title: Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes.
abstract: BACKGROUND
  The 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.).
  
  
  METHODS
  Mitochondrial 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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  These results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes.
authors.affiliation: 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, Beijing, 100193, China. successtmy@163.com.
authors.forename: Mingyong
authors.initials: M
authors.lastname: Tang
authors.affiliation: 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, Beijing, 100193, China. chenzhiwen6168@aliyun.com.
authors.forename: Zhiwen
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA50011, USA. corrinne@iastate.edu.
authors.forename: Corrinne E
authors.initials: CE
authors.lastname: Grover
authors.affiliation: Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China. yumeiwang001@126.com.
authors.forename: Yumei
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Present address: Saskatchewan Cancer Agency, Division of Oncology, Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada. lishuang2070114@163.com.
authors.forename: Shuangshuang
authors.initials: S
authors.lastname: Li
authors.affiliation: 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. 13717895021@126.com.
authors.forename: Guozheng
authors.initials: G
authors.lastname: Liu
authors.affiliation: College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China. mzhy@mail.hebau.edu.cn.
authors.forename: Zhiying
authors.initials: Z
authors.lastname: Ma
authors.affiliation: Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA50011, USA. jfw@iastate.edu.
authors.forename: Jonathan F
authors.initials: JF
authors.lastname: Wendel
authors.affiliation: 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, Beijing, 100193, China. jinping_hua@cau.edu.cn.
authors.forename: Jinping
authors.initials: J
authors.lastname: Hua
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D019143:Evolution, Molecular; D015321:Gene Rearrangement; D022761:Gene Transfer, Horizontal; D050259:Genes, Mitochondrial; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D003368:Gossypium / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D011544:Pseudogenes; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D026801:Synteny / Q000235:genetics
chemical_list: D012343:RNA, Transfer