Complete chloroplast genome sequence of Hedychium coronarium

Abstract

The first complete chloroplast genome of Hedychium coronarium (Zingiberaceae) was reported in this study. The H. coronarium chloroplast genome was 163,949 bp in length and comprised a pair of inverted repeat (IR) regions of 29,780 bp each, a large single-copy (LSC) region of 88,581 bp and a small single-copy (SSC) region of 15,808 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and eight rRNA genes (four rRNA species). The nucleotide composition was asymmetric (31.68% A, 18.35% C, 17.74% G, 32.23% T) with an overall AT content of 63.92%. Phylogenetic analysis showed that H. coronarium was classified into a monophyletic group within the genus Hedychium in family Zingiberaceae.

Hedychium coronarium is one species of the genus Hedychium (Zingiberaceae), which distributes predominantly in southeast, south to southwest of China, south to southeast Asia and Australia (Wu et al. 2016). Hedychium coronarium pseudostems are 1–3 m tall; leaves sessile; ligule 2–3 cm, membranous; leaf blade oblong-lanceolate, 20–40 × 4.5–8 cm, adaxially glabrous, abaxially finely pubescent or thinly hairy, base acute, apex long acuminate (Wu and Larsen 2000). Hedychium coronarium plants are cultivated for their ornamental, medicinal and aromatic values (Wu and Larsen 2000; Wu et al. 2016). Within genus Hedychium, no complete chloroplast genome for Hedychium species has been reported so far (Li et al. 2019a), hindering species identification of Hedychium species based on chloroplast genomes.

Hedychium coronarium was collected from Guangzhou, Guangdong province, and stored at the resource garden of environmental horticulture research institute (specimen accession no. Hc2015), Guangdong academy of agricultural sciences, Guangzhou, China. Total chloroplast DNA was extracted from about 100 g of fresh leaves of H. coronarium using the sucrose gradient centrifugation method (Li et al. 2012). Chloroplast DNA (accession no. HcDNA2017) was stored at −80 °C in Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China. Library construction was using Illumina (Illumina, CA, USA) and PacBio (Novogene, Beijing, China) sequencing, respectively. The Illumina and PacBio sequencing data were deposited in the NCBI sequence read archive under accession numbers SRR8147014 and SRR8143983, respectively. After trimming, 69.4 M clean data of 150 bp paired-end reads and 0.65 M clean data of 8–10 kb subreads were generated. The chloroplast genome of H. coronarium was assembled and annotated using the reported methods (Li et al. 2019b). The annotated complete chloroplast genome sequence of H. coronarium was submitted to the GenBank (accession no. MK262736).

The complete chloroplast genome of H. coronarium was 163,949 bp in length and comprised a pair of inverted repeat (IR) regions of 29,780 bp each, a large single-copy (LSC) region of 88,581 bp, and a small single-copy (SSC) region of 15,808 bp. It was predicted to contain a total of 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA (28 tRNA species), and eight rRNA (four rRNA species). Twenty gene species occurred in double copies, including eight PCG species (ndhB, rpl2, rpl23, rps7, rps12, rps19, ycf1, and ycf2), eight tRNA species (trnA-UGC, trnH-GUG, trnI-CAU, trnI-GAU, trnL-CAA, trnV-GAC, trnR-ACG, and trnN-GUU), and all four rRNA species (rrn4.5, rrn5, rrn16, and rrn23). All these 20 gene species were located in the IR regions. The ycf1 gene crossed the boundary of SSC-IRb region, whereas the rps12 gene was located its first exon in the LSC region and other two exons in the IRs regions. In addition, 10 PCG genes (atpF, ndhA, ndhB, rpoC1, petB, petD, rpl2, rpl16, rps12, and rps16) and six tRNA genes (trnK-UUU, trnG-GCC, trnL-UAA, trnV-UAC, trnI-GAU, and trnA-UGC) had a single intron, whereas two other genes (ycf3 and clpP) possessed two introns. The nucleotide composition was asymmetric (31.68% A, 18.35% C, 17.74% G, and 32.23% T) with an overall AT content of 63.92%. The AT contents of the LSC, SSC, and IR regions were 66.15%, 70.48%, and 58.85%, respectively.

To obtain its phylogenetic position within family Zingiberaceae, a phylogenetic tree was constructed using single nucleotide polymorphisms (SNPs) arrays from available 16 species chloroplast genomes using Costus viridis, Costus pulverulentus, and Canna indica as outgroup taxa. The SNP arrays were obtained as previously described method (Li et al. 2019a). For each chloroplast genome, all SNPs were connected in the same order to obtain a sequence in FASTA format. Multiple FASTA format sequences alignments were carried out using ClustalX version 1.81 (Thompson et al. 1997). A maximum-likelihood phylogenetic tree (Figure 1) was constructed using the SNPs from 16 chloroplast genomes alignment result with MEGA7 (Kumar et al. 2016). As shown in the phylogenetic tree (Figure 1), H. coronarium was classified into a monophyletic group (bootstrap value = 97%) within the genus Hedychium in family Zingiberaceae with available SNPs.

Figure 1.

Phylogenetic tree constructed with single nucleotide polymorphisms arrays from 16 species chloroplast genomes using maximum-likelihood method. The bootstrap values were based on 1000 replicates and are indicated next to the branches. Accession numbers: Alpinia zerumbet JX088668, Alpinia oxyphylla NC_035895.1, Curcuma flaviflora KR967361, Curcuma roscoeana NC_022928.1, Curcuma longa MK262732, Kaempferia galanga MK209001, Kaempferia elegans MK209002, Zingiber spectabile JX088661, Amomum kravanh NC_036935.1, Amomum compactum NC_036992.1, Amomum villosum MK262730, Stahlianthus involucratus MK262725, Hedychium coronarium MK262736, Costus pulverulentus KF601573, Costus viridis MK262733, and Canna indica KF601570.

Disclosure statement

No potential conflict of interest was reported by the authors.