| Chloroplast research have significant advantage of genomics and genome sequencing, and a new picture is emerging of how the chloroplast functions and communicates with other cellular compartments. As a world’s leading textile crop and a model system for studies of many biological processes, genomics research of cottons has advanced rapidly in the past few years. Gossypium contains5tetraploid (AD1to AD5,2n=4×) and47diploid species (designated A through G, plus K,2n=2×), but the origin and evolution of allotetraploid Gossypium has remained controversial. To further our understanding of this important crop, the chloroplast genome of three Gossypium species were determined in this study. The main results were as follows:1. The complete chloroplast genome sequences belong to three diploid species were determined and annotated. Bioinformatic analyses showed that, the chloroplast genomes of Gossypium were highly conserved. The three chloroplast genomes were typical circular chromosomes like those of most other higher plants, including the large single copy (LSC), the small single copy (SSC) and2IR regions. The whole genome size ranged between159,945bp (G. laxum; D9),159,973bp (G. turneri; D10) and160,122bp (G. shwendimanii; D11). Differences in the chloroplast genome size of Gossypium were mainly attributed to the length variations of IGS. The assignment of the potential genes identified140genes for each genome, including113functional gene (79of protein coding genes,30tRNA and4rRNA),2ORFs, four pseudogenes and21repeated genes. Four genes viz. infA, ycf68, ORF42and ORF56, in addition to earlier mentioned genes, were confirmed to be existed in studied genomes. The gene order was consistent with that of Nicotiana, which showed rearrangement did not exist. The GC content of the whole chloroplast genome calculated as37.27%,37.27%and37.25%for G. laxum (D9), G.turneri (D10) and G. shwendimanii (D11), respectively, which were similar to the other plants.2. SSRs totally varied from62to64, and the average rate was0.36SSRs/kb between the3genomes. The predominant mononucleotide repeats were A or T, which accounted for94.85%to97.28%of the mononucleotide repeats among the3genomes with a definition mononucleotide≥8bp. The SSR loci also contributed to the AT richness of the chloroplast DNA of Gossypium. The data obtained from this study indicated that SSR polymorphism is very rich in the chloroplast DNA of Gossypium and that the number of polymorphic SSRs would decrease along with SSR length decreasing or SSR motif elongation. 3. This study revealed that wide ranges of expansions and contractions of IR are very common evolutionary events among14Gossypium species which were compared in our research. The expansions/contractions of IR as observed in the IR/SSC/LSC borders are probably mediated by intra-molecular recombination between two short direct repeat sequences that frequently occur within the genes located at the borders.4. The phylogenetic analyses based on50protein coding genes for41angiosperms and four gymnosperm out groups (Cycas, Ginkgo, Pinus and Gnetum) were performed. Our phylogeny tree continued to strongly support that Theobroma cacao as the closest species to Gossypium inside eudicots. Phylogenetic trees with bootstrap values (BS) were built for fourteen Gossypium species. All methods of data analyses, means maximum-likelihood (ML), maximum parsimony (MP) and neighbor-joining (NJ) had no effect on the phylogenetic trees, and the resulted topology were highly similar in each dataset. Phylogenetic trees of three dataset in our study for fourteen Gossypium species were largely congruent with each other. |
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