Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production

Abstract

Background The whole chloroplast genomes of 3018 rice genotypes were assembled from available sequence data by alignment with a reference rice chloroplast genome sequence, providing high quality chloroplast genomes for analysis of diversity on a much larger scale than in any previous plant study. Results Updated annotation of the chloroplast genome identified 13 more tRNA genes and 30 more introns and defined the function of more of the genes. Domesticated rice had chloroplast genomes that were distinct from those in wild relatives. Analysis confirms an Australian chloroplast clade as a sister to the domesticated clade. All domesticated rice genotypes could be assigned to one of two main clades suggesting the domestication of two distinct maternal genome clades that diverged long before domestication. These clades were very distinct having 4 polymorphisms between all 1486 accession in clade A and all 1532 accessions in clade B. These would result in expression of 3 proteins with altered amino acid sequences and a tRNA with an altered sequence and may be associated with adaptive evolution of the two chloroplast types. Diversity within these pools may have been captured during domestication with subclades enriched in specific groups such as basmati, tropical japonica and temperate japonica. However the phylogenies of the chloroplast and nuclear genomes differed possibly due to modern rice breeding and reticulate evolution prior to domestication. Indica and aus genotypes were common in both chloroplast clades while japonica genotypes were more likely to be found in the same clade (cladeB). Conclusions The different evolutionary paths of the cytoplasmic and nuclear genomes of rice have resulted in the presence of apparently functional chloroplast genome diversity and the implications for rice crop performance require further investigation.

Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes

“…Furthermore, both the reference S. bicolor NC008602 and S. bicolor 112151 are different accessions from different seed sources of the same cultivar Tx623 B (maintainer) whereas S. bicolor 314746 is from the cultivar Tx623 A (male sterile) (Table 1), which are breeding lines of a single variety of Tx623. Recent studies revealed variations within chloroplast genome sequences (Moner et al, 2018(Moner et al, , 2020 that could be associated with multiple domestication events in rice (Oryza sativa L.). Although the nuclear phylogeny places the S. bicolor accessions in one clade, this does not exclude the possibility that more than one chloroplast type from wild progenitors has been captured by domesticated sorghum as has been found in rice (Moner et al, 2020).…”

“…Recent studies revealed variations within chloroplast genome sequences (Moner et al, 2018(Moner et al, , 2020 that could be associated with multiple domestication events in rice (Oryza sativa L.). Although the nuclear phylogeny places the S. bicolor accessions in one clade, this does not exclude the possibility that more than one chloroplast type from wild progenitors has been captured by domesticated sorghum as has been found in rice (Moner et al, 2020). Multiple domestications or chloroplast capture by reticulate evolution (Jackson et al, 1999) may be involved.…”

“…Chloroplast transfer or capture is common in closely related plant species and represents a clear example of reticulate evolution. Whole chloroplast genome sequencing has revealed this process in many plant groups (Guyeux et al., 2019; Healey et al., 2018; Moner et al., 2020). This analysis shows that Stiposorghum and Parasorghum are not monophyletic groups.…”

Comparative genomic study on the complete plastomes of four officinal Ardisia species in China

“…Introns, a group of self-catalytic ribozymes that could splice their own excision from mRNA, tRNA, and rRNA precursors, help to infer phylogenetic relationships. The length of exons and introns in genes was important information in plant chloroplast genome 24 , 25 . In this study, there were two genes ( ycf3 and clpP ) including two introns in four Ardisia chloroplast genome.…”

Table_1.XLSX

“…While much work has been dedicated to understanding the origin and evolution of domesticated rice the issue of multiple versus single origins is a topic of ongoing debate. Most recent studies have concluded that a multiple origin scenario is most likely however the number of domestication events wherein key grain domestication loci were acquired remains unresolved (Huang et al, 2012;Civan et al, 2015Civan et al, , 2019Choi et al, 2017;Choi and Purugganan, 2018;Civan and Brown, 2018;Wang W. S. et al, 2018;Moner et al, 2020). The two major type of cultivated rice, indica and japonica, originated from different ancestral wild rice populations, with gene flows observed from japonica to indica as well as two relatively small ecotypes, aus and aromatic rice.…”