In the current release of RicerelativesGD, three chromosome-level genome assemblies of Echinochloa species (Echinochloa crus-galli、Echinochloa colona、Echinochloa oryzicola)were provided by us (Wu et al., 2022). Based on the updated genomic data, 153,910 and 145,843 genes of 16 rice relatives were identified to be specific to the indica and japonica rice, respectively.
In the current release of RicerelativesGD, (1) two chromosome-level genome assemblies of weedy rice (Oryza sativa f. spontanea)(indica and japonica type) were provided by us (Wu et al., unpublished data); (2) the genome of a Oryza species, O. Granulate, was added (Wu et al., 2018). Based on the updated genomic data, 116,159 and 108,092 genes of 14 rice relatives were identified to be specific to the indica and japonica rice, respectively; (3) sequences and structures of two biosynthetic gene clusters for allelopathic and antimicrobial chemicals, the momilactone gene cluster in Calohypnum plumiforme, Echinochloa crus-galli, O. sativa, O. punctata, O. brachyantha, Leersia perrieri and the DIMBOA gene cluster in E. crus-galli, were added; (4) the genomic assembly and its annotated protein-coding genes of C. plumiforme (v2) which contains the genes in momilactone gene cluster were provided for download in this release.
In the second release of RicerelativesGD, genomic resources of Oryza sativa f. spontanea (weedy rice) (Sun et al., 2019) and new genome assembly (V2.0) of E. crus-galli (Ye et al., 2020) have been added/updated.
The bioinformatics pipeline for identification of specific genes was updated. The specific genes will be excluded if its BLASTP E-value is more than 1e-5 against the gene annotation set of indica/japonica rice (R498 and Nipponbare). Finally, 90,233 and 82,322 genes of 11 rice relatives were identified to be specific to the indica/japonica rice.
Genomic SNPs of 524 global weedy rice were integrated in this release by comparison with 479 representative local cultivated rice and wild rice (Qiu et al., 2020). The weedy rice’s specific SNPs were annotated with snpEff and their related genes were annotated with funRiceGenes (https://funricegenes.github.io/). Finally, 30,672 SNPs were annotated as HIGH/MODERATE effects and included in this release.
In this release, genome resources of 11 rice relatives including eight Oryza species (Oryza nivara, Oryza rufipogon, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, Oryza meridionalis, Oryza punctaca, Oryza brachyantha), Leersia perrieri, Zizania latifolia and Echinochloa crus-galli were selected (References list). Two rice reference genomes, indica R498 and japonica Nipponbare, were used. Interproscan, Mercator and Swiss-prot Uniport were used for gene annotation and GOATOOLS was used for GO enrichment analysis. As results, 9,107 stress response genes and 3,074 photosynthesis genes were identified based on their function annotations.
Specific genes in this release refer to those genes that have no orthologous genes in indica/japonica rice (R498 and Nipponbare). Based on gene families/orphan genes of all 13 species generated by Orthofinder, 179,480/152,658 genes were identified specific to the indica/japonica rice.
The RiceRelativesGD provides online tools including sequences BLAST, phylogenetic tree construction, genome browser and search for gene ID/symbol/GO term/Pfam term.