Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing

Abstract

BackgroundChloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic.ResultsA total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the indica and japonica in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of indica and japonica within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice.ConclusionsThe chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of indica and japonica within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0129-y) contains supplementary material, which is available to authorized users.

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

“…SSRs were widely dispersed in chloroplast genomes, and have been extensively used in population genetics and molecular phylogenetic researches [40,41]. In this study, 1205 SSRs were identified in five Alpinia chloroplast genomes, including two accessions of A. oxyphylla, A. katsumadai, A. zerumbet, and A. pumila ( Figure 3 and Table S6).…”

Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses

“…SSRs are These markers are widely used in population genetics and breeding program studies 44, 45 because of their high polymorphism even within species, due to slipped-strand mispairing on a single DNA strand during DNA replication 46 . In this study, 1,043 SSRs were identified in sixteen Lilium cp genomes.…”

Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

“…The identification of genomic SNPs provides an opportunity to apply these data to genome-based association studies in the future. Recent studies have utilized whole mitochondrial or plastid genome approaches to detect SNPs in plants, which showed that organellar SNP markers are a powerful genetic resource for germplasm differentiation, purification, and population genetics (Mcpherson et al, 2013;Sabir et al, 2014;Wei et al, 2016;Shen et al, 2017). The Pyropia species is characterized by a high proportion of organellar DNA and a small organellar genome size, which makes sequencing the organellar genomes affordable and convenient without the need 1 http://www.fao.org/fishery/factsheets/en for prior isolation or amplification (Wang et al, 2013;Kong et al, 2014;Xu et al, 2018a).…”