title: Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids.
abstract: BACKGROUND
  Cotton (Gossypium spp.) is a model system for the analysis of polyploidization. Although ascertaining the donor species of allotetraploid cotton has been intensively studied, sequence comparison of Gossypium chloroplast genomes is still of interest to understand the mechanisms underlining the evolution of Gossypium allotetraploids, while it is generally accepted that the parents were A- and D-genome containing species. Here we performed a comparative analysis of 13 Gossypium chloroplast genomes, twelve of which are presented here for the first time.
  
  
  RESULTS
  The size of 12 chloroplast genomes under study varied from 159,959 bp to 160,433 bp. The chromosomes were highly similar having >98% sequence identity. They encoded the same set of 112 unique genes which occurred in a uniform order with only slightly different boundary junctions. Divergence due to indels as well as substitutions was examined separately for genome, coding and noncoding sequences. The genome divergence was estimated as 0.374% to 0.583% between allotetraploid species and A-genome, and 0.159% to 0.454% within allotetraploids. Forty protein-coding genes were completely identical at the protein level, and 20 intergenic sequences were completely conserved. The 9 allotetraploids shared 5 insertions and 9 deletions in whole genome, and 7-bp substitutions in protein-coding genes. The phylogenetic tree confirmed a close relationship between allotetraploids and the ancestor of A-genome, and the allotetraploids were divided into four separate groups. Progenitor allotetraploid cotton originated 0.43-0.68 million years ago (MYA).
  
  
  CONCLUSIONS
  Despite high degree of conservation between the Gossypium chloroplast genomes, sequence variations among species could still be detected. Gossypium chloroplast genomes preferred for 5-bp indels and 1-3-bp indels are mainly attributed to the SSR polymorphisms. This study supports that the common ancestor of diploid A-genome species in Gossypium is the maternal source of extant allotetraploid species and allotetraploids have a monophyletic origin. G. hirsutum AD1 lineages have experienced more sequence variations than other allotetraploids in intergenic regions. The available complete nucleotide sequences of 12 Gossypium chloroplast genomes should facilitate studies to uncover the molecular mechanisms of compartmental co-evolution and speciation of Gossypium allotetraploids.
authors.affiliation: College of Agronomy & Biotechnology, China Agricultural University, Beijing, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Xu
authors.forename: Guanjun
authors.initials: G
authors.lastname: Xiong
authors.forename: Pengbo
authors.initials: P
authors.lastname: Li
authors.forename: Fei
authors.initials: F
authors.lastname: He
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.forename: Kunbo
authors.initials: K
authors.lastname: Wang
authors.forename: Zhaohu
authors.initials: Z
authors.lastname: Li
authors.forename: Jinping
authors.initials: J
authors.lastname: Hua
mesh_terms: D001482:Base Composition; D019143:Evolution, Molecular; D023061:Gene Order; D054628:Genome, Chloroplast; D003368:Gossypium / Q000145:classification / Q000235:genetics*; D054643:INDEL Mutation; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D057891:Tetraploidy; D020506:Untranslated Regions
chemical_list: D020506:Untranslated Regions