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) 2.0 was updated with the near-complete reference genome assemblies of ZS97RS2 and MH63RS2. ZS97RS2 contained 20 contigs (387.32 Mb), and six chromosomes (i.e. Chr02/Chr06/Chr07/Chr08/Chr10/Chr12) were assembled into single contigs. MH63RS2 contained 19 contigs (387.42 Mb), and seven (i.e. Chr03/Chr04/ Chr05/Chr06/Chr08/Chr10/Chr12) were assembled into single contigs. In addition, 12 and 10 chromosomes contained both telomeres and centromeres in ZS97RS2 and MH63RS2, respectively. 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 ZS97RS2 and MH63RS2 genomes
| ZS97RS2 | MH63RS2 | |
|---|---|---|
| Total size of assembled contigs (bp) | 387,324,985 | 387,422,159 |
| Numbers of gene models/transcripts | 60,897/84,957 | 60,123/83,258 |
| Number of non-TE gene loci | 37,651 | 38,047 |
| 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 (RIGW): A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Molecular Plant. 2018, 11(3): 505-507. 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.