Table 1.
The 33 primers used to amplify the complete cp genome of the Populus.
Table 2.
The barcode sequences for the five Populus accessions.
Fig 1.
Gene map of the four Populus cp genomes.
The genes that are drawn outside the circle are transcribed clockwise, whereas those that are drawn inside the circle are transcribed counterclockwise. The large single copy (LSC), small single copy (SSC) and inverted repeat (IRA and IRB) regions are indicated.
Table 3.
Summary of the features of the complete cp genomes of the seven Populus accessions.
Fig 2.
Gene arrangement map of the seven cp genomes using MAUVE software in Geneious R8.
Annotations of rRNA, protein coding and tRNA genes are shown in red, white and green boxes, respectively.
Table 4.
Base composition of the CDS sequences.
Fig 3.
Comparison of the LSC, IR, and SSC border regions among the seven Populus cp genomes.
Fig 4.
Amino acid frequencies of the seven Populus cp genomes based on 58 protein-coding sequences.
Fig 5.
Comparison of SSRs among the seven cp genomes.
(A) The number of SSRs detected in seven Populus cp genomes. (B) The number of SSR types detected in seven Populus cp genomes: P1, mononucleotide repeat; P2, dinucleotide repeat, P3, trinucleotide repeat and C, compound repeat (C) Frequencies of identified SSRs.
Fig 6.
Analysis of repeat sequences in the seven cp genomes.
(A) Frequency of repeat types. Forward repeat (F), reverse repeat (R), palindrome repeat (P) and complement repeat (C). (B) Frequency of repeats ≥30 bp in length.
Table 5.
Numbers of nucleotide substitutions and indels in the seven cp genomes.
Fig 7.
Whole cp genome alignments of the seven Populus accessions using the mVISTA program, with P. adenopoda as the reference.
The Y-axis indicates identity from 50% to 100% and gray arrows indicate the position and direction of each gene. Red indicates noncoding sequences (CNS), blue indicates the exons of protein-coding genes (exon) and green indicates tRNA or rRNA genes.
Fig 8.
Comparison of the nucleotide variability values of the seven cp genomes of Populus.
The genetic divergences among the Populus cp genomes were calculated with the DnaSP software (window length, 600 bp; step size, 200 bp). X-axis, position of the midpoint of a window; Y-axis, nucleotide diversity of each window.
Table 6.
Pairwise nucleotide divergences of the eight cp genomes of Populus.
Fig 9.
Phylogeny of the 12 Populus species inferred from ML and BI analysis of the cp genome dataset.
Numbers between the lines on the left indicate the ML bootstrap values for clades with >50% support, and the numbers on the right indicate the Bayesian posterior probabilities.