The complete chloroplast genome sequence of Heritiera javanica

Abstract

The first complete chloroplast genome (cpDNA) sequence of Heritiera javanica was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 161,419 bp in length, contains a large single copy region (LSC) of 89,334 bp and a small single copy region (SSC) of 19,231 bp, which were separated by a pair of inverted repeats (IR) regions of 26,427 bp. The genome contains 129 genes, including 84 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Further phylogenomic analysis showed that H. javanica in a unique clade in Heritiera genus.

Keywords:

• Heritiera javanica
• chloroplast
• Illumina sequencing
• phylogenetic analysis

Heritiera javanica belongs to the genus Heritiera within the family Malvaceae (Larano and Buot 2010). Heritiera javanica is a timber tree species and can be used as particleboard (Sahromi et al. 2015). Other species of Heritiera genus showed anti-inflammatory principles (Tewtrakul et al. 2010), antitumor and antioxidant activities (Hu et al. 2018). Therefore, H. javanica have potential medical value. However, there have been no genomic studies on H. javanica.

Herein, we reported and characterized the complete H. javanica plastid genome. The GenBank accession number is MN823696. One H. javanica individual (specimen number: 201907028) was collected from Puwen, Yunnan Province of China (23°31’19” N, 101°37’31” E). The specimen is stored at Yunnan Academy of Forestry Herbarium, Kunming, China, and the accession number is ZJFEP117. DNA was extracted from its fresh leaves using DNA Plantzol Reagent (Invitrogen, Carlsbad, CA, USA).

Paired-end reads were sequenced using Illumina HiSeq system (Illumina, San Diego, CA). In total, about 22.4 million high-quality clean reads were generated with adaptors trimmed. Aligning, assembly, and annotation were conducted using CLC de novo assembler (CLC Bio, Aarhus, Denmark), BLAST, GeSeq (Tillich et al. 2017), and GENEIOUS v 11.0.5 (Biomatters Ltd, Auckland, New Zealand). To confirm the phylogenetic position of H. javanica, the other four species of Heritiera genus from NCBI were aligned using MAFFT v.7 (Katoh and Standley 2013). The Auto algorithm in the MAFFT alignment software was used to align the seven complete genome sequences and the G-INS-i algorithm was used to align the partial complex sequences. The maximum-likelihood (ML) bootstrap analysis was conducted using RAxML (Stamatakis 2006); bootstrap probability values were calculated from 1000 replicates. Gossypium sturtianum (JF317356) and Gossypium stocksii (JF317355) were served as the out-group.

The complete H. javanica plastid genome is a circular DNA molecule with the length of 161,419 bp, contains a large single copy region (LSC) of 89,334 bp and a small single copy region (SSC) of 19,231 bp, which were separated by a pair of inverted repeats (IR) regions of 26,427 bp. The overall GC content of the whole genome is 37.0%, and the corresponding values of the LSC, SSC, and IR regions are 34.9%, 31.2%, and 42.8%, respectively. The plastid genome contained 129 genes, including 84 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis showed that H. javanica clustered in a unique clade in Heritiera genus (Figure 1). The determination of the complete plastid genome sequences provided new molecular data to illuminate the Heritiera genus evolution.

Figure 1. The maximum-likelihood tree based on the five chloroplast genomes of Heritiera genus. The bootstrap value based on 1000 replicates is shown on each node.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This study was financially supported by Sub-projects of the National Key Research and Development Plan [2017YFD0601101-5] and Ten Thousand Industry Leaders Plan Talent of Yunnan Province.