Dataset Information

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.

SUBMITTER: Chen Z

PROVIDER: S-EPMC4911064 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Chen Zhiwen Z Feng Kun K Grover Corrinne E CE Li Pengbo P Liu Fang F Wang Yumei Y Xu Qin Q Shang Mingzhao M Zhou Zhongli Z Cai Xiaoyan X Wang Xingxing X Wendel Jonathan F JF Wang Kunbo K Hua Jinping J

PloS one 20160616 6

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 ...[more]

PMID: 27309527

Similar Datasets

Project description:BackgroundSome Gynura species have been reported to be natural anti-diabetic plants. Improvement of their traits towards application relies on hybridization. Clearly, phylogenetic relationships could optimize compatible hybridizations. For flowerings plants, chloroplast genomes have been used to solve many phylogenetic relationships. To date, the chloroplast genome sequences of 4 genera of the tribe Senecioneae have been uploaded to GenBank. The internal relationships within the genus Gynura and the relationship of the genus Gynura with other genera in the tribe Senecioneae need further research.ResultsThe chloroplast genomes of 4 Gynura species were sequenced, assembled and annotated. In comparison with those of 12 other Senecioneae species, the Gynura chloroplast genome features were analysed in detail. Subsequently, differences in the microsatellite and repeat types in the tribe were found. From the comparison, it was found that IR expansion and contraction are conserved in the genera Gynura, Dendrosenecio and Ligularia. Compared to other regions on the chloroplast genome, the region from 25,000 to 50,000 bp was not conserved. Seven ndh genes in this region are under purifying selection, with small changes in amino acids. The whole chloroplast genome sequences of 16 Senecioneae species were used to build a phylogenetic tree. Based on the oldest Artemisia pollen fossil, the divergence time was estimated.ConclusionsSequencing the chloroplast genomes of 4 Gynura species helps us to solve many problems. The phylogenetic relationships and divergence time among 4 Gynura and 16 Senecioneae species were evaluated by comparing their chloroplast genomes. The phylogenetic relationship of the genera Gynura and Ligularia was different from that observed previous work. In a previous phylogenetic tree, the genus Ligularia belonged to the Tussilagininae subtribe, which was in a lineage that diverged earlier than other genera. Further morphology and genome-wide analyses are needed to clarify the genus relationships.

Project description:BackgroundWild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the largest textile natural fiber.ResultsA total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thurberi (D1), G. klotzschianum (D3-k), G. raimondii (D5) and G. trilobum (D8) to reference genome. The numbers of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was mined out by gene co-expression analysis. A total of 47,180-55,548 unique genes were identified in four diploid species by De novo assembly. Furthermore, 163, 344, 330, and 161 positively selected genes (PSGs) were detected in thurberi, G. klotzschianum, G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5-17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What's more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum showed the best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network.ConclusionOur study provided new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaptation during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca2+ signal transduction and oxidation-reduction mechanisms. Our work establishes a transcriptomic selection mechanism for altering gene expression of the four diploid D-genome cotton and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets