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The complete chloroplast genome of japonica type weedy rice (Oryza sativa f. spontanea).

ABSTRACT: As a noxious weed, weedy rice (Oryza sativa f. spontanea Roshev. 1931) has threatened global food security and sustainable crop production. On the other hand, weedy rice has a strong tolerance for abiotic stresses and the potential to provide rich resources for rice genetic improvement. Thus, for a more comprehensive understanding of its speciation, we sequenced and assembled the first complete chloroplast genome of Oryza sativa f. spontanea (japonica type). The complete chloroplast genome was 134,555 bp in length and encoded 133 genes, including 83 protein-coding genes, 42 tRNA genes and 8 rRNA genes. Phylogenetic analysis revealed that the indica-japonica differentiation of weedy rice was closely related to cultivated rice, and Oryza sativa f. spontanea (japonica type) was genetically more closely clustered with cultivated rice O. sativa (japonica type) than O. nivara or other wild rice.

SUBMITTER: Hu Y

PROVIDER: S-EPMC9347469 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of japonica type weedy rice (Oryza sativa f. spontanea).

Hu Yiyu Y Dong Chenfeng C Ye Chuyu C Fan Longjiang L Tang Wei W

Mitochondrial DNA. Part B, Resources 20220801 8

As a noxious weed, weedy rice (Oryza sativa f. spontanea Roshev. 1931) has threatened global food security and sustainable crop production. On the other hand, weedy rice has a strong tolerance for abiotic stresses and the potential to provide rich resources for rice genetic improvement. Thus, for a more comprehensive understanding of its speciation, we sequenced and assembled the first complete chloroplast genome of Oryza sativa f. spontanea (japonica type). Th ...[more]

PMID: 35937906

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The complete chloroplast genome of weedy rice Oryza sativa f. spontanea.

Project description:The emergence of weedy rice (Oryza sativa f. spontanea) has been considered as a serious global agricultural problem in recent decades. To better understand its speciation, here we assembled the complete chloroplast genome of O. sativa f. spontanea with the length of 134,502 bp. The assembly contains a large single-copy (LSC, 80,549 bp), a small single-copy (SSC, 12,347 bp) and a pair of inverted repeats (IRa and IRb, 20,803 bp each). A total of 132 unique genes were annotated, including 82 protein-coding genes, 42 tRNA genes and eight rRNA genes. Phylogenetic analysis showed that O. sativa f. spontanea (indica type) appears closely related to cultivated indica rice rather than wild rice, supporting the hypothesis that weedy rice originated from cultivated rice.

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Parallel reaction monitoring revealed tolerance to drought proteins in weedy rice (Oryza sativa f. spontanea).

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Gene flow from cultivated rice (Oryza sativa) to its weedy and wild relatives.

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