Affiliations 

  • 1 Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
  • 2 China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900, Sepang, Selangor, Malaysia
  • 3 Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
  • 4 Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
  • 5 Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. rozimohd@upm.edu.my
Sci Rep, 2020 08 03;10(1):13034.
PMID: 32747724 DOI: 10.1038/s41598-020-70030-0

Abstract

Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.