Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships

Muhammad Syahmi Hishamuddin,Shiou Yih Lee,Shairul Izan Ramlee,Wei Lun Ng,Rozi Mohamed,Dhilia Udie Lamasudin

doi:10.1038/s41598-020-70030-0

Muhammad Syahmi Hishamuddin, Shiou Yih Lee + Show 4 more

Open Access

https://doi.org/10.1038/s41598-020-70030-0

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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.

Highlights

Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation
All newly sequenced cp genomes of Aquilaria species with gene annotations have been deposited into the GenBank (A. beccariana, MN125347; A. crassna, MN125348; A. hirta, MN125349; A. microcarpa, MN125350; A. rostrata, MN125351; A. sinensis, MN147870; A. subintegra, MN147871)
We report new complete cp genomes sequences from seven Aquilaria species and analyzed these genomes including another, which we recently published

Summary

Introduction

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. Aquilaria Lam., is a tropical tree genus from the family Thymelaeaceae Members of this taxon are widely distributed in the Indomalesia region, but their numbers are declining in the wild. They have entered various Red List categories of the International Union for Conservation of Nature (IUCN). A recent phylogenetic analysis utilizing five non-coding cp DNA regions from 15 species (Aquilarieae) yielded inconclusive resolution due to the high percentage of conserved s ites[11]. It has been suggested that genome-scale data could provide a better resolution and thorough information of a studied genus pertaining to taxonomical aspects, genetic diversity, and pattern of evolution[11]

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