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

Ivy Yee Yen Chew; Hung Hui Chung; Leonard Whye Kit Lim; Melinda Mei Lin Lau; Han Ming Gan; Boon Siong Wee; Siong Fong Sim

doi:10.1016/j.dib.2023.109029

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

Data Brief. 2023 Mar 4:47:109029. doi: 10.1016/j.dib.2023.109029. eCollection 2023 Apr.

Authors

Ivy Yee Yen Chew¹, Hung Hui Chung¹, Leonard Whye Kit Lim¹, Melinda Mei Lin Lau¹, Han Ming Gan^{2

3}, Boon Siong Wee¹, Siong Fong Sim¹

Affiliations

¹ Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
² Patriot Biotech Sdn Bhd, 47500 Subang Jaya, Selangor, Malaysia.
³ Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.

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.