The first complete chloroplast sequence of a major tropical timber tree in the Meranti family: Vatica odorata (Dipterocarpaceae)

Abstract

Dipterocarpaceae are one of the economically most important native tree families for timber production in tropical Asia. We report the complete chloroplast genome of Vatica odorata (Griff.) Symington, the first in the family Dipterocarpaceae. The chloroplast genome was 151,465 bp in length, with a large single-copy (LSC) region of 83,538 bp and a small single-copy (SSC) region of 20,095 bp, separated by two inverted repeat (IRs) regions of 23,916 bp. It contained 126 genes, including 90 coding genes, 30 tRNA genes, and 8 rRNA genes. The overall GC content was 37.2%, and 43.1%, 35.2%, and 33.3% in the IRs, LSC and SSC regions, respectively. A phylogenetic tree showed Vatica accumulated more variation when compared with Tilia, and that internal relationships in Malvales need to be reassessed.

Keywords:

• Dipterocarpaceae
• complete chloroplast genome
• Vatica odorata
• malvales
• Tropical hardwood

Dipterocarpaceae, comprising more than 550 species, are spread throughout tropical Asia, Africa, and South America (Gottwald & Parameswaran 1966; Ashton 1982), with their centre of diversity in Malaysia (Ashton 1988). In China, Dipterocarpaceae are represented by 5 genera and 12 species (Xi-wen et al. 2007).

Despite a number of previous studies using single or multiple marker approaches (both cp- and nDNA) for Dipterocarpaceae (Kajita et al. 1998; Gamage et al. 2006; Yulita 2013), no studies to date have generated and used complete genomes (nuclear or chloroplast).

The genus Vatica comprises about 65 species (Xi-wen et al. 2007). Its timber is especially valuable as it is very hard and resistant to insect attacks. However, at the current rate of forest exploitation, 65 million ha of forest are projected to be cleared for agriculture between 2012 and 2030 (FAO 2012). Here, we report the complete chloroplast sequence of Vatica odorata to provide genomic resources for timber identification and quality improvement.

Genomic DNA of one individual of Vatica odorata was extracted from fresh leaves collected in XTBG Botanical Garden (22°35′24″N, 99°30′01″E Yunnan, China – voucher STRIJK_1594 deposited in the herbarium of the College of Forestry of Guangxi University, Nanning, China), using a SDS protocol (modified from Healey et al. 2014). Library construction and sequencing were performed by Novogene (Beijing, China), following Illumina HiSeq2500 system manufacturer instructions. De novo assembly of the cp genome was conducted using org.asm v0.2.05 (ORG.ASM 2016) and annotation using cpGAVAS (Liu et al. 2016).

The complete cp genome of Vatica odorata (GenBank accession KX966283) was 151,465 bp in length, with a large single-copy (LSC) region of 83,538 bp and a small single-copy (SSC) region of 20,095 bp, separated by two inverted repeat (IRs) regions of 23,916 bp. The genome contained 126 genes, including 90 coding genes, 30 tRNA genes, and 8 rRNA genes. The overall GC content of the cp genome was 37.2% and 43.1% in IRs, which was greater than LSC (35.2%) and SSC (33.3%) regions.

The chloroplast genome of Vatica odorata is the first to be published for the family and to confirm the phylogenetic position within the broader Malvales order, we reconstructed phylogenetic relationships using other plastome sequences available in GenBank using PHYML (Guindon et al. 2005). Phylogenetic tree shows the particularly long branch of Vatica, as opposed to Tilia, and the short branches underlying the nodes of the preceding clades (Figure 1). However, Malvaceae in its current circumscription are not monophyletic. Our results also suggest that the merger of Tiliaceae with other Malvaceae (sensu Chase & Reveal 2009) does not aid in resolving the phylogenetic quagmire in the family.

Figure 1. ML phylogenetic tree of the six Malvales in available chloroplast sequences in GenBank, plus the chloroplast sequence of Vatica odorata. The tree is rooted with the Brassicales (Arabidopsis thaliana). Bootstraps (100 replicates) are shown at the nodes. Scale in substitution per site.

This is the first study to report the complete chloroplast genome of a Dipterocarpaceae species and will be of great interest in further studies on genomic diversity, origin, and evolution of Dipterocarpaceae.

Acknowledgements

We would like to acknowledge B. Kingsley, M. Roeder and the horticultural staff of Xishuangbanna Tropical Botanical Garden (Chinese Academy of Sciences) for their assistance in sampling material of Vatica odorata.

Disclosure statement

This work was supported by grants from Guangxi University (Nanning), the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (GXU) and the provincial government of Guangxi Province (“100 Talents” Program; recruitment of overseas talents for colleges and universities in Guangxi) to JSS, and grants from China Postdoctoral Science Foundation (No. 2015M582481 and 2016T90822) to DDH. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by grants from Guangxi University (Nanning), the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (GXU) and the provincial government of Guangxi Province (“100 Talents” Program; recruitment of overseas talents for colleges and universities in Guangxi) to JSS, and grants from China Postdoctoral Science Foundation (No. 2015M582481 and 2016T90822) to DDH.