Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

Abstract

The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

“…Table 1 shows a comparison of the predicted protein coding and tRNA gene content of four sequenced Oryza species, including O. glaberrima. The gene number in O. glaberrima falls between that of Oryza brachyantha 15 (30,952 genes) and that of the gold standard, O. sativa RefSeq 11 (41,620 …”

Genome Size and the Role of Transposable Elements

“…Parts a and b are modified and reprinted from (Schulman 2013) with permission from Elsevier genome is comprised of 81 % transposable elements and 77 % LTR retrotransposons, the vast majority of which inserted following the origin of the species (Staton et al 2012). Comparisons of the genomes of several Oryza (rice) species showed that differences in LTR retrotransposon abundance considerably explained variations in genome size in the genus (Chen et al 2013;Zhang et al 2007). Spectacularly, the genome of O. australiensis doubled in size over three million years due to gain of 90,000 copies of three LTR retrotransposons families, specifically RIRE1 of superfamily Copia and Kangourou and Wallabi of superfamily Gypsy (Piegu et al 2006).…”

Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice

“…The results showed that the TE insertion in the promoter region of RAV6 is conserved in all cultivated rice accessions (data not shown). To further confirm this, we aligned the sequences of the MITEs, as well as the 59 region of RAV6, in four known assembled rice genomes, including three cultivated rice strains, cv Nipponbare, 93-11, and Kasalath, and the wild rice Oryza brachyantha (Yu et al, 2002;International Rice Genome Sequencing Project, 2005;Chen et al, 2013;Sakai et al, 2014). The MITE insertion was conserved in the cultivated rice genomes but was absent in O. brachyantha (Fig.…”

“…All four known genome sequences of Oryza spp. were collected, including japonica rice 'Nipponbare' (International Rice Genome Sequencing Project, 2005), indica rice '93-11' (Yu et al, 2002), aus rice 'Kasalath' (Sakai et al, 2014), and the wild rice Oryza brachyantha (Chen et al, 2013). The genomic DNA sequence of the OsRAV6 gene body and 230-bp upstream region was used as a query sequence, and homologous regions were searched in the other three genomes of Oryza spp.…”