A chloroplast variation map generated using whole genome re-sequencing of Korean landrace rice reveals phylogenetic relationships amongOryza sativasubspecies

Abstract

Although the overall structure of the chloroplast genome is generally conserved, several sequence variations have been identified that are valuable for plant population and evolutionary studies. Here, we constructed a chloroplast variation map of 30 landrace rice strains of Korean origin, using the Oryza rufipogon chloroplast genome (GenBank: ) as a reference. Differential distribution of single‐nucleotide polymorphisms and INDELs across the rice chloroplast genome is suggestive of a region‐specific variation. Population structure clustering revealed the existence of two clear subgroups (indica and japonica) and an admixture group (aus). Phylogenetic analysis of the 30 landrace rice strains and six rice chloroplast references suggested and supported independent evolution of O. sativa indica and japonica. Interestingly, two aus type accessions, which were thought to be indica type, shared a closer relationship with the japonica type. One hypothesis is that ‘Korean aus’ was intentionally introduced and may have obtained japonica chloroplasts during cultivation. We also calculated the nucleotide diversity of 30 accessions and compared the results to six rice chloroplast references. These data demonstrated that although nucleotide diversity is low in all strains tested, aus and indica have a higher nucleotide diversity than japonica.

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

“…japonica is closed to Oryza rufipogon in Asian cultivated and wild rice (Brozynska et al 2014 ) and the African rice ( Oryza glaberrima and Oryza barthii ) were cluster together but in separate group with the Asian rice (Wambugu et al 2015 ). Our previous studies indicated that the use of chloroplast genome variation to study diversity, population genetics, and phylogenetic analysis was quite convincing and also supported some previous outcomes (Tong et al 2015 ). Despite these chloroplast-related studies, a large number of accessions must be applied to extend these studies from limited collections and specific varieties.…”

“…indica and japonica , which were thought to be originated from O. nivara and O. rufipogon , respectively. According to a chloroplast whole genome sequence investigation from several references, we previously found that the indica and japonica were closer with O. nivara and O. rufipogon , respectively, which also indicated the independent origin of Asian cultivated rice (Tong et al 2015 ). Population structure of a KRICE_CORE set, which hold 137 accessions in current collection, also supported the hypothesis of the independent origin of indica and japonica in nuclear genome (Kim et al 2016 ).…”

Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

“…However, both inadequate informative sites of DNA sequences and a limited number of taxon sampling have sometimes led to poor phylogenetic resolution and inappropriate taxonomic treatment. The whole chloroplast genome, containing more informative sites, has been regarded as a powerful data source for resolving the phylogenetic relationships of different taxonomic ranks, especially taxa with notorious difficulty in species delimitation (Knox & Palmer, 1999;Goremykin et al, 2004;Shaw et al, 2007;Tong et al, 2015;Wen et al, 2018;Liu et al, 2019). With the development of next-generation sequencing technologies as well as the decreasing cost, it has become practical to resolve difficult phylogenies using the whole chloroplast genome (Wilkinson et al, 2017;Valcárcel & Wen, 2019).…”

Genetic diversity of Australian wild rice

“…This suggest that the maternal genomes of aus come from two different origins. (Kumagai et al, 2016) (Civáň et al, 2015;Kim et al, 2015;Tong et al, 2015;Tong et al, 2016) Despite the existence of distinct clades based upon chloroplast sequence the accessions did not show a strong geographic isolation being spread widely across the south and east of Asia. Divergence may have been caused by a past period of geographic isolation creating distinct populations that became the progenitors for domestication of indica and japonica rice.…”

“…However, accessions in the O. sativa japonica sub clade extended further west into India, while the O. sativa subsp. indica were more abundant further to the south and east (Civáň et al, 2015;Garris et al, 2005;Kim et al, 2014b;Tong et al, 2015;Tong et al, 2016).…”