Fig 1.
Gene map of the Pinus taeda plastid genome.
Thick lines in the red area indicate the extent of the inverted repeat regions (IRa and IRb; 850 bp), which separate the genome into small (SSC; 42,258 bp) and large (LSC; 77,614 bp) single copy regions. Genes drawn inside the circle are transcribed clockwise, and those outside are transcribed counter clockwise. Genes belonging to different functional groups are color-coded. The dark grey in the inner circle corresponds to the GC content and the light grey corresponds to the AT content.
Table 1.
Summary of complete chloroplast genomes for 15 Pinus species.
Table 2.
Genes in the sequenced P. taeda chloroplast genome.
Table 3.
Genes with introns in the Pinus taeda chloroplast genome and length of exons and introns.
Fig 2.
Amino acid frequencies of the Pinus taeda chloroplast (cp) protein coding sequences.
The frequencies of amino acids were calculated for all 81 protein-coding genes from the start to the stop codon.
Table 4.
Base compositions in the Pinus taeda chloroplast (cp) genome.
Table 5.
Codon–anticodon recognition pattern and codon usage for the Pinus taeda chloroplast genome.
Fig 3.
Visual alignment of plastid genomes from Pinus taeda and six other Pinus species (five from the subgenus Pinus and one from the subgenus Strobus).
VISTA-based identity plot showing sequence identity among seven species, using P. taeda as a reference.
Fig 4.
Distance between adjacent genes and junctions of the small single-copy (SSC), large single-copy (LSC), and two inverted repeat (IR) regions among plastid genomes from six Pinus species.
Boxes above and below the main line indicate the adjacent border genes. The figure is not to scale regarding sequence length, and only shows relative changes at or near the IR/SC borders.
Table 6.
Repeat sequences in the Pinus taeda chloroplast genome.
Table 7.
Tandem repeat sequences in the Pinus taeda chloroplast genome.
Fig 5.
Analysis of simple sequence repeat (SSR) in the Pinus taeda plastid genome.
A, Number of SSR types in complete genome, coding, and non-coding regions; B, Frequency of identified SSR motifs in different repeat class types.
Table 8.
Simple sequence repeats (SSRs) in the Pinus taeda chloroplast genome.
Fig 6.
Phylogenetic trees of 15 Pinus species.
The entire genome dataset was analyzed using four different methods: Bayesian inference (BI), maximum parsimony (MP), maximum likelihood (ML), and neighbor-joining (NJ). Numbers above the branches represent bootstrap values in the MP, ML, and NJ trees and posterior probabilities in the BI trees, whereas the number below the branches represents branch length. The red dot represents the position of P. taeda (KY964286).