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The complete plastid genome of the wild rice species Oryza brachyantha (Poaceae).

ABSTRACT: 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.

SUBMITTER: Liu F

PROVIDER: S-EPMC7871827 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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

Liu Fengqi F Tembrock Luke R LR Sun Cheng C Han Guiqing G Guo Changhong C Wu Zhiqiang Z

Mitochondrial DNA. Part B, Resources 20160411 1

The whole plastid genome of wild rice (<i>Oryza brachyantha</i>) 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, ...[more]

PMID: 33644346

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Project description:BackgroundThe genus Oryza is being used as a model in plant genomic studies although there are several issues still to be resolved regarding the spatio-temporal evolution of this ancient genus. Particularly contentious is whether undated transoceanic natural dispersal or recent human interference has been the principal agent determining its present distribution and differentiation. In this context, we studied the origin and distribution history of the allotetraploid CD rice genome. It is endemic to the Neotropics but the genus is thought to have originated in the Paleotropics, and there is relatively little genetic divergence between some orthologous sequences of the C genome component and their Old World counterparts.Methodology/principal findingsBecause of its allotetraploidy, there are several potential pitfalls in trying to date the formation of the CD genome using molecular data and this could lead to erroneous estimates. Therefore, we rather chose to rely on historical evidence to determine whether or not the CD genome was present in the Neotropics before the arrival of Columbus. We searched early collections of herbarium specimens and studied the reports of explorers of the tropical Americas for references to rice. In spite of numerous collectors traveling inland and collecting Oryza, plants determined as CD genome species were not observed away from cultivated rice fields until 1869. Various arguments suggest that they only consisted of weedy forms until that time.Conclusions/significanceThe spatio-temporal distribution of herbarium collections fits a simple biogeographical scenario for the emergence in cultivated rice fields followed by radiation in the wild of the CD genome in the Neotropics during the last four centuries. This probably occurred from species introduced to the Americas by humans and we found no evidence that the CD genome pre-existed in the Old World. We therefore propose a new evolutionary hypothesis for such a recent origin of the CD genome. Moreover, we exemplify how an historical approach can provide potentially important information and help to disentangle the timing of evolutionary events in the history of the Oryza genomes.

Dataset Information

The complete plastid genome of the wild rice species Oryza brachyantha (Poaceae).

Publications

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

Similar Datasets

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