Fig 1.
Phylogenetic analysis of conifer cp genomes.
ML analysis was performed based on 47 cp protein-coding genes with a GTR + I + G model. G. biloba and C. revolute were set as outgroups. Support values for each branch based on a bootstrap analysis of 1,000 nonparametric replicates are shown. The scale of branch length is indicated in the bottom left corner.
Table 1.
Chloroplast genome features of G. pensilis.
Fig 2.
Chloroplast genome rearrangement estimates among cupressophytes and Pinaceae.
The topologies of clades cupressophytes (A) and Pinaceae (B) constructed from phylogenetic analysis were used as suggested actual trees and rearrangements were inferred from the matrices of cp genome LCBs. The estimated number of rearrangements for branches to taxa are shown above branches and corresponding rearrangements per million years were shown in brackets. The cp genome of G. biloba with removing IRA and IRB separately was used as a rooted genome in these two comparisons, respectively.
Fig 3.
The G. pensilis cp genome lost IRA in comparison with G. biloba and C. revolute.
Outer to inner circles correspond to the cp genome maps of C. revolute, G. biloba and G. pensilis, respectively. The bold blue and green lines in the C. revolute and G. biloba cp genome circles correspond to the IRA and IRB regions, respectively. The blue solid boxes correspond to the rpl23-rps3 cluster, which is always downstream of the IRB region, and the green solid boxes correspond to psbA, which is always upstream of the IRA region in a clockwise direction.
Fig 4.
The distribution of palindromic repeats and estimated number of rearrangement events in conifer cp genomes.
The full binomial species names for the species in this figure are listed in S2 Table. Dots colored in blue and red belong to the Pinaceae and cupressophytes, respectively and represent a pair of palindromic repeats with the size of the repeat unit corresponding to the value on the left y-axis. Dots colored in orange represent the estimated number of rearrangement events required for transforming corresponding species cp genome into that of G.biloba and correspond to the value on the right y-axis.
Fig 5.
SSR analysis in the G. pensilis cp genome.
(A) Frequency of identified SSR motifs in different repeat type classes. There were four kinds of SSR motifs identified in the G. pensilis cp genome. Most of the mononucleotides (109 of 111) are composed of A/T, and the majority of dinucleotides (30 of 50) are composed of AT/TA, whereas the other two kinds of SSRs have a high A/T content. (B) G. pensilis cp genome composition and SSR motifs distribution. SSRs are more abundant in the intergenic sequences (IGS, 55.93%) than in protein-coding regions (CDS, 28.94%), which account for 22.94 and 61.77% of the G. pensilis cp genome, respectively.