Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species

Abstract

The cotton genus (Gossypium spp.) contains 8 monophyletic diploid genome groups (A, B, C, D, E, F, G, K) and a single allotetraploid clade (AD). To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome in this group, we performed a comparative analysis of 19 Gossypium chloroplast genomes, six reported here for the first time. Nucleotide distance in non-coding regions was about three times that of coding regions. As expected, distances were smaller within than among genome groups. Phylogenetic topologies based on nucleotide and indel data support for the resolution of the 8 genome groups into 6 clades. Phylogenetic analysis of indel distribution among the 19 genomes demonstrates contrasting evolutionary dynamics in different clades, with a parallel genome downsizing in two genome groups and a biased accumulation of insertions in the clade containing the cultivated cottons leading to large (for Gossypium) chloroplast genomes. Divergence time estimates derived from the cpDNA sequence suggest that the major diploid clades had diverged approximately 10 to 11 million years ago. The complete nucleotide sequences of 6 cpDNA genomes are provided, offering a resource for cytonuclear studies in Gossypium.

Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

“…Allopolyploid Gossypium is the result of the transoceanic dispersal of an A‐genome species (resembling G. arboreum ), which subsequently hybridised with a native D‐genome species (resembling G. raimondii ) in the New World and experienced chromosome doubling (Wendel ; Chen et al . ). Cotton nuclear genome sequences have now been published for these model diploid progenitors of the polyploid species, G. raimondii (D 5 ; Wang et al .…”

“…; Chen et al . ). Here, we sequenced two diploid mitochondrial genomes, G. raimondii (D 5 ) and G. arboreum (A 2 ), whose progenitors are the putative contributors to the Dt subgenome and At subgenome of allotetraploid species, respectively.…”

“…The genus originated approximately 5-10 million years ago (Mya), subsequently diversifying into~46 diploid species (divided into eight monophyletic genome groups, designated A-G and K) and seven allotetraploid species Gallagher et al in press). Allopolyploid Gossypium is the result of the transoceanic dispersal of an A-genome species (resembling G. arboreum), which subsequently hybridised with a native D-genome species (resembling G. raimondii) in the New World and experienced chromosome doubling (Wendel 1989;Chen et al 2016). Cotton nuclear genome sequences have now been published for these model diploid progenitors of the polyploid species, G. raimondii (D 5 ; Wang et al 2012;Paterson et al 2012) and G. arboreum (A 2 ; Li et al 2014), as well as for the two agronomically important allopolyploids, G. hirsutum Zhang et al 2015) and G. barbadense Yuan et al 2015).…”

“…Cotton nuclear genome sequences have now been published for these model diploid progenitors of the polyploid species, G. raimondii (D 5 ; Wang et al 2012;Paterson et al 2012) and G. arboreum (A 2 ; Li et al 2014), as well as for the two agronomically important allopolyploids, G. hirsutum Zhang et al 2015) and G. barbadense Yuan et al 2015). In addition, the mitochondrial genomes Tang et al 2015) and chloroplast (Ibrahim et al 2006;Lee et al 2006) genomes of both cultivated polyploid species have been sequenced, the latter in conjunction with representatives of most Gossypium chloroplast species (Lee et al 2006;Xu et al 2012;Chen et al 2016). Here, we sequenced two diploid mitochondrial genomes, G. raimondii (D 5 ) and G. arboreum (A 2 ), whose progenitors are the putative contributors to the Dt subgenome and At subgenome of allotetraploid species, respectively.…”

TheGossypium longicalyxgenome as a resource for cotton breeding and evolution

“…Discovered only 60 years ago (Hutchinson and B. J. S. Lee 1958), it is both cytogenetically differentiated from members of the other genome groups (Phillips 1966) and morphologically isolated (Fryxell 1971, 1992). Importantly, G. longicalyx is sister to the A-genome cottons (Wendel and Albert 1992; Wendel and Grover 2015; Chen et al 2016), i.e., G. arboreum and G. herbaceum , the only diploids with long, spinnable fiber.…”