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. 2021 Mar 15;6(3):755–757. doi: 10.1080/23802359.2021.1878954

The complete chloroplast genome of Madhuca hainanensis (Sapotaceae), an endemic and endangered timber species in Hainan Island, China

Yong Wang a, Hai-Tao Wang b, Yu-Kai Chen a,✉, Jing Yu c,✉, Yong Yang a
PMCID: PMC7971245  PMID: 33796645

Abstract

Madhuca hainanensis Chun & F.C.How is an endangered and endemic species in Hainan Island, and it was ranked as a VU (Vulnerable) species in China. In this study, we reported its complete chloroplast (cp) genome sequence based on high throughput sequencing data. The complete cp genome was 159,630 bp in length, containing two short inverted repeat (IRs) of 26,093 bp, a large single copy (LSC) region of 88,846 bp and a small single copy (SSC) region of 18,598 bp. Totally, the cp genome contained 131 genes, including 86 protein coding genes (PCG), eight rRNA genes and 37 tRNAs. The GC contents of this genome was 36.8%. A maximum likelihood (ML) phylogenetic analysis indicates that M. hainanensis is closely related to Sinosideroxylon wightianum.

Keywords: Madhuca hainanensis, chloroplast genome, Illumina sequencing, phylogenetic analysis

The genus Madhuca in family Sapotaceae is widely distributed in South and Southeast Asia, including 85 species in the world. Among these, 2 species (Madhuca hainanensis and Madhuca pasquieri) are only distributed in Southern China, and Madhuca hainanensis Chun & F.C.How (https://www.ipni.org/n/787485-1) is endemic species in Hainan Island, China (Francisco-Ortega et al. 2010; Dai et al. 2013; Lin et al. 2018). It is extremely narrow distribution, occuring only in tropical, montane rain forests and evergreen forest at high altitudes of about 1000 m in Hainnan Island (Li and Huang 1996; Zhang and Ma 2008). In China, M. hainanensis, a valuable tropical timber species, is always used for shipbuilding, axles, sports equipment, mechanical appliance, furniture and bridges, because it has excellent characteristics such as dark reddish brown in appearance, dense in structure, tough in texture, and resistant to rot (Chen 1990; Huang et al. 2011). In addition, its seed is rich in oil, up to 55%, which can be used for food and soap making, and its bark contains rich tannin (Huang et al. 2011). However, M. hainanensis natural resources have been depleted due to long term use and unreasonable harvesting (Mo et al. 2007; Dai et al. 2013). At present, M. hainanensis was ranked as a VU (Vulnerable) species in China (World Conservation Monitoring Centre 1998), and only few researches related to its communitties, seedling conservation and human impacts on genetic diversity (Dai et al. 2013; Zhai et al. 2015). In this study, we herein assembled the complete chloroplast genome of M. hainanensis (GeneBank: MT909828) based on sequences data obtained with the Illumina HiSeq platform. Its cp genome sequence would contribute fundamental information to further phylogenetical and protective studies of this plant.

The sample of M. hainanensis was collected from Bawangling national nature reserve (N19°05′, E109°10′), Hainan Island, China, and deposited at the botany laboratory of Hainan Normal University, Haikou, China (Sample accession number: HS-1068). Total DNA was extracted from fresh leaves using the modified CTAB method (Doyle 1987).The genome was sequenced on an Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) with 150 bp paired-end reads. In total, approximately 4.88 Gb of clean reads data with an average coverage of 516× were obtained after quality filtering and trimming. The cp genome were assembled by SPAdes v.3.11.0 software (Bankevich et al. 2012) with cp genome of Lucuma. nervosa (MH018545) as reference. The assembled cp genome genes were then annotated using PGA (Qu et al. 2019), coupled with manual check and adjustment.

The complete cpDNA of M. hainanensis was 159,630 bp in length. The genome was a typical quadripartite structure, containing a pair of short inverted repeat (IRs) of 26,093 bp, which was separated by a large single copy (LSC) region of 88,846 bp and a small single copy (SSC) region of 18,598 bp. The complete cp genome contained 131 genes, including 86 protein coding genes (PCG), 8 rRNA genes and 37 tRNAs. Among these genes, 15 genes (trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC and ndhA) harbored a single intron and two genes (clpP, ycf3) had two introns. The majority of genes in M. hainanensis occurred as a single copy. The overall GC content of M. hainanensis cp genome is 36.8%.

To clarify the phylogenetic of M. hainanensis, a maximum likelihood (ML) phylogenetic tree was reconstructed by MAGA7 software using concatenated protein sequences of 64 single copy genes which were found in all 14 chloroplast genomes of Ebenales and Magnolia pyramidata (Magnoliaceae) as an out-group (Figure 1). The result showed that M. hainanensis is closely related to Sinosideroxylon wightianum, and all representatives of Ebenales were clustered into one monophyletic clade. Our result will provide useful information for genetic evolution and convervation genetics of this endangered plant.

Figure 1.

Figure 1.

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Maximum likelihood tree of M. hainanensis based on concatenated protein sequences of 64 single copy genes found in all 15 chloroplast genome. Numbers in the nodes were bootstrap values from 1000 replicates.

Funding Statement

This study was supported by the National Science Foundation of Hainan Province [318QN237].

Disclosure statement

No potential conflict of interest was reported by the author(s). Yong Wang and Hai-Tao Wang should be regarded as co-first authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession number MT909828. The associated BioProject, SRA and Bio-Sample numbers are PRJNA668681, SRP287064, and SAMN16418375 respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession number MT909828. The associated BioProject, SRA and Bio-Sample numbers are PRJNA668681, SRP287064, and SAMN16418375 respectively.

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