Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

Abstract

Background: In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as "Bingpian" in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency.

Methods: In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci.

Results: The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae.

Conclusions: Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.

Keywords: Chloroplast genomes; Comparative genomics; DNA barcoding; Dipterocarpoideae; Phylogenetics; Selected selection.

Fig. 1

Gene map of S. leprosula chloroplast genomes. Genes inside the circle are transcribed clockwise, genes outside are transcribed counter-clockwise. Genes are color-coded to indicate functional groups. The dark gray area in the inner circle corresponds to guanine-cytosine (GC) content while the light gray corresponds to the adenine-thymine (AT) content of the genome. The small (SSC) and large (LSC) single-copy regions and inverted repeat (IRa and IRb) regions are noted in the inner circle

Fig. 2

The chloroplast genomes of all 23 different species were analyzed by shuffle-LAGAN program. The percentage of identity is shown on the vertical axis, which ranges from 50–100%, while the horizontal axis represents the position in the chloroplast genome. Each arrow indicates the annotated gene in the reference genome and the direction of its transcription. Genomic regions are color-coded into exons, tRNA, conserved non-coding sequences, and mRNA

Fig. 3

Changes in chloroplast GC content of all 23 species

Fig. 4

Comparison of the borders of the all regions among 20 chloroplast genomes of Dipterocarpoideae

Fig. 5

The repetitive sequence in eleven Dipterocarpoideae cp genomes used TandemRepeatFinder and RepeatMasker

Fig. 6

A comparison of pairwise K_a/K_s values of 23 species concatenated all single copy gene sequences

Fig. 7

Phylogenetic relationships of genus Dipterocarpoideae species with related species based on 50 single-copy genes. The topology is indicated with BI/ML/NJ bootstrap support values at each node. Roman scrip (I/II/III/IV) represent positively selected branches

Fig. 8

Comparison of partial site under positive selection of different genes