Project description: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.

| S-EPMC3615480 | biostudies-literature

The complete plastid genome of the wild rice species <i>Oryza brachyantha</i> (Poaceae).

Project description:The whole plastid genome of wild rice (Oryza brachyantha) is characterized in this study. The genome is 134?604?bp in length and is arranged in a typical circular structure, including a pair of inverted repeats (IRs) of 20?832?bp in size separated by a large single-copy region (LSC) of 80?411?bp in length and a small single-copy region (SSC) of 12?529?bp in length. The overall GC content of the genome is 38.98%. One hundred and ten unique genes were annotated from the chloroplast genome, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. A total of 20 of these genes are duplicated in the IR regions, 13 genes contain 1 intron and 2 genes (rps12 and ycf3) have 2 introns.

| S-EPMC7871827 | biostudies-literature

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