Table 1.
General features of six Gossypium chloroplast genomes.
Fig 1.
A consensus map of six newly sequenced Gossypium chloroplast genomes.
Genes on the outside of the outer circle are transcribed in the clockwise direction and genes on the inside of the outer circle are transcribed in the counterclockwise direction. The inner circle delineates the inverted repeat regions (IRa and IRb), the small single-copy region (SSC), and the large single-copy region (LSC). Functional categories of genes are color-coded.
Fig 2.
Maximum likelihood (ML) phylogenetic tree of 19 Gossypium species based on several analyses, including whole genome sequences, 78 concatenated chloroplast protein-coding exons sequences and indel-coded data.
Theobroma cacao was used as outgroup. Bootstrap values for all major divergences were high (>90%) on the corresponding nodes (Bayesian tree is similar, and therefore not displayed).
Fig 3.
Three types of junction region models for Gossypium chloroplast genome.
Type I, rps19 and trnH, entirely located in LSC region with no any overlap fragments in IR region. Type II, rps19 across the point of JLB, part fragment of 5’rps19 located in IRa region, trnH perfectly located in LSC region. Type III, rps19 across the point of JLB and trnH across the point of JLA, part fragment of 5’rps19 and 3’trnH located in IRa and IRb region, respectively. Also see S1 Fig for phylogenetic placement of each IR junction type.
Fig 4.
Inferred gains and losses of chloroplast genomic features during the evolution of Gossypium diploid species.
Genomic characters were mapped on the tree. Gains and losses of characters are indicated by solid and hollow symbols, respectively. *: the indels length aligned with G. hirsutum. The number in parentheses represents the length of indels.
Fig 5.
Chronogram showing Gossypium phylogeny and divergence time with T. cacao as an outgroup.
Consensus tree presenting divergence dates produces by the PhyloBayes analysis of the 78 concatenated chloroplast protein-coding exons dataset using three fossil calibration points (S8 Table), the autocorrelated Lognormal relaxed-clock mode, the site-heterogeneous mixture CAT+GTR substitution model, and soft bound 10%. A geological time scale is shown at the bottom. The arrows represent for three calibration points.