Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats

Li-Zhi Gao,Yuan Liu,Evan E Eichler,Shu-Yan Mao,Dan Zhang,Wei Li,Kui Li,Jun-Ying Jiao,Yuan Zhao,Chao Shi,Ju Gao,Cheng-Wen Gao,Yun-Long Liu,You-Jie Zhao

doi:10.1038/s42003-019-0531-2

Abstract

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences.

Highlights

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation
Besides Chloroplast DNA (cpDNA) sequences that have been applied to determining phylogenetic relationships among Oryza species[12,19,20,21,22,23], the completion of 10 Oryza plastomes (O. australiensis, O. barthii, O. glaberrima, O. glumaepatula, O. longistaminata, O. meridionalis, O. nivara, O. officinalis, O. rufipogon, and O. sativa)[24,25,26,27,28,29,30], and for example, the fully sequenced rice chloroplast genomes[24,31] have been extensively used to phylogenetic and population genetic studies in cultivated rice and wild relatives[32,33,34]
Illumina paired-end reads, after excluding non-chloroplast genome reads, were first mapped to the O. sativa ssp. japonica chloroplast genome (NC_001320) (AA- genome) as a reference, and these 21 chloroplast genomes were generated with genome sizes varying from 134,074 bp (L. japonica) to 136,133 bp (O. meyeriana) (GG- genome; Supplementary Table 2)

Summary

Introduction

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Indica to 48 bp in O. australiensis (EE- genome); a trivial difference in junction positions was observed among the 22 Oryza and L. japonica chloroplast genomes (Supplementary Fig. 6).

Results

Conclusion