Pleurosigma provides insights into the evolutionary adaptations of pelagic diatoms.

Jian J, Chen C, Fang X, Workman CT, Ostenfeld Larsen T, Li Y, Sonnenschein EC. Jian J, et al. DNA Res. 2026 Jan 9;33(1):dsaf037. doi: 10.1093/dnares/dsaf037. DNA Res. 2026. PMID: 41388796 Free PMC article.

8

The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity.

Ge F, Guo Y, Xu L, Low WY, Ma H, Li Q, Wang Z, Zhu B, Xu L, Gao X, Zhang L, Gao H, Li J, Chen Y. Ge F, et al. DNA Res. 2026 Jan 9;33(1):dsaf034. doi: 10.1093/dnares/dsaf034. DNA Res. 2026. PMID: 41311030 Free PMC article.

9

Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales.

Hensen N, Hiltunen Thorén M, Johannesson H. Hensen N, et al. DNA Res. 2025 Dec 1;32(6):dsaf036. doi: 10.1093/dnares/dsaf036. DNA Res. 2025. PMID: 41327873 Free PMC article.

10

Nuclear genome sequencing reveals the highly intron-rich architecture of the chlorarachniophyte alga Amorphochlora amoebiformis.

Aoki D, Saiki H, Yamamoto K, Suzuki S, Hirakawa Y. Aoki D, et al. DNA Res. 2025 Dec 1;32(6):dsaf035. doi: 10.1093/dnares/dsaf035. DNA Res. 2025. PMID: 41311095 Free PMC article.

11

Whole-genome sequencing of wild and ancestral Dura provides insight into the untapped genomic information of undomesticated oil palm (Elaeis guineensis Jacq.).

Aditama R, Siregar HA, Tanjung ZA, Dinarti D, Ardie SW, Suwarno WB, Suprianto E, Utomo C, Liwang T, Sudarsono S. Aditama R, et al. DNA Res. 2025 Dec 1;32(6):dsaf033. doi: 10.1093/dnares/dsaf033. DNA Res. 2025. PMID: 41268641 Free PMC article.

12

Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.

Kifushi M, Nishikawa Y, Hosokawa M, Anai T, Takeyama H. Kifushi M, et al. DNA Res. 2025 Dec 1;32(6):dsaf032. doi: 10.1093/dnares/dsaf032. DNA Res. 2025. PMID: 41206461 Free PMC article.

13

Chromosome-scale genomes of two wild flowering cherries (Cerasus itosakura and Cerasus jamasakura) provide insights into structural evolution in Cerasus.

Fujiwara K, Toyoda A, Katsuki T, Sato Y, Biswa BB, Kishida T, Tsuruta M, Nakamura Y, Mochizuki T, Kimura N, Kawamoto S, Ohta T, Nonomura KI, Niki H, Yano H, Umehara K, Suzuki C, Koide T. Fujiwara K, et al. DNA Res. 2025 Dec 1;32(6):dsaf031. doi: 10.1093/dnares/dsaf031. DNA Res. 2025. PMID: 41163577 Free PMC article.

14

Life inside a bag: multiomics insights into the bagworm species Eumeta crameri.

Chakraborty A, Mahajan S, Prasoodanan P K V, Khamkar AS, Sharma VK. Chakraborty A, et al. DNA Res. 2025 Dec 1;32(6):dsaf029. doi: 10.1093/dnares/dsaf029. DNA Res. 2025. PMID: 41132005 Free PMC article.

15

MedakaBase as a unified genomic resource platform for medaka fish biology.

Morikami K, Tanizawa Y, Yagura M, Sakamoto M, Kawamoto S, Nakamura Y, Yamaguchi K, Shigenobu S, Naruse K, Ansai S, Kuraku S. Morikami K, et al. DNA Res. 2025 Dec 1;32(6):dsaf030. doi: 10.1093/dnares/dsaf030. DNA Res. 2025. PMID: 41122912 Free PMC article.

16

Genome assembly and insights into globally invasive Red-vented Bulbul (Pycnonotus cafer).

Puthumana MA, Bisht MS, Singh M, Sharma VK. Puthumana MA, et al. DNA Res. 2025 Dec 1;32(6):dsaf027. doi: 10.1093/dnares/dsaf027. DNA Res. 2025. PMID: 41063535 Free PMC article.

17

Full-length hybrid transcriptome of the olfactory rosette in Senegalese sole (Solea senegalensis): an essential genomic resource for improving reproduction on farms.

Torres-Sabino D, Blanco-Hortas A, Villamayor PR, Rasines I, Martín I, Bouza C, Robledo D, Martínez P. Torres-Sabino D, et al. DNA Res. 2025 Dec 1;32(6):dsaf028. doi: 10.1093/dnares/dsaf028. DNA Res. 2025. PMID: 41055041 Free PMC article.

18

Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.

Yoshida S, Uchiyama I, Fukuyo M, Kato M, Rao DN, Konno M, Fujiwara SI, Azuma T, Kobayashi I, Kishino H. Yoshida S, et al. DNA Res. 2025 Dec 1;32(6):dsaf025. doi: 10.1093/dnares/dsaf025. DNA Res. 2025. PMID: 40971938 Free PMC article.

19

Localization of the origin of transfer for Salmonella genomic island 4 from Salmonella enterica serovar I 4,[5],12:i:

Neupane DP, Bearson BL, Bearson SMD. Neupane DP, et al. DNA Res. 2025 Dec 1;32(6):dsaf023. doi: 10.1093/dnares/dsaf023. DNA Res. 2025. PMID: 40971805 Free PMC article.

20

Satellite DNAs rising from the transposon graveyards.

Šatović-Vukšić E, Majcen P, Plohl M. Šatović-Vukšić E, et al. DNA Res. 2025 Sep 2;32(5):dsaf026. doi: 10.1093/dnares/dsaf026. DNA Res. 2025. PMID: 41022669 Free PMC article. Review.

21

Can classical statistics and deep learning converge on explainable, causally driven target discovery?

Chen L. Chen L. DNA Res. 2025 Sep 2;32(5):dsaf024. doi: 10.1093/dnares/dsaf024. DNA Res. 2025. PMID: 40971794 Free PMC article. Review.

22

Chromosome-scale genome assembly of Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history.

Xiao TW, Wang XF, Wang ZF, Yan HF. Xiao TW, et al. DNA Res. 2025 Sep 2;32(5):dsaf022. doi: 10.1093/dnares/dsaf022. DNA Res. 2025. PMID: 40916496 Free PMC article.

23

Diversity, evolution, and transcription of endogenous retroviruses in Chiroptera genomes.

Zhou ZJ, Xiao Y, Fang J, Yao YX, Yang CH, Dacheux L, Luo DS, Qiu Y, Ge XY. Zhou ZJ, et al. DNA Res. 2025 Sep 2;32(5):dsaf021. doi: 10.1093/dnares/dsaf021. DNA Res. 2025. PMID: 40853364 Free PMC article.

24

Genome survey and evolutionary analysis of 8 Lamprotula species: SSR profiling, mitochondrial characterization, and population dynamics inference.

Jiang M, Liu Q, Jiang C, Zhan M, Wen H, Shu F, Xie L, Liu T, Ren C, Tang W, Liu K. Jiang M, et al. DNA Res. 2025 Sep 2;32(5):dsaf020. doi: 10.1093/dnares/dsaf020. DNA Res. 2025. PMID: 40795895 Free PMC article.

25

Thin-diaPASEF: diaPASEF for maximizing proteome coverage in single-shot proteomics.

Konno R, Ishikawa M, Nakajima D, Inukai K, Ohara O, Kawashima Y. Konno R, et al. DNA Res. 2025 Jul 4;32(4):dsaf019. doi: 10.1093/dnares/dsaf019. DNA Res. 2025. PMID: 40704459 Free PMC article.

26

Dynamic integration and evolutionary trajectory of endogenous IHHNV elements in crustacean genomes.

Zhong X, Yuan J, Zhang X, Li S, Liu C, Si S, Hu J, Prachumwat A, Sritunyalucksana K, Li F. Zhong X, et al. DNA Res. 2025 Jul 4;32(4):dsaf018. doi: 10.1093/dnares/dsaf018. DNA Res. 2025. PMID: 40693514 Free PMC article.

27

Nearly T2T, phased genome assemblies of corals reveal haplotype diversity and the evolutionary process of gene expansion.

Takeuchi T, Suzuki Y, Shoguchi E, Fujie M, Kawamitsu M, Shinzato C, Satoh N, Myers EW. Takeuchi T, et al. DNA Res. 2025 Jul 4;32(4):dsaf017. doi: 10.1093/dnares/dsaf017. DNA Res. 2025. PMID: 40590610 Free PMC article.

28

Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.

Tanaka T, Haraguchi Y, Todoroki T, Saisho D, Abiko T, Kai H. Tanaka T, et al. DNA Res. 2025 Jul 4;32(4):dsaf016. doi: 10.1093/dnares/dsaf016. DNA Res. 2025. PMID: 40577690 Free PMC article.

29

Manipulating alternative end-joining alters carbon-ion beam-induced genome mutation profiles in Arabidopsis thaliana.

Long J, Zhao J, Chen J, Ding J, Liu X, Li Z, Bian P, Wang T, Jin W, Lu X, Zhang Y, Zhou L, Du Y. Long J, et al. DNA Res. 2025 Jul 4;32(4):dsaf014. doi: 10.1093/dnares/dsaf014. DNA Res. 2025. PMID: 40448271 Free PMC article.

30

Correction to: Chromosome-level genome assembly of the medicinal insect Blaps rhynchopetera using Nanopore and Hi-C technologies.

[No authors listed] [No authors listed] DNA Res. 2025 May 28;32(3):dsaf013. doi: 10.1093/dnares/dsaf013. DNA Res. 2025. PMID: 40464361 Free PMC article. No abstract available.

31

Hybrid genome assembly of the widespread bat Rhinolophus lepidus provides insights into susceptibility to SARS-CoV-2 infection and climate change threat.

Garg KM, Low DHW, Lee G, Lee BPY, Mendenhall IH, Rheindt FE, Smith GJD, Chattopadhyay B. Garg KM, et al. DNA Res. 2025 May 28;32(3):dsaf015. doi: 10.1093/dnares/dsaf015. DNA Res. 2025. PMID: 40458961 Free PMC article.

32

Integrative transcriptomic analysis reveals alternative splicing complexity and transcriptomic diversity in porcine placentas across altitudes.

Li CY, Meng XT, Liu ZP, Zhang X, Zhou B, Pubuzhaxi, Zhao HY, Zhao JD, Fu GW, Chang YC, Gong SR, Huo JL, Zhao GY. Li CY, et al. DNA Res. 2025 May 28;32(3):dsaf008. doi: 10.1093/dnares/dsaf008. DNA Res. 2025. PMID: 40445954 Free PMC article.

33

Whole-genome sequencing of the ant Crematogaster osakensis (Hymenoptera: Formicidae: Myrmicinae).

Gotoh A, Toyoda A, Yamabe T, Itoh T. Gotoh A, et al. DNA Res. 2025 May 28;32(3):dsaf012. doi: 10.1093/dnares/dsaf012. DNA Res. 2025. PMID: 40392114 Free PMC article.

34

A high-quality genome assembly of Annona squamosa (custard apple) provides functional insights into an emerging fruit crop.

Bisht MS, Mahajan S, Chakraborty A, Sharma VK. Bisht MS, et al. DNA Res. 2025 May 28;32(3):dsaf007. doi: 10.1093/dnares/dsaf007. DNA Res. 2025. PMID: 40371876 Free PMC article.

35

Comparative genomics of endophytic fungi Apiospora malaysiana with related ascomycetes indicates adaptation attuned to lifestyle choices with potential sustainable cellulolytic activity.

Kant S, Das S, Dutta S, Mandal K, Upadhyay A, Sarangi AN, Majumder R, Tripathy S. Kant S, et al. DNA Res. 2025 May 28;32(3):dsaf011. doi: 10.1093/dnares/dsaf011. DNA Res. 2025. PMID: 40346017 Free PMC article.

36

Four chromosome-scale ampullariid genomes: high-quality resources for ecological, evolutionary, and invasion biology studies.

Xiong J, Gao Y, Zhou Y, Ip JC, Ituarte S, Heras H, Qiu JW, Sun J. Xiong J, et al. DNA Res. 2025 May 28;32(3):dsaf010. doi: 10.1093/dnares/dsaf010. DNA Res. 2025. PMID: 40344091 Free PMC article.

37

Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria.

Urriza M, Dimaria G, de Oliveira LO, Catara V, Murillo J. Urriza M, et al. DNA Res. 2025 May 28;32(3):dsaf009. doi: 10.1093/dnares/dsaf009. DNA Res. 2025. PMID: 40273218 Free PMC article.

38

Chromosome-scale genome assembly of Phyllanthus emblica L. 'Yingyu'.

Zhang L, Yuan J, Pu T, Qu W, Lei X, Ma K, Qian K, Zhao Q, Liao C, Jin J. Zhang L, et al. DNA Res. 2025 Mar 1;32(2):dsaf006. doi: 10.1093/dnares/dsaf006. DNA Res. 2025. PMID: 40070358 Free PMC article.

39

Genome assembly of the temporary socially parasitic spiny ant Polyrhachis lamellidens and its host Camponotus japonicus.

Iwai H, Kurihara Y, Kono N, Hojo MK, Yamaguchi K, Shigenobu S, Ozaki M, Koto A, Arakawa K. Iwai H, et al. DNA Res. 2025 Mar 1;32(2):dsaf005. doi: 10.1093/dnares/dsaf005. DNA Res. 2025. PMID: 40036880 Free PMC article.

40

Comparative transcriptome and mutation analyses of the pancreatic islets of a rat model of obese type 2 diabetes identifies a frequently distributed nonsense mutation in the lipocalin 2 gene.

Yokoi N, Adachi N, Hirokoji T, Nakano K, Yoshihara M, Shigenaka S, Urakawa R, Taniguchi Y, Yoshida Y, Yokose S, Suyama M, Okamura T. Yokoi N, et al. DNA Res. 2025 Mar 1;32(2):dsaf004. doi: 10.1093/dnares/dsaf004. DNA Res. 2025. PMID: 40036227 Free PMC article.

41

Chromosome-level genome assembly of Pontederia cordata L. provides insights into its rapid adaptation and variation of flower colours.

Wang JL, Zhang WD, Yang XD, Zhao PG, Wang XY, Zhao SY, Chen LY. Wang JL, et al. DNA Res. 2025 Mar 1;32(2):dsaf002. doi: 10.1093/dnares/dsaf002. DNA Res. 2025. PMID: 39878035 Free PMC article.

42

Identification of a candidate sex determination region and sex-specific molecular markers based on whole-genome re‑sequencing in the sea star Asterias amurensis.

Wang Y, Yang H, Wang Y, Li Y, Ni G, Cummins SF, Chen M. Wang Y, et al. DNA Res. 2024 Dec 27;32(1):dsaf003. doi: 10.1093/dnares/dsaf003. DNA Res. 2024. PMID: 39792457 Free PMC article.

43

Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader.

Ramdass AC, Rampersad SN. Ramdass AC, et al. DNA Res. 2024 Dec 27;32(1):dsaf001. doi: 10.1093/dnares/dsaf001. DNA Res. 2024. PMID: 39758036 Free PMC article.

44

Correction to: Chromosome-level genome assembly of the medicinal insect Blaps rhynchopetera using Nanopore and Hi-C technologies.

[No authors listed] [No authors listed] DNA Res. 2024 Dec 27;32(1):dsae037. doi: 10.1093/dnares/dsae037. DNA Res. 2024. PMID: 39729083 Free PMC article. No abstract available.

45

Near-complete telomere-to-telomere de novo genome assembly in Egyptian clover (Trifolium alexandrinum).

Sato MP, Arafa RA, Rakha MT, Emeran AA, Isobe S, Shirasawa K. Sato MP, et al. DNA Res. 2024 Dec 27;32(1):dsae036. doi: 10.1093/dnares/dsae036. DNA Res. 2024. PMID: 39693366 Free PMC article.

46

The haplotype-phased genome assembly facilitated the deciphering of the bud dormancy-related QTLs in Prunus mume.

Hsiang TF, Yamane H, Lin YJ, Sugimori M, Nishiyama S, Nagasaka K, Nakano R, Tao R. Hsiang TF, et al. DNA Res. 2024 Dec 27;32(1):dsae034. doi: 10.1093/dnares/dsae034. DNA Res. 2024. PMID: 39656749 Free PMC article.

47

A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium yellows resistance QTL.

Todd OE, Simpson S, Scheffler B, Dorn KM. Todd OE, et al. DNA Res. 2024 Dec 27;32(1):dsae032. doi: 10.1093/dnares/dsae032. DNA Res. 2024. PMID: 39589284 Free PMC article.

48

De novo sequencing allows genome-wide identification of genes involved in galactomannan synthesis in locust bean (Ceratonia siliqua).

Akutsu M, Shinozawa A, Nishiyama T, Sakata Y, Hiwatashi Y. Akutsu M, et al. DNA Res. 2024 Dec 1;31(6):dsae033. doi: 10.1093/dnares/dsae033. DNA Res. 2024. PMID: 39673409 Free PMC article.

49

Epigenetic control of tetrapyrrole biosynthesis by m4C DNA methylation in a cyanobacterium.

Schmidt N, Stappert N, Nimura-Matsune K, Watanabe S, Sobotka R, Hagemann M, Hess WR. Schmidt N, et al. DNA Res. 2024 Dec 1;31(6):dsae035. doi: 10.1093/dnares/dsae035. DNA Res. 2024. PMID: 39657587 Free PMC article.

50

Time-dependent changes in genome-wide gene expression and post-transcriptional regulation across the post-death process in silkworm.

Yang LY, Tang DR, Luo SQ, Li WW, Jiang YH, Lin LB, Zhang QL. Yang LY, et al. DNA Res. 2024 Dec 1;31(6):dsae031. doi: 10.1093/dnares/dsae031. DNA Res. 2024. PMID: 39546332 Free PMC article.

51

The burst of satellite DNA in Leptidea wood white butterflies and their putative role in karyotype evolution.

Cabral-de-Mello DC, Yoshido A, Milani D, Šíchová J, Sahara K, Marec F. Cabral-de-Mello DC, et al. DNA Res. 2024 Dec 1;31(6):dsae030. doi: 10.1093/dnares/dsae030. DNA Res. 2024. PMID: 39460673 Free PMC article.

52

Chromosome-scale genome assembly of acerola (Malpighia emarginata DC.).

Shirasawa K, Harada K, Haramoto N, Aoki H, Kammera S, Yamamoto M, Nishizawa Y. Shirasawa K, et al. DNA Res. 2024 Dec 1;31(6):dsae029. doi: 10.1093/dnares/dsae029. DNA Res. 2024. PMID: 39374107 Free PMC article.

53

Chromosome-level genome assembly of the medicinal insect Blaps rhynchopetera using Nanopore and Hi-C technologies.

Zhang W, Li Y, Wang Q, Yu Q, Ma Y, Huang L, Zhang C, Yang Z, Wang J, Xiao H. Zhang W, et al. DNA Res. 2024 Dec 1;31(6):dsae027. doi: 10.1093/dnares/dsae027. DNA Res. 2024. PMID: 39250428 Free PMC article.

54

Functional landscape of genome-wide postzygotic somatic mutations between monozygotic twins.

Yamamoto K, Lee Y, Masuda T, Ozono K, Iwatani Y, Watanabe M, Okada Y, Sakai N. Yamamoto K, et al. DNA Res. 2024 Oct 1;31(5):dsae028. doi: 10.1093/dnares/dsae028. DNA Res. 2024. PMID: 39306676 Free PMC article.

55

Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples.

Švara A, Sun H, Fei Z, Khan A. Švara A, et al. DNA Res. 2024 Oct 1;31(5):dsae026. doi: 10.1093/dnares/dsae026. DNA Res. 2024. PMID: 39185728 Free PMC article.

56

Propagation path of a flowering cherry (Cerasus × yedoensis) cultivar 'Somei-Yoshino' traced by somatic mutations.

Shirasawa K, Esumi T, Itai A, Hatakeyama K, Takashina T, Yakuwa T, Sumitomo K, Kurokura T, Fukai E, Sato K, Shimada T, Shiratake K, Hosokawa M, Monden Y, Kusaba M, Ikegami H, Isobe S. Shirasawa K, et al. DNA Res. 2024 Oct 1;31(5):dsae025. doi: 10.1093/dnares/dsae025. DNA Res. 2024. PMID: 39115130 Free PMC article.

57

Insights from the first chromosome-level genome assembly of the alpine gentian Gentiana straminea Maxim.

Kelsang GA, Ni L, Zhao Z. Kelsang GA, et al. DNA Res. 2024 Oct 1;31(5):dsae022. doi: 10.1093/dnares/dsae022. DNA Res. 2024. PMID: 39017645 Free PMC article.

58

Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum).

Nagasaki H, Shirasawa K, Hoshikawa K, Isobe S, Ezura H, Aoki K, Hirakawa H. Nagasaki H, et al. DNA Res. 2024 Oct 1;31(5):dsae016. doi: 10.1093/dnares/dsae016. DNA Res. 2024. PMID: 38845356 Free PMC article.

59

Pan-lineage Mycobacterium tuberculosis reference genome for enhanced molecular diagnosis.

Bahk K, Sung J, Seki M, Kim K, Kim J, Choi H, Whang J, Mitarai S. Bahk K, et al. DNA Res. 2024 Aug 1;31(4):dsae023. doi: 10.1093/dnares/dsae023. DNA Res. 2024. PMID: 39127874 Free PMC article.

60

A high-quality genome assembly reveals adaptations underlying glossy, wax-coated leaves in the heat-tolerant wild raspberry Rubus leucanthus.

Wu W, Wang L, Huang W, Zhang X, Li Y, Guo W. Wu W, et al. DNA Res. 2024 Aug 1;31(4):dsae024. doi: 10.1093/dnares/dsae024. DNA Res. 2024. PMID: 39101533 Free PMC article.

61

A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China.

Gong S, Gan H, Chu J, Wang Z, Sun J. Gong S, et al. DNA Res. 2024 Aug 1;31(4):dsae021. doi: 10.1093/dnares/dsae021. DNA Res. 2024. PMID: 38946223 Free PMC article.

62

Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758).

Galià-Camps C, Carreras C, Pascual M, Greve C, Schell T, Turon X, Palacín C, Pérez-Portela R, Wangensteen OS, Pegueroles C. Galià-Camps C, et al. DNA Res. 2024 Aug 1;31(4):dsae020. doi: 10.1093/dnares/dsae020. DNA Res. 2024. PMID: 38908014 Free PMC article.

63

A haplotype-resolved reference genome of a long-distance migratory bat, Pipistrellus nathusii (Keyserling & Blasius, 1839).

Driller M, Brown T, Currie SE, Hiller M, Winkler S, Pippel M, Voigt CC, Fickel J, Mazzoni CJ. Driller M, et al. DNA Res. 2024 Aug 1;31(4):dsae018. doi: 10.1093/dnares/dsae018. DNA Res. 2024. PMID: 38847751 Free PMC article.

64

High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus.

Huang XZ, Gong SD, Shang XH, Gao M, Zhao BY, Xiao L, Shi PL, Zeng WD, Cao S, Wu ZD, Song JM, Chen LL, Yan HB. Huang XZ, et al. DNA Res. 2024 Jun 1;31(3):dsae017. doi: 10.1093/dnares/dsae017. DNA Res. 2024. PMID: 38809753 Free PMC article.

65

Characterization of transcriptome changes in saline stress adaptation on Leuciscus merzbacheri using PacBio Iso-Seq and RNA-Seq.

Yu D, Zhou M, Chen W, Ding Z, Wang C, Qian Y, Liu Y, He S, Yang L. Yu D, et al. DNA Res. 2024 Jun 1;31(3):dsae019. doi: 10.1093/dnares/dsae019. DNA Res. 2024. PMID: 38807352 Free PMC article.

66

Correction to: Assessing genetic diversity and geographical differentiation in a global collection of wild soybean (Glycine soja Sieb. et Zucc.) and assigning a mini-core collection.

[No authors listed] [No authors listed] DNA Res. 2024 Jun 1;31(3):dsae015. doi: 10.1093/dnares/dsae015. DNA Res. 2024. PMID: 38717118 Free PMC article. No abstract available.

67

Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea.

Daware A, Mohanty JK, Narnoliya L, Singh A, Rathore D, Thakro V, Francis A, Singh NP, Francis P, Tripathi S, Chattopadhyay D, Parida SK. Daware A, et al. DNA Res. 2024 Jun 1;31(3):dsae013. doi: 10.1093/dnares/dsae013. DNA Res. 2024. PMID: 38702947 Free PMC article.

68

Chromosome-level genome assembly of the yeast Lodderomyces beijingensis reveals the genetic nature of metabolic adaptations and identifies subtelomeres as hotspots for amplification of mating type loci.

Brejová B, Hodorová V, Mutalová S, Cillingová A, Tomáška Ľ, Vinař T, Nosek J. Brejová B, et al. DNA Res. 2024 Jun 1;31(3):dsae014. doi: 10.1093/dnares/dsae014. DNA Res. 2024. PMID: 38686638 Free PMC article.

69

Telomere-to-telomere genome assembly of Oldenlandia diffusa.

Gao Y, Xu D, Hu Z. Gao Y, et al. DNA Res. 2024 Jun 1;31(3):dsae012. doi: 10.1093/dnares/dsae012. DNA Res. 2024. PMID: 38600880 Free PMC article.

70

Chromosome-level genome assembly and characterization of the Calophaca sinica genome.

Cao J, Zhu H, Gao Y, Hu Y, Li X, Shi J, Chen L, Kang H, Ru D, Ren B, Liu B. Cao J, et al. DNA Res. 2024 Jun 1;31(3):dsae011. doi: 10.1093/dnares/dsae011. DNA Res. 2024. PMID: 38590243 Free PMC article.

71

Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira).

Nakamura Y, Yasuike M, Fuji T, Suyama S, Mekuchi M. Nakamura Y, et al. DNA Res. 2024 Jun 1;31(3):dsae010. doi: 10.1093/dnares/dsae010. DNA Res. 2024. PMID: 38566577 Free PMC article.

72

Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal.

Fukuta K, Kato DI, Maeda J, Tsuruta A, Suzuki H, Nagano Y, Tsukamoto H, Niwa K, Terauchi M, Toyoda A, Fujiyama A, Noguchi H. Fukuta K, et al. DNA Res. 2024 Apr 1;31(2):dsae006. doi: 10.1093/dnares/dsae006. DNA Res. 2024. PMID: 38494174 Free PMC article.

73

Assessing genetic diversity and geographical differentiation in a global collection of wild soybean (Glycine soja Sieb. et Zucc.) and assigning a mini-core collection.

Li F, Sayama T, Yokota Y, Hiraga S, Hashiguchi M, Tanaka H, Akashi R, Ishimoto M. Li F, et al. DNA Res. 2024 Apr 1;31(2):dsae009. doi: 10.1093/dnares/dsae009. DNA Res. 2024. PMID: 38490815 Free PMC article.

74

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology.

Sato M, Fukuda K, Kadota M, Makino-Itou H, Tatsumi K, Yamauchi S, Kuraku S. Sato M, et al. DNA Res. 2024 Apr 1;31(2):dsae004. doi: 10.1093/dnares/dsae004. DNA Res. 2024. PMID: 38451834 Free PMC article.

75

Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig.

Zong W, Zhao R, Wang X, Zhou C, Wang J, Chen C, Niu N, Zheng Y, Chen L, Liu X, Hou X, Zhao F, Wang L, Wang L, Song C, Zhang L. Zong W, et al. DNA Res. 2024 Apr 1;31(2):dsae008. doi: 10.1093/dnares/dsae008. DNA Res. 2024. PMID: 38447059 Free PMC article.

76

High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis.

Huang Z, Liu Q, Zeng X, Ni G. Huang Z, et al. DNA Res. 2024 Apr 1;31(2):dsae007. doi: 10.1093/dnares/dsae007. DNA Res. 2024. PMID: 38416146 Free PMC article.

77

A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis.

Murata T, Gotoh Y, Hayashi T. Murata T, et al. DNA Res. 2024 Feb 1;31(1):dsae002. doi: 10.1093/dnares/dsae002. DNA Res. 2024. PMID: 38300630 Free PMC article.

78

The chromosome-level genome of the submerged plant Cryptocoryne crispatula provides insights into the terrestrial-freshwater transition in Araceae.

Qian ZH, Li W, Wang QF, Liang SC, Wu S, Li ZZ, Chen JM. Qian ZH, et al. DNA Res. 2024 Feb 1;31(1):dsae003. doi: 10.1093/dnares/dsae003. DNA Res. 2024. PMID: 38245835 Free PMC article.

79

Hybrid de novo genome assembly of the sexually dimorphic Lady Amherst's pheasant.

Garg KM, Dovih P, Chattopadhyay B. Garg KM, et al. DNA Res. 2024 Feb 1;31(1):dsae001. doi: 10.1093/dnares/dsae001. DNA Res. 2024. PMID: 38168719 Free PMC article.

80

ZSCAN4-binding motif-TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes.

Akiyama T, Ishiguro KI, Chikazawa N, Ko SBH, Yukawa M, Ko MSH. Akiyama T, et al. DNA Res. 2024 Feb 1;31(1):dsad029. doi: 10.1093/dnares/dsad029. DNA Res. 2024. PMID: 38153767 Free PMC article.

81

Chromosome-level genome assembly and demographic history of Euryodendron excelsum in monotypic genus endemic to China.

Wang ZF, Fu L, Yu EP, Zhu WG, Zeng SJ, Cao HL. Wang ZF, et al. DNA Res. 2024 Feb 1;31(1):dsad028. doi: 10.1093/dnares/dsad028. DNA Res. 2024. PMID: 38147541 Free PMC article.

82

MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison.

Furuta T, Yamamoto T. Furuta T, et al. DNA Res. 2024 Feb 1;31(1):dsad027. doi: 10.1093/dnares/dsad027. DNA Res. 2024. PMID: 38134958 Free PMC article.

83

Churros: a Docker-based pipeline for large-scale epigenomic analysis.

Wang J, Nakato R. Wang J, et al. DNA Res. 2024 Feb 1;31(1):dsad026. doi: 10.1093/dnares/dsad026. DNA Res. 2024. PMID: 38102723 Free PMC article.

84

The genome of a globally invasive passerine, the common myna, Acridotheres tristis.

Stuart KC, Johnson RN, Major RE, Atsawawaranunt K, Ewart KM, Rollins LA, Santure AW, Whibley A. Stuart KC, et al. DNA Res. 2024 Jan 1;31(2):dsae005. doi: 10.1093/dnares/dsae005. DNA Res. 2024. PMID: 38366840 Free PMC article.

85

Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains.

Ramdass AC, Rampersad SN. Ramdass AC, et al. DNA Res. 2023 Dec 1;30(6):dsad025. doi: 10.1093/dnares/dsad025. DNA Res. 2023. PMID: 37952165 Free PMC article.

86

Metagenomic Thermometer.

Kurokawa M, Higashi K, Yoshida K, Sato T, Maruyama S, Mori H, Kurokawa K. Kurokawa M, et al. DNA Res. 2023 Dec 1;30(6):dsad024. doi: 10.1093/dnares/dsad024. DNA Res. 2023. PMID: 37940329 Free PMC article.

87

Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon.

Sato MP, Iwakami S, Fukunishi K, Sugiura K, Yasuda K, Isobe S, Shirasawa K. Sato MP, et al. DNA Res. 2023 Oct 1;30(5):dsad023. doi: 10.1093/dnares/dsad023. DNA Res. 2023. PMID: 37943179 Free PMC article.

88

Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome.

Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Pons J, Alós J, Barcelo-Serra M. Cruz F, et al. DNA Res. 2023 Oct 1;30(5):dsad021. doi: 10.1093/dnares/dsad021. DNA Res. 2023. PMID: 37797305 Free PMC article.

89

Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes.

Yang X, Song Y, Zhang R, Yu M, Guo X, Guo H, Du X, Sun S, Li C, Mao X, Fan G, Liu X. Yang X, et al. DNA Res. 2023 Oct 1;30(5):dsad022. doi: 10.1093/dnares/dsad022. DNA Res. 2023. PMID: 37788574 Free PMC article.

90

Evolution of the viral genomes of SARS-CoV-2 in association with the changes in local condition: a genomic epidemiological study of a suburban city of Japan.

Kashima Y, Mizutani T, Okimoto Y, Maeda M, Musashino K, Nishide RI, Matsukura A, Nagase J, Suzuki Y. Kashima Y, et al. DNA Res. 2023 Oct 1;30(5):dsad020. doi: 10.1093/dnares/dsad020. DNA Res. 2023. PMID: 37712596 Free PMC article.

91

Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum.

Koshimizu S, Masuda S, Shibata A, Ishii T, Shirasu K, Hoshino A, Arita M. Koshimizu S, et al. DNA Res. 2023 Oct 1;30(5):dsad019. doi: 10.1093/dnares/dsad019. DNA Res. 2023. PMID: 37691489 Free PMC article.

92

Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits.

Zhang S, Song Y, Liu M, Yuan Z, Zhang M, Zhang H, Seim I, Fan G, Liu S, Liu X. Zhang S, et al. DNA Res. 2023 Oct 1;30(5):dsad018. doi: 10.1093/dnares/dsad018. DNA Res. 2023. PMID: 37590994 Free PMC article.

93

Genetic basis of lineage-specific evolution of fruit traits in hexaploid persimmon.

Horiuchi A, Masuda K, Shirasawa K, Onoue N, Matsuzaki R, Tao R, Kubo Y, Ushijima K, Akagi T. Horiuchi A, et al. DNA Res. 2023 Oct 1;30(5):dsad015. doi: 10.1093/dnares/dsad015. DNA Res. 2023. PMID: 37326063 Free PMC article.

94

GINGER: an integrated method for high-accuracy prediction of gene structure in higher eukaryotes at the gene and exon level.

Taniguchi T, Okuno M, Shinoda T, Kobayashi F, Takahashi K, Yuasa H, Nakamura Y, Tanaka H, Kajitani R, Itoh T. Taniguchi T, et al. DNA Res. 2023 Aug 1;30(4):dsad017. doi: 10.1093/dnares/dsad017. DNA Res. 2023. PMID: 37478310 Free PMC article.

95

Self-grafting-induced epigenetic changes leading to drought stress tolerance in tomato plants.

Fuentes-Merlos MI, Bamba M, Sato S, Higashitani A. Fuentes-Merlos MI, et al. DNA Res. 2023 Aug 1;30(4):dsad016. doi: 10.1093/dnares/dsad016. DNA Res. 2023. PMID: 37452722 Free PMC article.

96

Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma.

Uchida T, Yoshioka Y, Yoshida Y, Fujie M, Yamaki A, Sasaki A, Inoue K, Shinzato C. Uchida T, et al. DNA Res. 2023 Aug 1;30(4):dsad014. doi: 10.1093/dnares/dsad014. DNA Res. 2023. PMID: 37358253 Free PMC article.

97

Genome assembly of the pioneer species Plantago major L. (Plantaginaceae) provides insight into its global distribution and adaptation to metal-contaminated soil.

Lyu S, Mei Q, Liu H, Wang B, Wang J, Lambers H, Wang Z, Dong B, Liu Z, Deng S. Lyu S, et al. DNA Res. 2023 Aug 1;30(4):dsad013. doi: 10.1093/dnares/dsad013. DNA Res. 2023. PMID: 37228100 Free PMC article.

98

Chromosome-level genome assembly of an endangered plant Prunus mongolica using PacBio and Hi-C technologies.

Zhu Q, Wang Y, Yao N, Ni X, Wang C, Wang M, Zhang L, Liang W. Zhu Q, et al. DNA Res. 2023 Aug 1;30(4):dsad012. doi: 10.1093/dnares/dsad012. DNA Res. 2023. PMID: 37220653 Free PMC article.

99

Base-excision restriction enzymes: expanding the world of epigenetic immune systems.

Kojima KK, Kobayashi I. Kojima KK, et al. DNA Res. 2023 Aug 1;30(4):dsad009. doi: 10.1093/dnares/dsad009. DNA Res. 2023. PMID: 37148195 Free PMC article.

100

Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.

Mori H, Kato T, Ozawa H, Sakamoto M, Murakami T, Taylor TD, Toyoda A, Ohkuma M, Kurokawa K, Ohno H. Mori H, et al. DNA Res. 2023 Jun 1;30(3):dsad010. doi: 10.1093/dnares/dsad010. DNA Res. 2023. PMID: 37253538 Free PMC article.

101

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

Gomez-Garrido J, Cruz F, Alioto TS, Feiner N, Uller T, Gut M, Sanchez Escudero I, Tavecchia G, Rotger A, Otalora Acevedo KE, Baldo L. Gomez-Garrido J, et al. DNA Res. 2023 Jun 1;30(3):dsad008. doi: 10.1093/dnares/dsad008. DNA Res. 2023. PMID: 37137526 Free PMC article.

102

Genome sequence and salinity adaptation of the desert shrub Nitraria sibirica (Nitrariaceae, Sapindales).

Ma X, Ru D, Morales-Briones DF, Mei F, Wu J, Liu J, Wu S. Ma X, et al. DNA Res. 2023 May 11;30(3):dsad011. doi: 10.1093/dnares/dsad011. Online ahead of print. DNA Res. 2023. PMID: 37167434 Free PMC article.

103

Detection of tandem repeats in the Capsicum annuum genome.

Rudenko V, Korotkov E. Rudenko V, et al. DNA Res. 2023 Apr 25;30(3):dsad007. doi: 10.1093/dnares/dsad007. Online ahead of print. DNA Res. 2023. PMID: 37186267 Free PMC article.

104

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake).

Kurokochi H, Tajima N, Sato MP, Yoshitake K, Asakawa S, Isobe S, Shirasawa K. Kurokochi H, et al. DNA Res. 2023 Apr 25;30(3):dsad006. doi: 10.1093/dnares/dsad006. Online ahead of print. DNA Res. 2023. PMID: 37186136 Free PMC article.

105

The genome sequence and demographic history of Przewalskia tangutica (Solanaceae), an endangered alpine plant on the Qinghai-Tibet Plateau.

Wu Y, Yang J, Yang Y, Liu J. Wu Y, et al. DNA Res. 2023 Apr 1;30(2):dsad005. doi: 10.1093/dnares/dsad005. DNA Res. 2023. PMID: 37014116 Free PMC article.

106

Chromosome-level genome assembly of the endangered plant Tetraena mongolica.

Liu B, Zhao X, Wang Z, Liu H, Huang X, Yang P. Liu B, et al. DNA Res. 2023 Apr 1;30(2):dsad004. doi: 10.1093/dnares/dsad004. DNA Res. 2023. PMID: 36999569 Free PMC article.

107

Chromosome-level genome assembly of Phrynocephalus forsythii using third-generation DNA sequencing and Hi-C analysis.

Qi Y, Zhao W, Zhao Y, Niu C, Cao S, Zhang Y. Qi Y, et al. DNA Res. 2023 Apr 1;30(2):dsad003. doi: 10.1093/dnares/dsad003. DNA Res. 2023. PMID: 36882113 Free PMC article.

108

Correction to: Mituru Takanami, 1929-2022.

[No authors listed] [No authors listed] DNA Res. 2023 Feb 1;30(1):dsad002. doi: 10.1093/dnares/dsad002. DNA Res. 2023. PMID: 36692106 Free PMC article. No abstract available.

109

A chromosome-level genome assembly of the Henosepilachna vigintioctomaculata provides insights into the evolution of ladybird beetles.

Zhu W, Chi S, Wang Y, Li H, Wang Z, Gu S, Sun T, Xiang H, You P, Ren Y. Zhu W, et al. DNA Res. 2023 Feb 1;30(1):dsad001. doi: 10.1093/dnares/dsad001. DNA Res. 2023. PMID: 36645207 Free PMC article.

110

The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes.

Kobayashi Y, Shibata TF, Hirakawa H, Nishiyama T, Yamada A, Hasebe M, Shigenobu S, Kawaguchi M. Kobayashi Y, et al. DNA Res. 2023 Feb 1;30(1):dsac053. doi: 10.1093/dnares/dsac053. DNA Res. 2023. PMID: 36610744 Free PMC article.

111

Characterization of proteogenomic signatures of differentiation of CD4+ T cell subsets.

Kanno T, Konno R, Miyako K, Nakajima T, Yokoyama S, Sasamoto S, Asou HK, Ohzeki J, Kawashima Y, Hasegawa Y, Ohara O, Endo Y. Kanno T, et al. DNA Res. 2023 Feb 1;30(1):dsac054. doi: 10.1093/dnares/dsac054. DNA Res. 2023. PMID: 36579714 Free PMC article.

112

Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.

Shirasawa K, Hosokawa M, Yasui Y, Toyoda A, Isobe S. Shirasawa K, et al. DNA Res. 2023 Feb 1;30(1):dsac052. doi: 10.1093/dnares/dsac052. DNA Res. 2023. PMID: 36566389 Free PMC article.

113

Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae.

Dong C, Wang S, Zhang H, Liu J, Li M. Dong C, et al. DNA Res. 2023 Feb 1;30(1):dsac051. doi: 10.1093/dnares/dsac051. DNA Res. 2023. PMID: 36521020 Free PMC article.

114

Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii.

Hasegawa Y, Watanabe T, Otsuka R, Toné S, Kubota S, Hirakawa H. Hasegawa Y, et al. DNA Res. 2023 Feb 1;30(1):dsac047. doi: 10.1093/dnares/dsac047. DNA Res. 2023. PMID: 36519838 Free PMC article.

115

The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau.

Ning Y, Li Y, Dong SB, Yang HG, Li CY, Xiong B, Yang J, Hu YK, Mu XY, Xia XF. Ning Y, et al. DNA Res. 2023 Feb 1;30(1):dsac049. doi: 10.1093/dnares/dsac049. DNA Res. 2023. PMID: 36503982 Free PMC article.

116

Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis.

Wang H, Xu D, Wang S, Wang A, Lei L, Jiang F, Yang B, Yuan L, Chen R, Zhang Y, Fan W. Wang H, et al. DNA Res. 2023 Feb 1;30(1):dsac050. doi: 10.1093/dnares/dsac050. DNA Res. 2023. PMID: 36473054 Free PMC article.

117

The methanogen core and pangenome: conservation and variability across biology's growth temperature extremes.

Prondzinsky P, Toyoda S, McGlynn SE. Prondzinsky P, et al. DNA Res. 2023 Feb 1;30(1):dsac048. doi: 10.1093/dnares/dsac048. DNA Res. 2023. PMID: 36454681 Free PMC article.

118

Comparison of CRISPR-Cas9-mediated megabase-scale genome deletion methods in mouse embryonic stem cells.

Miyata M, Yoshida J, Takagishi I, Horie K. Miyata M, et al. DNA Res. 2023 Feb 1;30(1):dsac045. doi: 10.1093/dnares/dsac045. DNA Res. 2023. PMID: 36448318 Free PMC article.

119

A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan.

Tamura K, Sakamoto M, Tanizawa Y, Mochizuki T, Matsushita S, Kato Y, Ishikawa T, Okuhara K, Nakamura Y, Bono H. Tamura K, et al. DNA Res. 2023 Feb 1;30(1):dsac044. doi: 10.1093/dnares/dsac044. DNA Res. 2023. PMID: 36383440 Free PMC article.

120

A chromosomal-scale reference genome of the New World Screwworm, Cochliomyia hominivorax.

Tandonnet S, Krsticevic F, Basika T, Papathanos PA, Torres TT, Scott MJ. Tandonnet S, et al. DNA Res. 2023 Feb 1;30(1):dsac042. doi: 10.1093/dnares/dsac042. DNA Res. 2023. PMID: 36370138 Free PMC article.

121

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.).

McGrath JM, Funk A, Galewski P, Ou S, Townsend B, Davenport K, Daligault H, Johnson S, Lee J, Hastie A, Darracq A, Willems G, Barnes S, Liachko I, Sullivan S, Koren S, Phillippy A, Wang J, Liu T, Pulman J, Childs K, Shu S, Yocum A, Fermin D, Mutasa-Göttgens E, Stevanato P, Taguchi K, Naegele R, Dorn KM. McGrath JM, et al. DNA Res. 2023 Feb 1;30(1):dsac033. doi: 10.1093/dnares/dsac033. DNA Res. 2023. PMID: 36208288 Free PMC article.

122

Correction to: The genome of Prunus humilis provides new insights to drought adaption and population diversity.

[No authors listed] [No authors listed] DNA Res. 2022 Dec 1;29(6):dsac038. doi: 10.1093/dnares/dsac038. DNA Res. 2022. PMID: 36562116 Free PMC article. No abstract available.

123

Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis.

Rai A, Hirakawa H, Rai M, Shimizu Y, Shirasawa K, Kikuchi S, Seki H, Yamazaki M, Toyoda A, Isobe S, Muranaka T, Saito K. Rai A, et al. DNA Res. 2022 Dec 1;29(6):dsac043. doi: 10.1093/dnares/dsac043. DNA Res. 2022. PMID: 36535891 Free PMC article.

124

Improved assembly and annotation of the sesame genome.

Wang M, Huang J, Liu S, Liu X, Li R, Luo J, Fu Z. Wang M, et al. DNA Res. 2022 Dec 1;29(6):dsac041. doi: 10.1093/dnares/dsac041. DNA Res. 2022. PMID: 36355766 Free PMC article.

125

A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster.

Takeuchi T, Suzuki Y, Watabe S, Nagai K, Masaoka T, Fujie M, Kawamitsu M, Satoh N, Myers EW. Takeuchi T, et al. DNA Res. 2022 Dec 1;29(6):dsac035. doi: 10.1093/dnares/dsac035. DNA Res. 2022. PMID: 36351462 Free PMC article.

126

De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'.

Shirasawa K, Hirakawa H, Azuma A, Taniguchi F, Yamamoto T, Sato A, Ghelfi A, Isobe SN. Shirasawa K, et al. DNA Res. 2022 Dec 1;29(6):dsac040. doi: 10.1093/dnares/dsac040. DNA Res. 2022. PMID: 36342351 Free PMC article.

127

Assembly-free discovery of human novel sequences using long reads.

Li Q, Yan B, Lam TW, Luo R. Li Q, et al. DNA Res. 2022 Dec 1;29(6):dsac039. doi: 10.1093/dnares/dsac039. DNA Res. 2022. PMID: 36308393 Free PMC article.

128

Rapid transcriptomic and physiological changes in the freshwater pennate diatom Mayamaea pseudoterrestris in response to copper exposure.

Suzuki S, Ota S, Yamagishi T, Tuji A, Yamaguchi H, Kawachi M. Suzuki S, et al. DNA Res. 2022 Dec 1;29(6):dsac037. doi: 10.1093/dnares/dsac037. DNA Res. 2022. PMID: 36197113 Free PMC article.

129

De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids.

Zhou T, Bai G, Hu Y, Ruhsam M, Yang Y, Zhao Y. Zhou T, et al. DNA Res. 2022 Dec 1;29(6):dsac034. doi: 10.1093/dnares/dsac034. DNA Res. 2022. PMID: 36197098 Free PMC article.

130

Chromosome-level genome of a leaf vegetable Glebionis coronaria provides insights into the biosynthesis of monoterpenoids contributing to its special aroma.

Wang S, Wang A, Wang H, Jiang F, Xu D, Fan W. Wang S, et al. DNA Res. 2022 Dec 1;29(6):dsac036. doi: 10.1093/dnares/dsac036. DNA Res. 2022. PMID: 36197084 Free PMC article.

131

Genome assembly of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea.

Nawae W, Sonthirod C, Yoocha T, Waiyamitra P, Soisook P, Tangphatsornruang S, Pootakham W. Nawae W, et al. DNA Res. 2022 Aug 23;29(5):dsac026. doi: 10.1093/dnares/dsac026. DNA Res. 2022. PMID: 36214371 Free PMC article.

132

Comprehensive analysis of 124 transcriptomes from 31 tissues in developing, juvenile, and adult Japanese Black cattle.

Arishima T, Wakaguri H, Nakashima R, Sakakihara S, Kawashima K, Sugimoto Y, Suzuki Y, Sasaki S. Arishima T, et al. DNA Res. 2022 Aug 23;29(5):dsac032. doi: 10.1093/dnares/dsac032. DNA Res. 2022. PMID: 36047829 Free PMC article.

133

Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping.

Sekine D, Oku S, Nunome T, Hirakawa H, Tsujimura M, Terachi T, Toyoda A, Shigyo M, Sato S, Tsukazaki H. Sekine D, et al. DNA Res. 2022 Aug 23;29(5):dsac020. doi: 10.1093/dnares/dsac020. DNA Res. 2022. PMID: 36007888 Free PMC article.

134

Chromosomal-level genome of velvet bean (Mucuna pruriens) provides resources for L-DOPA synthetic research and development.

Hao S, Ge Q, Shao Y, Tang B, Fan G, Qiu C, Wu X, Li L, Liu X, Shi C, Lee SM. Hao S, et al. DNA Res. 2022 Aug 23;29(5):dsac031. doi: 10.1093/dnares/dsac031. DNA Res. 2022. PMID: 35980175 Free PMC article.

135

Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana.

Mo C, Wu Z, Shang X, Shi P, Wei M, Wang H, Xiao L, Cao S, Lu L, Zeng W, Yan H, Kong Q. Mo C, et al. DNA Res. 2022 Aug 23;29(5):dsac030. doi: 10.1093/dnares/dsac030. DNA Res. 2022. PMID: 35961033 Free PMC article.

136

Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons.

Aziz R, Sen P, Beura PK, Das S, Tula D, Dash M, Namsa ND, Deka RC, Feil EJ, Satapathy SS, Ray SK. Aziz R, et al. DNA Res. 2022 Jun 25;29(4):dsac023. doi: 10.1093/dnares/dsac023. DNA Res. 2022. PMID: 35920776 Free PMC article.

137

Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations.

Manggabarani AM, Hashiguchi T, Hashiguchi M, Hayashi A, Kikuchi M, Mustamin Y, Bamba M, Kodama K, Tanabata T, Isobe S, Tanaka H, Akashi R, Nakaya A, Sato S. Manggabarani AM, et al. DNA Res. 2022 Jun 25;29(4):dsac024. doi: 10.1093/dnares/dsac024. DNA Res. 2022. PMID: 35916715 Free PMC article.

138

BLSSpeller to discover novel regulatory motifs in maize.

Rahmani RS, Decap D, Fostier J, Marchal K. Rahmani RS, et al. DNA Res. 2022 Jun 25;29(4):dsac029. doi: 10.1093/dnares/dsac029. DNA Res. 2022. PMID: 35904558 Free PMC article.

139

High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations.

Carlson CR, Ter Horst AM, Johnston JS, Henry E, Falk BW, Kuo YW. Carlson CR, et al. DNA Res. 2022 Jun 25;29(4):dsac027. doi: 10.1093/dnares/dsac027. DNA Res. 2022. PMID: 35866687 Free PMC article.

140

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome.

Zhu C, Liu H, Pan Z, Cheng L, Sun Y, Wang H, Chang G, Wu N, Ding H, Zhao H, Zhang L, Yu X. Zhu C, et al. DNA Res. 2022 Jun 25;29(4):dsac028. doi: 10.1093/dnares/dsac028. DNA Res. 2022. PMID: 35861402 Free PMC article.

141

Chromosome-level genome of Tibetan naked carp (Gymnocypris przewalskii) provides insights into Tibetan highland adaptation.

Tian F, Liu S, Zhou B, Tang Y, Zhang Y, Zhang C, Zhao K. Tian F, et al. DNA Res. 2022 Jun 25;29(4):dsac025. doi: 10.1093/dnares/dsac025. DNA Res. 2022. PMID: 35861387 Free PMC article.

142

Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness.

Yang JS, Qian ZH, Shi T, Li ZZ, Chen JM. Yang JS, et al. DNA Res. 2022 Jun 25;29(4):dsac022. doi: 10.1093/dnares/dsac022. DNA Res. 2022. PMID: 35751614 Free PMC article.

143

The genome of Prunus humilis provides new insights to drought adaption and population diversity.

Wang Y, Xie J, Zhang H, Li W, Wang Z, Li H, Tong Q, Qiao G, Liu Y, Tian Y, Wei Y, Li P, Wang R, Chen W, Liang Z, Xu M. Wang Y, et al. DNA Res. 2022 Jun 25;29(4):dsac021. doi: 10.1093/dnares/dsac021. DNA Res. 2022. PMID: 35751601 Free PMC article.

144

Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica.

Kamiyama T, Shimada-Niwa Y, Tanaka H, Katayama M, Kuwabara T, Mori H, Kunihisa A, Itoh T, Toyoda A, Niwa R. Kamiyama T, et al. DNA Res. 2022 Jun 25;29(4):dsac019. doi: 10.1093/dnares/dsac019. DNA Res. 2022. PMID: 35686927 Free PMC article.

145

Environmental DNA analysis for macro-organisms: species distribution and more.

Minamoto T. Minamoto T. DNA Res. 2022 May 27;29(3):dsac018. doi: 10.1093/dnares/dsac018. DNA Res. 2022. PMID: 35652724 Free PMC article. Review.

146

Universal Surface Biotinylation: a simple, versatile and cost-effective sample multiplexing method for single-cell RNA-seq analysis.

Sugimoto M, Tada Y, Shichino S, Koyamatsu S, Tsumaki N, Abe K. Sugimoto M, et al. DNA Res. 2022 May 27;29(3):dsac017. doi: 10.1093/dnares/dsac017. DNA Res. 2022. PMID: 35652718 Free PMC article.

147

Inventory of ATP-binding cassette proteins in Lithospermum erythrorhizon as a model plant producing divergent secondary metabolites.

Li H, Matsuda H, Tsuboyama A, Munakata R, Sugiyama A, Yazaki K. Li H, et al. DNA Res. 2022 May 27;29(3):dsac016. doi: 10.1093/dnares/dsac016. DNA Res. 2022. PMID: 35640979 Free PMC article.

148

Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production.

Yamamoto J, Chumsakul O, Toya Y, Morimoto T, Liu S, Masuda K, Kageyama Y, Hirasawa T, Matsuda F, Ogasawara N, Shimizu H, Yoshida KI, Oshima T, Ishikawa S. Yamamoto J, et al. DNA Res. 2022 May 27;29(3):dsac015. doi: 10.1093/dnares/dsac015. DNA Res. 2022. PMID: 35608323 Free PMC article.

149

A chromosome-level genome assembly of the pollinating fig wasp Valisia javana.

Chen L, Feng C, Wang R, Nong X, Deng X, Chen X, Yu H. Chen L, et al. DNA Res. 2022 May 27;29(3):dsac014. doi: 10.1093/dnares/dsac014. DNA Res. 2022. PMID: 35595238 Free PMC article.

150

Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad.

Liedtke HC, Cruz F, Gómez-Garrido J, Fuentes Palacios D, Marcet-Houben M, Gut M, Alioto T, Gabaldón T, Gomez-Mestre I. Liedtke HC, et al. DNA Res. 2022 May 27;29(3):dsac013. doi: 10.1093/dnares/dsac013. DNA Res. 2022. PMID: 35583263 Free PMC article.

151

Chromosome-level genome assembly and characterization of Sophora Japonica.

Lei W, Wang Z, Cao M, Zhu H, Wang M, Zou Y, Han Y, Wang D, Zheng Z, Li Y, Liu B, Ru D. Lei W, et al. DNA Res. 2022 May 27;29(3):dsac009. doi: 10.1093/dnares/dsac009. DNA Res. 2022. PMID: 35466378 Free PMC article.

152

Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex.

Mixão V, Del Olmo V, Hegedűsová E, Saus E, Pryszcz L, Cillingová A, Nosek J, Gabaldón T. Mixão V, et al. DNA Res. 2022 Feb 27;29(2):dsac010. doi: 10.1093/dnares/dsac010. DNA Res. 2022. PMID: 35438177 Free PMC article.

153

Chromosomal-level genome assembly of the orchid tree Bauhinia variegata (Leguminosae; Cercidoideae) supports the allotetraploid origin hypothesis of Bauhinia.

Zhong Y, Chen Y, Zheng D, Pang J, Liu Y, Luo S, Meng S, Qian L, Wei D, Dai S, Zhou R. Zhong Y, et al. DNA Res. 2022 Feb 27;29(2):dsac012. doi: 10.1093/dnares/dsac012. DNA Res. 2022. PMID: 35438173 Free PMC article.

154

MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.).

Nishimura K, Motoki K, Yamazaki A, Takisawa R, Yasui Y, Kawai T, Ushijima K, Nakano R, Nakazaki T. Nishimura K, et al. DNA Res. 2022 Feb 27;29(2):dsac011. doi: 10.1093/dnares/dsac011. DNA Res. 2022. PMID: 35412600 Free PMC article.

155

The chromosome-level genome assembly of Gentiana dahurica (Gentianaceae) provides insights into gentiopicroside biosynthesis.

Li T, Yu X, Ren Y, Kang M, Yang W, Feng L, Hu Q. Li T, et al. DNA Res. 2022 Feb 27;29(2):dsac008. doi: 10.1093/dnares/dsac008. DNA Res. 2022. PMID: 35380665 Free PMC article.

156

Spatial and single-cell transcriptome analysis reveals changes in gene expression in response to drug perturbation in rat kidney.

Onoda N, Kawabata A, Hasegawa K, Sakakura M, Urakawa I, Seki M, Zenkoh J, Suzuki A, Suzuki Y. Onoda N, et al. DNA Res. 2022 Feb 27;29(2):dsac007. doi: 10.1093/dnares/dsac007. DNA Res. 2022. PMID: 35325072 Free PMC article.

157

Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron.

Wang M, Zhang L, Tong S, Jiang D, Fu Z. Wang M, et al. DNA Res. 2022 Feb 27;29(2):dsac006. doi: 10.1093/dnares/dsac006. DNA Res. 2022. PMID: 35266513 Free PMC article.

158

A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae).

Tang L, Liao X, Tembrock LR, Ge S, Wu Z. Tang L, et al. DNA Res. 2022 Feb 27;29(2):dsac005. doi: 10.1093/dnares/dsac005. DNA Res. 2022. PMID: 35171284 Free PMC article.

159

The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs.

Liu HL, Harris AJ, Wang ZF, Chen HF, Li ZA, Wei X. Liu HL, et al. DNA Res. 2022 Jan 28;29(1):dsac003. doi: 10.1093/dnares/dsac003. DNA Res. 2022. PMID: 35137004 Free PMC article.

160

A chromosome-level genome assembly of an alpine plant Crucihimalaya lasiocarpa provides insights into high-altitude adaptation.

Feng L, Lin H, Kang M, Ren Y, Yu X, Xu Z, Wang S, Li T, Yang W, Hu Q. Feng L, et al. DNA Res. 2022 Jan 28;29(1):dsac004. doi: 10.1093/dnares/dsac004. DNA Res. 2022. PMID: 35094078 Free PMC article.

161

Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species.

Shirasawa K, Ueta S, Murakami K, Abdelrahman M, Kanno A, Isobe S. Shirasawa K, et al. DNA Res. 2022 Jan 28;29(1):dsac002. doi: 10.1093/dnares/dsac002. DNA Res. 2022. PMID: 35040911 Free PMC article.

162

Chromosome-scale assembly of barley cv. 'Haruna Nijo' as a resource for barley genetics.

Sakkour A, Mascher M, Himmelbach A, Haberer G, Lux T, Spannagl M, Stein N, Kawamoto S, Sato K. Sakkour A, et al. DNA Res. 2022 Jan 28;29(1):dsac001. doi: 10.1093/dnares/dsac001. DNA Res. 2022. PMID: 35022669 Free PMC article.

163

Erratum to: Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads.

Kiguchi Y, Nishijima S, Kumar N, Hattori M, Suda W. Kiguchi Y, et al. DNA Res. 2021 Oct 11;28(6):dsab025. doi: 10.1093/dnares/dsab025. DNA Res. 2021. PMID: 34882767 Free PMC article. No abstract available.

164

Genome sequencing and analysis of two early-flowering cherry (Cerasus × kanzakura) varieties, 'Kawazu-zakura' and 'Atami-zakura'.

Shirasawa K, Itai A, Isobe S. Shirasawa K, et al. DNA Res. 2021 Oct 11;28(6):dsab026. doi: 10.1093/dnares/dsab026. DNA Res. 2021. PMID: 34792565 Free PMC article.

165

Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade.

Hirose Y, Ohtsubo Y, Misawa N, Yonekawa C, Nagao N, Shimura Y, Fujisawa T, Kanesaki Y, Katoh H, Katayama M, Yamaguchi H, Yoshikawa H, Ikeuchi M, Eki T, Nakamura Y, Kawachi M. Hirose Y, et al. DNA Res. 2021 Oct 11;28(6):dsab024. doi: 10.1093/dnares/dsab024. DNA Res. 2021. PMID: 34677568 Free PMC article.

166

Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714.

Riediger M, Hernández-Prieto MA, Song K, Hess WR, Futschik ME. Riediger M, et al. DNA Res. 2021 Oct 11;28(6):dsab023. doi: 10.1093/dnares/dsab023. DNA Res. 2021. PMID: 34672328 Free PMC article.

167

High-quality genome assembly of an important biodiesel plant, Euphorbia lathyris L.

Wang M, Gu Z, Fu Z, Jiang D. Wang M, et al. DNA Res. 2021 Oct 11;28(6):dsab022. doi: 10.1093/dnares/dsab022. DNA Res. 2021. PMID: 34664644 Free PMC article.

168

Genome-wide simple sequence repeat markers in potato: abundance, distribution, composition, and polymorphism.

Jian Y, Yan W, Xu J, Duan S, Li G, Jin L. Jian Y, et al. DNA Res. 2021 Oct 11;28(6):dsab020. doi: 10.1093/dnares/dsab020. DNA Res. 2021. PMID: 34609514 Free PMC article.

169

The time is ripe to investigate human centromeres by long-read sequencing†.

Suzuki Y, Morishita S. Suzuki Y, et al. DNA Res. 2021 Oct 11;28(6):dsab021. doi: 10.1093/dnares/dsab021. DNA Res. 2021. PMID: 34609504 Free PMC article.

170

Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads.

Kiguchi Y, Nishijima S, Kumar N, Hattori M, Suda W. Kiguchi Y, et al. DNA Res. 2021 Oct 11;28(6):dsab019. doi: 10.1093/dnares/dsab019. DNA Res. 2021. PMID: 34586399 Free PMC article.

171

Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate.

Liu H, Li X, Zhang Q, Yuan P, Liu L, King GJ, Ding G, Wang S, Cai H, Wang C, Xu F, Shi L. Liu H, et al. DNA Res. 2021 Sep 13;28(5):dsab011. doi: 10.1093/dnares/dsab011. DNA Res. 2021. PMID: 34514497 Free PMC article.

172

Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis.

Huang D, Ming R, Xu S, Wang J, Yao S, Li L, Huang R, Tan Y. Huang D, et al. DNA Res. 2021 Sep 13;28(5):dsab018. doi: 10.1093/dnares/dsab018. DNA Res. 2021. PMID: 34499150 Free PMC article.

173

A high-quality chromosome-level genome of wild Rosa rugosa.

Zang F, Ma Y, Tu X, Huang P, Wu Q, Li Z, Liu T, Lin F, Pei S, Zang D, Zhang X, Zheng Y, Yu Y. Zang F, et al. DNA Res. 2021 Sep 13;28(5):dsab017. doi: 10.1093/dnares/dsab017. DNA Res. 2021. PMID: 34499118 Free PMC article.

174

Exploring the evolutionary process of alkannin/shikonin O-acyltransferases by a reliable Lithospermum erythrorhizon genome.

Tang C. Tang C. DNA Res. 2021 Sep 13;28(5):dsab015. doi: 10.1093/dnares/dsab015. DNA Res. 2021. PMID: 34424327 Free PMC article.

175

Transcriptomes and DNA methylomes in apomictic cells delineate nucellar embryogenesis initiation in citrus.

Jia HH, Xu YT, Yin ZP, Wu XM, Qing M, Fan YJ, Song X, Xie KD, Xie ZZ, Xu Q, Deng XX, Guo WW. Jia HH, et al. DNA Res. 2021 Sep 13;28(5):dsab014. doi: 10.1093/dnares/dsab014. DNA Res. 2021. PMID: 34424285 Free PMC article.

176

Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids.

Shirasawa K, Nishio S, Terakami S, Botta R, Marinoni DT, Isobe S. Shirasawa K, et al. DNA Res. 2021 Sep 13;28(5):dsab016. doi: 10.1093/dnares/dsab016. DNA Res. 2021. PMID: 34424280 Free PMC article.

177

Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense.

Shirasawa K, Kobayashi N, Nakatsuka A, Ohta H, Isobe S. Shirasawa K, et al. DNA Res. 2021 Sep 13;28(5):dsab010. doi: 10.1093/dnares/dsab010. DNA Res. 2021. PMID: 34289022 Free PMC article.

178

Understanding small ORF diversity through a comprehensive transcription feature classification.

Guerra-Almeida D, Tschoeke DA, Nunes-da-Fonseca R. Guerra-Almeida D, et al. DNA Res. 2021 Sep 13;28(5):dsab007. doi: 10.1093/dnares/dsab007. DNA Res. 2021. PMID: 34240112 Free PMC article. Review.

179

Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae.

Bonilla E, Costa AR, van den Berg DF, van Rossum T, Hagedoorn S, Walinga H, Xiao M, Song W, Haas PJ, Nobrega FL, Brouns SJJ. Bonilla E, et al. DNA Res. 2021 Aug 25;28(4):dsab013. doi: 10.1093/dnares/dsab013. DNA Res. 2021. PMID: 34390569 Free PMC article.

180

Elucidation of the speciation history of three sister species of crown-of-thorns starfish (Acanthaster spp.) based on genomic analysis.

Yuasa H, Kajitani R, Nakamura Y, Takahashi K, Okuno M, Kobayashi F, Shinoda T, Toyoda A, Suzuki Y, Thongtham N, Forsman Z, Bronstein O, Seveso D, Montalbetti E, Taquet C, Eyal G, Yasuda N, Itoh T. Yuasa H, et al. DNA Res. 2021 Aug 25;28(4):dsab012. doi: 10.1093/dnares/dsab012. DNA Res. 2021. PMID: 34387305 Free PMC article.

181

The complete mitogenome assemblies of 10 diploid potato clones reveal recombination and overlapping variants.

Achakkagari SR, Tai HH, Davidson C, De Jong H, Strömvik MV. Achakkagari SR, et al. DNA Res. 2021 Aug 25;28(4):dsab009. doi: 10.1093/dnares/dsab009. DNA Res. 2021. PMID: 34254134 Free PMC article.

182

Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar 'Fielder'.

Sato K, Abe F, Mascher M, Haberer G, Gundlach H, Spannagl M, Shirasawa K, Isobe S. Sato K, et al. DNA Res. 2021 Jun 25;28(3):dsab008. doi: 10.1093/dnares/dsab008. DNA Res. 2021. PMID: 34254113 Free PMC article.

183

A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits.

Hirakawa H, Toyoda A, Itoh T, Suzuki Y, Nagano AJ, Sugiyama S, Onodera Y. Hirakawa H, et al. DNA Res. 2021 Jun 25;28(3):dsab004. doi: 10.1093/dnares/dsab004. DNA Res. 2021. PMID: 34142133 Free PMC article.

184

Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations.

Mixão V, Hegedűsová E, Saus E, Pryszcz LP, Cillingová A, Nosek J, Gabaldón T. Mixão V, et al. DNA Res. 2021 Jun 25;28(3):dsab006. doi: 10.1093/dnares/dsab006. DNA Res. 2021. PMID: 34129020 Free PMC article.

185

Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq.

Li X, Wu J, Xiao X, Rong Y, Yang H, Li J, Zhou Q, Zhou W, Shi J, Qi H, Du H. Li X, et al. DNA Res. 2021 Jun 25;28(3):dsab005. doi: 10.1093/dnares/dsab005. DNA Res. 2021. PMID: 33989386 Free PMC article.

186

Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle.

Yuan R, Zhang J, Wang Y, Zhu X, Hu S, Zeng J, Liang F, Tang Q, Chen Y, Chen L, Zhu W, Li M, Mo D. Yuan R, et al. DNA Res. 2021 May 2;28(2):dsab003. doi: 10.1093/dnares/dsab003. DNA Res. 2021. PMID: 34009337 Free PMC article.

187

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758).

Gomes-Dos-Santos A, Lopes-Lima M, Machado AM, Marcos Ramos A, Usié A, Bolotov IN, Vikhrev IV, Breton S, Castro LFC, da Fonseca RR, Geist J, Österling ME, Prié V, Teixeira A, Gan HM, Simakov O, Froufe E. Gomes-Dos-Santos A, et al. DNA Res. 2021 May 2;28(2):dsab002. doi: 10.1093/dnares/dsab002. DNA Res. 2021. PMID: 33755103 Free PMC article.

188

Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety 'Nijisseiki'.

Shirasawa K, Itai A, Isobe S. Shirasawa K, et al. DNA Res. 2021 May 2;28(2):dsab001. doi: 10.1093/dnares/dsab001. DNA Res. 2021. PMID: 33638981 Free PMC article.

189

Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections.

Kajiya-Kanegae H, Nagasaki H, Kaga A, Hirano K, Ogiso-Tanaka E, Matsuoka M, Ishimori M, Ishimoto M, Hashiguchi M, Tanaka H, Akashi R, Isobe S, Iwata H. Kajiya-Kanegae H, et al. DNA Res. 2021 Jan 19;28(1):dsaa032. doi: 10.1093/dnares/dsaa032. DNA Res. 2021. PMID: 33492369 Free PMC article.

190

Building pan-genome infrastructures for crop plants and their use in association genetics.

Jayakodi M, Schreiber M, Stein N, Mascher M. Jayakodi M, et al. DNA Res. 2021 Jan 19;28(1):dsaa030. doi: 10.1093/dnares/dsaa030. DNA Res. 2021. PMID: 33484244 Free PMC article. Review.

191

De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme, by long-read sequencing.

Takei H, Shirasawa K, Kuwabara K, Toyoda A, Matsuzawa Y, Iioka S, Ariizumi T. Takei H, et al. DNA Res. 2021 Jan 19;28(1):dsaa029. doi: 10.1093/dnares/dsaa029. DNA Res. 2021. PMID: 33475141 Free PMC article.

192

The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes.

Kushwaha B, Pandey M, Das P, Joshi CG, Nagpure NS, Kumar R, Kumar D, Agarwal S, Srivastava S, Singh M, Sahoo L, Jayasankar P, Meher PK, Shah TM, Hinsu AT, Patel N, Koringa PG, Das SP, Patnaik S, Bit A, Iquebal MA, Jaiswal S, Jena J. Kushwaha B, et al. DNA Res. 2021 Jan 19;28(1):dsaa031. doi: 10.1093/dnares/dsaa031. DNA Res. 2021. PMID: 33416875 Free PMC article.

193

The physiological potential of anammox bacteria as revealed by their core genome structure.

Okubo T, Toyoda A, Fukuhara K, Uchiyama I, Harigaya Y, Kuroiwa M, Suzuki T, Murakami Y, Suwa Y, Takami H. Okubo T, et al. DNA Res. 2021 Jan 19;28(1):dsaa028. doi: 10.1093/dnares/dsaa028. DNA Res. 2021. PMID: 33367889 Free PMC article.

194

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype.

Nashima K, Shirasawa K, Ghelfi A, Hirakawa H, Isobe S, Suyama T, Wada T, Kurokura T, Uemachi T, Azuma M, Akutsu M, Kodama M, Nakazawa Y, Namai K. Nashima K, et al. DNA Res. 2021 Jan 19;28(1):dsaa026. doi: 10.1093/dnares/dsaa026. DNA Res. 2021. PMID: 33175097 Free PMC article.

195

The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding.

Gonda I, Faigenboim A, Adler C, Milavski R, Karp MJ, Shachter A, Ronen G, Baruch K, Chaimovitsh D, Dudai N. Gonda I, et al. DNA Res. 2020 Dec 3;27(5):dsaa027. doi: 10.1093/dnares/dsaa027. DNA Res. 2020. PMID: 33340318 Free PMC article.

196

Characterization of G-quadruplex antibody reveals differential specificity for G4 DNA forms.

Javadekar SM, Nilavar NM, Paranjape A, Das K, Raghavan SC. Javadekar SM, et al. DNA Res. 2020 Dec 3;27(5):dsaa024. doi: 10.1093/dnares/dsaa024. DNA Res. 2020. PMID: 33084858 Free PMC article.

197

Whole genome sequencing identifies allelic ratio distortion in sperm involving genes related to spermatogenesis in a swine model.

Gòdia M, Casellas J, Ruiz-Herrera A, Rodríguez-Gil JE, Castelló A, Sánchez A, Clop A. Gòdia M, et al. DNA Res. 2020 Dec 3;27(5):dsaa019. doi: 10.1093/dnares/dsaa019. DNA Res. 2020. PMID: 32931559 Free PMC article.

198

Corrigendum to: Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae.

Bornowski N, Hamilton JP, Liao P, Wood JC, Dudareva N, Buell CR. Bornowski N, et al. DNA Res. 2020 Aug 1;27(4):dsaa025. doi: 10.1093/dnares/dsaa025. DNA Res. 2020. PMID: 33146674 Free PMC article. No abstract available.

199

The genotype-dependent phenotypic landscape of quinoa in salt tolerance and key growth traits.

Mizuno N, Toyoshima M, Fujita M, Fukuda S, Kobayashi Y, Ueno M, Tanaka K, Tanaka T, Nishihara E, Mizukoshi H, Yasui Y, Fujita Y. Mizuno N, et al. DNA Res. 2020 Aug 1;27(4):dsaa022. doi: 10.1093/dnares/dsaa022. DNA Res. 2020. PMID: 33051662 Free PMC article.

200

History and future perspectives of barley genomics.

Sato K. Sato K. DNA Res. 2020 Aug 1;27(4):dsaa023. doi: 10.1093/dnares/dsaa023. DNA Res. 2020. PMID: 32979265 Free PMC article. Review.

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