Complete chloroplast genome data of Shorea macrophylla (Engkabang): Structural features, comparative and phylogenetic analysis

Abstract

Shorea macrophylla belongs to the Shorea genus under the Dipterocarpaceae family. It is a woody tree that grows in the rainforest in Southeast Asia. The complete chloroplast (cp) genome sequence of S. macrophylla is reported here. The genomic size of S. macrophylla is 150,778 bp and it possesses a circular structure with conserved constitute regions of large single copy (LSC, 83,681 bp) and small single copy (SSC, 19,813 bp) regions, as well as a pair of inverted repeats with a length of 23,642 bp. It has 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The genome exhibits a similar GC content, gene order, structure, and codon usage when compared to previously reported chloroplast genomes from other plant species. The chloroplast genome of S. macrophylla contained 262 SSRs, the most prevalent of which was A/T, followed by AAT/ATT. Furthermore, the sequences contain 43 long repeat sequences, practically most of them are forward or palindrome type long repeats. The genome structure of S. macrophylla was compared to the genomic structures of closely related species from the same family, and eight mutational hotspots were discovered. The phylogenetic analysis demonstrated a close relationship between Shorea and Parashorea species, indicating that Shorea is not monophyletic. The complete chloroplast genome sequence analysis of S. macrophylla reported in this paper will contribute to further studies in molecular identification, genetic diversity, and phylogenetic research.

Keywords: Chloroplast genome; Dipterocarpaceae; Monophyletic; Phylogenetic analysis; Shorea macrophylla.

Fig. 1

Gene map of S. macrophylla chloroplast genome. The genes inside and outside the outer circle are transcribed in clockwise and anticlockwise directions. Genes belonging to different functional groups are coloured with different colours. The inner circle indicates the four regions of the chloroplast genome. IRa, inverted repeat region A; IRb, inverted repeat region B; LSC, large single-copy region; SSC, small single-copy region. The line chart in grey colour shows GC content along the genome.

Fig. 2

Comparison of the borders of the LSC, SSC and IR regions among the eight chloroplast genomes.

Fig. 3

Nucleotide diversity analysis of the whole chloroplast genome. Window length: 600 bp; Step size: 200 bp. X-axis: midpoint positions of a window; Y-axis: nucleotide diversity between S. macrophylla and five other Shorea and two Parashorea species.

Fig. 4

The shuffle-LAGAN program analyzed the comparative analysis of S. macrophylla with Shorea and Parashorea species. The percentage of identity is shown on the vertical axis, which ranges from 50 to 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(purple), UTR (neon blue) and CNS (pink).

Fig. 5

Phylogenetic relationships of S. macrophylla with other Dipterocarpaceae family species and two outgroups based on their protein-coding genes. The bootstrap value based on 1000 replicates is shown on each node. The subclades are drawn with Shorea sp. subclade drawn in red colour and Parashorea sp. subclade drawn in green colour. The result shown Shorea genus is not monophyletic.