BnPIR: Brassica napus pan-genome information resource for 1689 accessions

doi:10.1111/pbi.13491

. 2021 Mar;19(3):412-414.

doi: 10.1111/pbi.13491. Epub 2020 Dec 6.

BnPIR: Brassica napus pan-genome information resource for 1689 accessions

Jia-Ming Song^{1

2}, Dong-Xu Liu^{1

3}, Wen-Zhao Xie^{1

3}, Zhiquan Yang^{1

3}, Liang Guo¹, Kede Liu¹, Qing-Yong Yang^{1

3}, Ling-Ling Chen^{1

2

3}

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
² College of Life Science and Technology, Guangxi University, Nanning, China.
³ Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.

PMID: 33068485
PMCID: PMC7955874
DOI: 10.1111/pbi.13491

BnPIR: Brassica napus pan-genome information resource for 1689 accessions

Jia-Ming Song et al. Plant Biotechnol J. 2021 Mar.

. 2021 Mar;19(3):412-414.

doi: 10.1111/pbi.13491. Epub 2020 Dec 6.

Authors

Jia-Ming Song^{1

2}, Dong-Xu Liu^{1

3}, Wen-Zhao Xie^{1

3}, Zhiquan Yang^{1

3}, Liang Guo¹, Kede Liu¹, Qing-Yong Yang^{1

3}, Ling-Ling Chen^{1

2

3}

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
² College of Life Science and Technology, Guangxi University, Nanning, China.
³ Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.

PMID: 33068485
PMCID: PMC7955874
DOI: 10.1111/pbi.13491

No abstract available

Keywords: Brassica napus; gene index; homolog; pan-genome; presence/absence variations (PAVs); rapeseed population.

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Conflict of interest statement

No conflict of interest declared.

Figures

**Figure 1**
The architecture and representative resources of BnPIR. (a) The pipeline of ‘PVs + map‐to‐pan’ strategy to construct the pan‐genome of *B. napus*. (b) The phylogenetic tree of 1689 rapeseed accessions. (c) The three‐layer architecture of BnPIR. (d) Pan‐genome browser. (e) Population variations. (f) Gene information page. (g) Gbrowser. (h) Gbrowse synteny of multiple genomes. (i) 1689 rapeseed accessions. (j) Gene expression. T0: 24 days postsowing; T1: 54 days postsowing; T2: 82 days postsowing; T3: 115 days postsowing; T4: 147 days postsowing. (k) KEGG pathway. (l) Literature of rapeseed.

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References

1. Altschul, S.F. , Gish, W. , Miller, W. , Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410. - PubMed
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1. Chalhoub, B. , Denoeud, F. , Liu, S. , Parkin, I.A. , Tang, H. , Wang, X. et al. (2014) Early allopolyploid evolution in the post‐Neolithic Brassica napus oilseed genome. Science, 345, 950–953. - PubMed
1. Gan, X. , Stegle, O. , Behr, J. , Steffen, J.G. , Drewe, P. , Hildebrand, K.L. et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana . Nature, 477, 419–423. - PMC - PubMed
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[1] Altschul, S.F. , Gish, W. , Miller, W. , Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410. - PubMed

[2] Altschul, S.F. , Gish, W. , Miller, W. , Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410. - PubMed

[3] Buels, R. , Yao, E. , Diesh, C.M. , Hayes, R.D. , Munoz‐Torres, M. , Helt, G. et al. (2016) JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 17, 66. - PMC - PubMed

[4] Buels, R. , Yao, E. , Diesh, C.M. , Hayes, R.D. , Munoz‐Torres, M. , Helt, G. et al. (2016) JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 17, 66. - PMC - PubMed

[5] Chalhoub, B. , Denoeud, F. , Liu, S. , Parkin, I.A. , Tang, H. , Wang, X. et al. (2014) Early allopolyploid evolution in the post‐Neolithic Brassica napus oilseed genome. Science, 345, 950–953. - PubMed

[6] Chalhoub, B. , Denoeud, F. , Liu, S. , Parkin, I.A. , Tang, H. , Wang, X. et al. (2014) Early allopolyploid evolution in the post‐Neolithic Brassica napus oilseed genome. Science, 345, 950–953. - PubMed

[7] Gan, X. , Stegle, O. , Behr, J. , Steffen, J.G. , Drewe, P. , Hildebrand, K.L. et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana . Nature, 477, 419–423. - PMC - PubMed

[8] Gan, X. , Stegle, O. , Behr, J. , Steffen, J.G. , Drewe, P. , Hildebrand, K.L. et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana . Nature, 477, 419–423. - PMC - PubMed

[9] Kanehisa, M. , Goto, S. , Furumichi, M. , Tanabe, M. and Hirakawa, M. (2009) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355–D360. - PMC - PubMed

[10] Kanehisa, M. , Goto, S. , Furumichi, M. , Tanabe, M. and Hirakawa, M. (2009) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355–D360. - PMC - PubMed

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BnPIR: Brassica napus pan-genome information resource for 1689 accessions

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BnPIR: Brassica napus pan-genome information resource for 1689 accessions

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