RPAN: rice pan-genome browser for ∼3000 rice genomes. Sun, C., Hu, Z., Zheng, T., Lu, K., Zhao, Y., Wang, W., Shi, J., Wang, C., Lu, J., Zhang, D., Li, Z., & Wei, C. Nucleic Acids Research, 45(2):597–605, January, 2017. ![RPAN: rice pan-genome browser for ∼3000 rice genomes [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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.
@article{sun_rpan_2017,
title = {{RPAN}: rice pan-genome browser for ∼3000 rice genomes},
volume = {45},
issn = {0305-1048},
shorttitle = {{RPAN}},
url = {https://doi.org/10.1093/nar/gkw958},
doi = {10.1093/nar/gkw958},
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.},
number = {2},
urldate = {2022-09-16},
journal = {Nucleic Acids Research},
author = {Sun, Chen and Hu, Zhiqiang and Zheng, Tianqing and Lu, Kuangchen and Zhao, Yue and Wang, Wensheng and Shi, Jianxin and Wang, Chunchao and Lu, Jinyuan and Zhang, Dabing and Li, Zhikang and Wei, Chaochun},
month = jan,
year = {2017},
keywords = {high-level, methods, pangenome, pangenome browser, pangenome database, pangenome tools},
pages = {597--605},
}
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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. 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