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2020 6
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Oxford Nanopore MinION Sequencing and Genome Assembly.
Lu H, Giordano F, Ning Z. Lu H, et al. Genomics Proteomics Bioinformatics. 2016 Oct;14(5):265-279. doi: 10.1016/j.gpb.2016.05.004. Epub 2016 Sep 17. Genomics Proteomics Bioinformatics. 2016. PMID: 27646134 Free PMC article. Review.
The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises h …
The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technolo …
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW. Wenger AM, et al. Nat Biotechnol. 2019 Oct;37(10):1155-1162. doi: 10.1038/s41587-019-0217-9. Epub 2019 Aug 12. Nat Biotechnol. 2019. PMID: 31406327 Free PMC article.
The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. ...De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of &g …
The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. ...De
Long-read sequencing and de novo assembly of a Chinese genome.
Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, Lintner KE, Ding Q, Wang Z, Hu J, Wang D, Wang F, Wang L, Lyon GJ, Guan Y, Shen Y, Evgrafov OV, Knowles JA, Thibaud-Nissen F, Schneider V, Yu CY, Zhou L, Eichler EE, So KF, Wang K. Shi L, et al. Nat Commun. 2016 Jun 30;7:12065. doi: 10.1038/ncomms12065. Nat Commun. 2016. PMID: 27356984 Free PMC article.
Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-t …
Short-read sequencing has enabled the de novo assembly of several individual human genomes, but wi …
De novo genome assembly of a Han Chinese male and genome-wide detection of structural variants using Oxford Nanopore sequencing.
Cai R, Dong Y, Fang M, Guo C, Ma X. Cai R, et al. Mol Genet Genomics. 2020 Jul;295(4):871-876. doi: 10.1007/s00438-020-01672-y. Epub 2020 Apr 9. Mol Genet Genomics. 2020. PMID: 32274588
Here we report the sequencing and de novo assembly of a healthy male northern Han Chinese genome and detection of structural variants using only nanopore sequencing data. ...Third-generation sequencing technologies have many …
Here we report the sequencing and de novo assembly of a healthy male northern Han Chinese genome a …
De novo sequencing and chromosomal-scale genome assembly of leopard coral grouper, Plectropomus leopardus.
Zhou Q, Guo X, Huang Y, Gao H, Xu H, Liu S, Zheng W, Zhang T, Tian C, Zhu C, Lin H, Chen S. Zhou Q, et al. Mol Ecol Resour. 2020 Sep;20(5):1403-1413. doi: 10.1111/1755-0998.13207. Epub 2020 Jul 23. Mol Ecol Resour. 2020. PMID: 32521104
Here we report the de novo sequencing and assembly of the P. leopardus genome using a combination of 10 Genomics, high-throughput chromosome conformation capture (Hi-C) and PacBio long-read sequencing technologies. Th …
Here we report the de novo sequencing and assembly of the P. leopardus genome using a combination of 10 …
Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants.
He Y, Luo X, Zhou B, Hu T, Meng X, Audano PA, Kronenberg ZN, Eichler EE, Jin J, Guo Y, Yang Y, Qi X, Su B. He Y, et al. Nat Commun. 2019 Sep 17;10(1):4233. doi: 10.1038/s41467-019-12174-w. Nat Commun. 2019. PMID: 31530812 Free PMC article.
We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding approaches. ...We improve gene annotation by generating more …
We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta …
Misassembly of long reads undermines de novo-assembled ethnicity-specific genomes: validation in a Chinese Han population.
Mai Z, Liu W, Ding W, Zhang G. Mai Z, et al. Hum Genet. 2019 Jul;138(7):757-769. doi: 10.1007/s00439-019-02032-6. Epub 2019 Jun 5. Hum Genet. 2019. PMID: 31168775
However, the widely used 'standard human reference genome' GRCh37/38 is based on Caucasians. Therefore, de novo-assembled reference genomes for specific ethnicities would have advantages for genetics and precision medicine applications, especially with …
However, the widely used 'standard human reference genome' GRCh37/38 is based on Caucasians. Therefore, de novo-assembl …
De Novo Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen Puccinia hordei Identifies Candidates for Three Avirulence Genes.
Chen J, Wu J, Zhang P, Dong C, Upadhyaya NM, Zhou Q, Dodds P, Park RF. Chen J, et al. G3 (Bethesda). 2019 Oct 7;9(10):3263-3271. doi: 10.1534/g3.119.400450. G3 (Bethesda). 2019. PMID: 31444296 Free PMC article.
Puccinia hordei (Ph) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the genomics of this pathogen, and a reference genome is lacking. In this study, the first reference genome was assembled for an …
Puccinia hordei (Ph) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the gen
Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome-level reference genome for the family Meliaceae.
Ji YT, Xiu Z, Chen CH, Wang Y, Yang JX, Sui JJ, Jiang SJ, Wang P, Yue SY, Zhang QQ, Jin JL, Wang GS, Wei QQ, Wei B, Wang J, Zhang HL, Zhang QY, Liu J, Liu CJ, Jian JB, Qu CQ. Ji YT, et al. Mol Ecol Resour. 2021 May;21(4):1243-1255. doi: 10.1111/1755-0998.13318. Epub 2021 Jan 27. Mol Ecol Resour. 2021. PMID: 33421343
A total of 34,345 genes were predicted in the genome after homology-based and de novo annotation analyses. Evolutionary analysis showed that the genomes of T. sinensis and Populus trichocarpa diverged ~99.1-103.1 million years ago, and the T. si …
A total of 34,345 genes were predicted in the genome after homology-based and de novo annotation analyses. Evolutionary …
De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing.
Kang SH, Lee JY, Lee TH, Park SY, Kim CK. Kang SH, et al. PLoS One. 2018 Dec 11;13(12):e0208344. doi: 10.1371/journal.pone.0208344. eCollection 2018. PLoS One. 2018. PMID: 30533012 Free PMC article.
Adlay (Coix lacryma-jobi) is a tropical grass that has long been used in traditional Chinese medicine and is known for its nutritional benefits. Recent studies have shown that vitamin E compounds in adlay protect against chronic diseases such as cancer and heart dis …
Adlay (Coix lacryma-jobi) is a tropical grass that has long been used in traditional Chinese medicine and is known for its nut …
29 results