Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes

Zhiwen Chen,Jinping Hua,Yumei Wang,Hushuai Nie,Haili Pei,Lida Zhang,Shuangshuang Li

doi:10.1186/s12864-017-4282-5

Abstract

BackgroundCotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium.ResultsSix Gossypium mitochondrial genomes, including three diploid species from D and three allotetraploid species from AD genome groups (G. thurberi D1, G. davidsonii D3-d and G. trilobum D8; G. tomentosum AD3, G. mustelinum AD4 and G. darwinii AD5), were assembled as the single circular molecules of lengths about 644 kb in diploid species and 677 kb in allotetraploid species, respectively. The genomic structures of mitochondrial in D group species were identical but differed from the mitogenome of G. arboreum (A2), as well as from the mitogenomes of five species of the AD group. There mainly existed four or six large repeats in the mitogenomes of the A + AD or D group species, respectively. These variations in repeat sequences caused the major inversions and translocations within the mitochondrial genome. The mitochondrial genome complexity in Gossypium presented eight unique segments in D group species, three specific fragments in A + AD group species and a large segment (more than 11 kb) in diploid species. These insertions or deletions were most probably generated from crossovers between repetitive or homologous regions. Unlike the highly variable genome structure, evolutionary distance of mitochondrial genes was 1/6th the frequency of that in chloroplast genes of Gossypium. RNA editing events were conserved in cotton mitochondrial genes. We confirmed two near full length of the integration of the mitochondrial genome into chromosome 1 of G. raimondii and chromosome A03 of G. hirsutum, respectively, with insertion time less than 1.03 MYA.ConclusionTen Gossypium mitochondrial sequences highlight the insights to the evolution of cotton mitogenomes.

Highlights

Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD
Gossypium mitochondrial genomes from diploid and allotetraploid species Six Gossypium mitochondrial genomes were obtained in present study, including three diploid D species and three allotetraploid AD species
Complete mitochondrial DNA sequences were deposited in the GenBank database respectively: G. thurberi D1 (Accession No KR736343), G. davidsonii D3-d (Accession No KR736344), G. trilobum D8(Accession No KR736346), G. tomentosum AD3 (Accession No KX388135), G. mustelinum AD4 (Accession No KX388136) and G. darwinii AD5 (Accession No KX388137) (Table 1)

Summary

Introduction

Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. It is not clear how plant mitochondrial genomes rearrange so frequently or how the genome sizes can vary dramatically over relatively short evolutionary period This dynamic organization of the angiosperm mitochondrial genome provides unique information as well as an appropriate model system for studying genome structure and evolution. Compared to the highly conserved chloroplast genome structures [34,35,36], comparative analysis revealed rapid evolutionary divergence of Gossypium mitochondrial genomes [37,38,39], which proved that deep analyses of more mitochondrial genomes would provide new data to consider the evolutionary relationships and to explore the mechanism of cytoplasmic male sterility (CMS)

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