Rice Information GateWay (RIGW)
Rice is a major food for the world's population and serves as a model plant in cereal genome research. The Rice Information GateWay (RIGW) was constructed in 2016 upon the completion of the Oryza sativa ssp. indica cv. Zhenshan 97 and Minghui 63 genomes sequenced by Huazhong Agricultural University (HZAU) and Arizona Genomics Institute (AGI) with the aim of providing accurate and timely annotation of indica rice genome sequences. We have annotated the indica rice genomes ZS97 and MH63 for gene content, repetitive elements, non-coding RNA, SNPs, inversions, translocations, presence/absence variations, and segmental duplications, etc. Sequence polymorphisms between different rice subspecies indica and japonica have been identified. Designed as a basic platform for indica rice study, RIGW presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies.
Table 1. Characteristics of the ZS97RS1 and MH63RS1 genomes
| ZS97RS1 | MH63RS1 | |
|---|---|---|
| Total size of assembled contigs (bp) | 346,854,256 | 359,918,891 |
| Numbers of gene models/transcripts | 54,831/78,033 | 57,174/80,581 |
| Number of non-TE gene loci | 34,610 | 37,324 |
| Number of predicted PPI | 1,296,100 | 1,155,115 |
| Number of KEGG mapped transcripts | 11,272 | 11,334 |
| Number of ortholog genes | 29,814 | 30,980 |
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References
1. Song JM, Lei Y, Shu CC, Ding YD, Xing F, Liu H, Wang J, Xie WB, Zhang J*, Chen LL*. Rice Information GateWay: A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Molecular Plant. 2017, 11(3). doi: 10.1016/j.molp.2017.10.003.
2. Zhang J#, Chen LL#, Xing F#, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang Y, Sun S, Jiao WB, Lv F, Du B, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou ZW, Hurtado BE, Danowitz A, Wing RA*, Zhang Q*. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc Natl Acad Sci U S A. 2016, 113(35): E5163-71. doi: 10.1073/pnas.1611012113.
3. Zhang J#, Chen LL#, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao WB, Xing F, Lee S, Talag J, Song JM, Du B, Xie W, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Hurtado BE, Danowitz A, Wing RA*, Zhang Q*. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci Data. 2016, 3:160076. doi: 10.1038/sdata.2016.76.