RPAN: Rice Pan-genome Browser for ∼3000 Rice Genomes

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2016 Dec 13

PMID 27940610

Citations 72

Authors

Chen Sun

Zhiqiang Hu

Tianqing Zheng

Kuangchen Lu

Yue Zhao

Wensheng Wang

Jianxin Shi

Chunchao Wang

Jinyuan Lu

Dabing Zhang

Zhikang Li

Chaochun Wei

Affiliations

Soon will be listed here.

Abstract

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k.

Citing Articles

Pangenome graphs and their applications in biodiversity genomics.

Secomandi S, Gallo G, Rossi R, Rodriguez Fernandes C, Jarvis E, Bonisoli-Alquati A Nat Genet. 2025; 57(1):13-26.

PMID: 39779953 DOI: 10.1038/s41588-024-02029-6.

A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.

Kaur H, Shannon L, Samac D BMC Genomics. 2024; 25(1):1022.

PMID: 39482604 PMC: 11526573. DOI: 10.1186/s12864-024-10931-w.

Lactuca super-pangenome reduces bias towards reference genes in lettuce research.

van Workum D, Mehrem S, Snoek B, Alderkamp M, Lapin D, Mulder F BMC Plant Biol. 2024; 24(1):1019.

PMID: 39468479 PMC: 11514843. DOI: 10.1186/s12870-024-05712-2.

Evaluation of deep learning for predicting rice traits using structural and single-nucleotide genomic variants.

Vourlaki I, Ramos-Onsins S, Perez-Enciso M, Castanera R Plant Methods. 2024; 20(1):121.

PMID: 39127715 PMC: 11316328. DOI: 10.1186/s13007-024-01250-y.

A genome-wide association study of panicle blast resistance to in rice.

Jinlong H, Yu Z, Ruizhi W, Xiaoyu W, Zhiming F, Qiangqiang X Mol Breed. 2024; 44(7):49.

PMID: 39007057 PMC: 11236831. DOI: 10.1007/s11032-024-01486-5.

References

Huang X, Kurata N, Wei X, Wang Z, Wang A, Zhao Q . A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012; 490(7421):497-501. PMC: 7518720. DOI: 10.1038/nature11532. View

Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J . SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2013; 1(1):18. PMC: 3626529. DOI: 10.1186/2047-217X-1-18. View

Weigel D, Mott R . The 1001 genomes project for Arabidopsis thaliana. Genome Biol. 2009; 10(5):107. PMC: 2718507. DOI: 10.1186/gb-2009-10-5-107. View

Shi X, Peng J, Yu X, Zhang X, Li D, Liu B . PopGeV: a web-based large-scale population genome browser. Bioinformatics. 2015; 31(18):3048-50. DOI: 10.1093/bioinformatics/btv324. View

Seitzer P, Huynh T, Facciotti M . JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. BMC Bioinformatics. 2013; 14:18. PMC: 3560190. DOI: 10.1186/1471-2105-14-18. View

Kent W . BLAT--the BLAST-like alignment tool. Genome Res. 2002; 12(4):656-64. PMC: 187518. DOI: 10.1101/gr.229202. View

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

Hennig A, Bernhardt J, Nieselt K . Pan-Tetris: an interactive visualisation for Pan-genomes. BMC Bioinformatics. 2015; 16 Suppl 11:S3. PMC: 4547177. DOI: 10.1186/1471-2105-16-S11-S3. View

Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes R . SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res. 2014; 43(Database issue):D1023-7. PMC: 4383887. DOI: 10.1093/nar/gku1039. View

10.

Yao W, Li G, Zhao H, Wang G, Lian X, Xie W . Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol. 2015; 16:187. PMC: 4583175. DOI: 10.1186/s13059-015-0757-3. View

11.

Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A . The human genome browser at UCSC. Genome Res. 2002; 12(6):996-1006. PMC: 186604. DOI: 10.1101/gr.229102. View

12.

Wei X, Xu J, Guo H, Jiang L, Chen S, Yu C . DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol. 2010; 153(4):1747-58. PMC: 2923886. DOI: 10.1104/pp.110.156943. View

13.

Schatz M, Maron L, Stein J, Wences A, Gurtowski J, Biggers E . Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 2014; 15(11):506. PMC: 4268812. DOI: 10.1186/PREACCEPT-2784872521277375. View

14.

Zou J, Liu C, Liu A, Zou D, Chen X . Overexpression of OsHsp17.0 and OsHsp23.7 enhances drought and salt tolerance in rice. J Plant Physiol. 2012; 169(6):628-35. DOI: 10.1016/j.jplph.2011.12.014. View

15.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

16.

Vernikos G, Medini D, Riley D, Tettelin H . Ten years of pan-genome analyses. Curr Opin Microbiol. 2014; 23:148-54. DOI: 10.1016/j.mib.2014.11.016. View

17.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

18.

Sakai H, Lee S, Tanaka T, Numa H, Kim J, Kawahara Y . Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 2013; 54(2):e6. PMC: 3583025. DOI: 10.1093/pcp/pcs183. View

19.

Noll A, Grundmann N, Churakov G, Brosius J, Makalowski W, Schmitz J . GPAC-genome presence/absence compiler: a web application to comparatively visualize multiple genome-level changes. Mol Biol Evol. 2014; 32(1):275-86. DOI: 10.1093/molbev/msu276. View

20.

Yan W, Wang P, Chen H, Zhou H, Li Q, Wang C . A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant. 2010; 4(2):319-30. DOI: 10.1093/mp/ssq070. View