Abstract
BackgroundThe 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.ResultsUpdated 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).ConclusionsThe 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.
Highlights
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
A reliable whole genome sequence was generated from the total DNA sequence avoiding the complications of errors due to chloroplast insertions in the nucleus or mitochondria that have plagued earlier chloroplast studies [3]
This study has demonstrated that rice genetics is not a simple dichotomy with indica and japonica domestications but rather two domestications of distinct maternal genomes and introgression of many genes from wild populations
Summary
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. Rice is crop of critical importance to global food security. Enhancement of genetic diversity is a key strategy for improving crop resilience to climate change and characterization of that diversity is important in managing food security. A wide range of rice types are grown throughout the world to satisfy the diverse food tastes of different human populations. The 390 Mb nuclear genome of rice [1, 2] is responsible for the control of the traits that explain the differences in rice grain types. As in many other plant groups the maternal (chloroplast) and nuclear phylogenies may differ due to transfer of the maternal genome in rare cross pollination of plants from distinct populations
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