Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes

BMC Genomics

Research Article

Zhiying Ma¹  Jonathan F. Wendel²  Corrinne E. Grover²  Jinping Hua³  Mingyong Tang³  Zhiwen Chen³  Yumei Wang⁴  Guozheng Liu⁵  Shuangshuang Li⁶ 

[1] College of Agronomy, Hebei Agricultural University, 071001, Baoding, Hebei, China;Department of Ecology, Evolution and Organismal Biology, Iowa State University, IA50011, Ames, USA;Department of Plant Genetics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education /Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China;Institute of Cash Crops, Hubei Academy of Agricultural Sciences, 430064, Wuhan, Hubei, China;Present address: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt, Seeland, Germany;Present address: Saskatchewan Cancer Agency, Division of Oncology, Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada;

关键词: Mitochondrial genome;    Comparative genomics;    DNA rearrangement;    Duplicated copy;    Sequence transfer;   

DOI  :  10.1186/s12864-015-1988-0

 received in 2015-03-26, accepted in 2015-10-06,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced. To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.).MethodsMitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genome was sequenced with Solexa using paired-end, 90 bp read. The clean reads were assembled into contigs using ABySS and finished via additional fosmid and BAC sequencing. Finally, the genome was annotated and analyzed using different softwares.ResultsThe G. barbadense (Sea Island cotton) mitochondrial genome was fully sequenced (677,434-bp) and compared to the mitogenome of upland cotton. The G. barbadense mitochondrial DNA contains seven more genes than that of upland cotton, with a total of 40 protein coding genes (excluding possible pseudogenes), 6 rRNA genes, and 29 tRNA genes. Of these 75 genes, atp1, mttB, nad4, nad9, rrn5, rrn18, and trnD(GTC)-cp were each represented by two identical copies. A single 64 kb repeat was largely responsible for the 9 % difference in genome size between the two mtDNAs. Comparison of genome structures between the two mitochondrial genomes revealed 8 rearranged syntenic regions and several large repeats. The largest repeat was missing from the master chromosome in G. hirsutum. Both mitochondrial genomes contain a duplicated copy of rps3 (rps3-2) in conjunction with a duplication of repeated sequences. Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons.ConclusionThese results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes.

【 授权许可】

CC BY   
© Tang et al. 2015