Sinbase2.0 - Sesame Multi-Omics Database

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Resources>>Comparative Genomics>>Interspecies Comparison:

I. Phylogeny among 7 plant species

In this project, we selected 6 plant species, including Arabidopsis thaliana, Vitis vinifera, Solanum tuberosum, Solanum lycopersicum, Sorghum bicolor, Oryza sativa, for interspecies comparison with Sesamum indicum. These species contains important food crops, cash crops and model plants, from which researchers can obtain more useful information according to homologous relationship between Sesamum indicum and these species.

Note: WGT-Whole Genome Triplication (Ƴ) event of Angiosperm.

II. The identification of orthologous group by OrthoMCL

OrthoMCL provides a scalable method for constructing orthologous groups across multiple eukaryotic taxa, using a Markov Cluster algorithm to group (putative) orthologs and paralogs. The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences [1].

Species Orthologous Gruops Involved Genes in S. indicum

Sesamum indicum var. Zhongzhi13 12,569 20,941

III. The identification of collinear regions by MCScanX

MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses [2].

Species Collinear regions Involved Genes in S. indicum

Sesamum indicum var. Zhongzhi13 vs. Arabidopsis thaliana 587 5,754

Sesamum indicum var. Zhongzhi13 vs. Oryza sativa 66 466

Sesamum indicum var. Zhongzhi13 vs. Sorghum bicolor 133 892

Sesamum indicum var. Zhongzhi13 vs. Solanum lycopersicum 591 8,240

Sesamum indicum var. Zhongzhi13 vs. Solanum tuberosum 127 968

Sesamum indicum var. Zhongzhi13 vs. Vitis vinifera 519 7,906

Reference:

1. Li Li, Christian J. Stoeckert Jr., and David S. Roos. OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 2003, 13:2178-2189, https://doi.org/10.1101/gr.1224503.

2. Yupeng Wang, Haibao Tang, Jeremy D. DeBarry, Xu Tan, Jingping Li, Xiyin Wang, Tae-ho Lee, Huizhe Jin, Barry Marler, Hui Guo, Jessica C. Kissinger and Andrew H. Paterson. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 2012, Vol. 40, No.7, e49. https://doi.org/10.1093/nar/gkr1293.