The complete chloroplast genome sequence of Capsicum chinense Jacq. (Solanaceae).

Capsicum chinense is one of the domesticated pepper species and well known for its distinctive pungency. The complete chloroplast genome sequence of C. chinense was generated by de novo assembly using next generation sequencing data. The chloroplast genome is 156 807 bp long, containing large single-copy region of 87 290 bp and small single-copy region of 17 911 bp separated by a pair of inverted repeats of 25 803 bp. A total of 113 genes were predicted including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenomic analysis revealed that C. chinense chloroplast genome was most closely related to Capsicum annuum var. glabriusculum (American bird pepper), a wild progenitor of C. annuum.

Capsicum chinense is one of the five domesticated pepper species belonging to the Solanaceae family. Its fruits are known for distinctive pungency causing severe heat and nominated as the hottest pepper in the world with one million of the Scoville heat units (SHU) (Bosland & Baral 2007). Studies have mainly been focused on pungency-related compounds, capsaicinoids, using metabolic approach in C. chinense (Menichini et al. 2009; Wahyuni et al. 2013). Previously, two complete chloroplast genome sequences of Capsicum annuum L. were reported: the cultivated type and its wild progenitor (Jo et al. 2011; Zeng et al. 2016). However, complete chloroplast sequence of C. chinense has not yet been reported and only several partial chloroplast genome sequences were reported. In this study, we reported complete sequence of chloroplast genome of C. chinense to provide basic genetic information and help understand genomic diversity of pepper species.

The genomic DNA was extracted from leaves of C. chinense cultivated in the field of Pepper and Breeding Institute, Suwon, Korea. An Illumina pair-end (PE) genomic library of 300-bp insert was constructed by following the PE standard protocol (Illumina, USA) and sequenced using an Illumina Hiseq 2000 platform by THERAGEN ETEX BIO INSTITUTE (http://www.theragenetex.com), Suwon, Korea. High quality reads (Phred scores of 20 or more) of 0.5 Gbp were obtained and assembled using CLC genome assembler (ver 4.06 beta, CLC Inc, Rarhus, Denmark), by following the assembly method in Kim et al. (2015a,b). Contigs representing chloroplast genome were retrieved, ordered and joined into a single draft sequence by comparison of C. annuum chloroplast genome (Jo et al. 2011) as a reference. The draft sequence was confirmed and manually corrected by PE read mapping. The draft sequence was annotated using DOGMA (Wyman et al. 2004).

The complete chloroplast sequence of C. chinense had a length of 156 807 bp (GenBank accession no. KU041709) and consisted of four typical chloroplast parts, such large single copy (LSC) of 87 290 bp and small single copy (SSC) of 17 911 bp, separated by a pair of inverted repeats of 25 803 bp (IRa and IRb). Total GC contents were 37.7%, which was consistent with that of reported chloroplast genome of cultivated C. annuum (Jo et al. 2011). A total of 113 genes were predicted, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes of which 28 genes were duplicated in IR regions. The order and contents of genes in C. chinense chloroplast genome were identical to those of C. annuum chloroplast genome.

Phylogenomic analysis was performed with previously reported chloroplast genome sequences of 10 species belonging to the Solanaceae family using a neighbor-joining analysis of MEGA 6.0 (Tamura et al. 2013) with 1000 bootstrap replicates. As expected, the 10 species were classified into three groups in our phylogenetic tree according to their tribes, Capsiceae, Solaneae, and Nicotianeae (Figure 1). In the phylogenetic tree, C. chinense was included in Capsiceae tribe group, in which C. chinense was much closer to C. annuum var. glabriusculum (American bird pepper), a wild progenitor of C. annuum (Zeng et al. 2016), than other Capsicum species.

Figure 1.

Phylogenetic relationship of 11 complete chloroplast genome sequences belonging to the Solanaceae family based on the neighbour-joining analysis of MEGA6.0. Numbers around nodes indicate the bootstrap value from 1000 replicates. The chloroplast sequence of Ipomoea batatas (sweet potato) was set as the outgroup.