The complete chloroplast genome sequence of a Korean indigenous ornamental plant Hydrangea serrata for. fertilis Nakai (Hydrangeaceae).

De novo assembly with whole genome sequencing data of Hydrangea serrata for. fertilis, a great ornamental landscape plant species worldwide, facilitated to generate the complete chloroplast genome sequence in this study. The complete sequence was a circular DNA molecule of 157 730 bp in length, containing the large single-copy (LSC) region of 86 789 bp, small single-copy (SSC) region of 18 711 bp and two inverted repeats (IRs) regions of 26 115 bp. The genome encoded 114 genes consisting of 80 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis with matK gene-coding sequences of 19 species in family Hydrangeaceae showed a close relationship of H. serrata for. fertilis Nakai with H. macrophylla.

Hydrangea species are popular flowering shrubs and widely used as landscape plant with great ornamental value. The plants are famous for its inflorescences with both inconspicuous fertile and attractive neuter flowers (Reed 2002; Conolly et al. 2010; Samain et al. 2010). The increasing interests in Hydrangea species as decorative plants have led to increase availability of diverse Hydrangea species and cultivars with various coloured flowers and also to make the species one of the best-selling ornamental plants worldwide (Cerbah et al. 2001; Rinehart et al. 2006). There has been a taxonomically dispute in Hydrangea genus. Hydrangea serrata was classified as a subspecies of H. macrophylla by McClintock (1957), but recent publications on Hydrangea species have designated the two species as different species (Reed & Rinehart 2006). In this study, we generated the complete chloroplast genome sequence of H. serrata for. fertilis, called “Tamra Sansukuk” in Korea (Cho et al. 2014), to contribute to classification and authentication of Hydrangea species such as DNA marker application for ginseng cultivars (Kim et al. 2014).

A plant material of H. serrata for. fertilis collected from Mt. Halla, Jeju island, Korea, was provided from Hanteak Botanical Garden (http://www.hantaek.co.kr/), Yongin, Korea. Total genomic DNA was extracted from fresh leaves following a modified cetyltrimethylammonium bromide (CTAB) protocol (Allen et al. 2006). A pair-end (PE) library was constructed and sequenced using an Illumina MiSeq platform by Lab Genomics, Inc. (Seongnam, Korea). Raw sequence data of 1.12 Gb were filtered and de novo assembled by a CLC genome assembler (v. beta 4.6, CLC Inc., Rarhus, Denmark), as described in Kim et al (2015a,b). Six representative chloroplast contigs were ordered and merged into a single draft sequence compared with the chloroplast sequence of Zanthoxylum piperitum (KT153018, Lee et al. 2015) as a reference. The draft sequence was validated using manual correction by PE read mapping. DOGMA software was used for annotation of protein-coding genes in the chloroplast genome (Wyman et al. 2004), and the annotation result was manually validated by BLAST searches.

The complete chloroplast genome was a circular DNA molecule of 157 730 bp in length with 37.5% of GC content, which was separated into a large single copy (LSC) region of 86 789 bp, a small single copy (SSC) region of 18 711 bp and a pair of inverted repeats (IRa and IRb) of 26 115 bp. The genome contained a total of 114 genes including 80 protein-coding genes 30 tRNA genes and four rRNA genes. The complete chloroplast genome was deposited at GenBank with accession number KU140669, which is the first complete chloroplast genome reported in family Hydrangeaceae and even in order Cornales.

The phylogenetic analysis was performed by comparison with matK coding sequences derived from other 19 species in family Hydrangeaceae, registered in NCBI Genbank, by a maximum likelihood analysis with 1000 bootstrap replicates using MEGA 6.0 program (Tamura et al. 2013). All tested species were clustered into their own genus groups, in which H. serrata for. fertilis was placed mostly close to H. macrophylla (Figure 1).

Figure 1.

Maximum likelihood phylogenetic tree of H. serrata for. fertilis with other 19 species in Hydrangeaceae family based on matK coding sequences. Numbers in the nodes are the bootstrap values from 1000 replicates. The matK sequence of Zanthoxylum piperitum (KT153018) in family Rutaceae was set as an outgroup.

Declaration of interest

This research was supported by the Bio & Medical Technology Development Program of the NRF funded by the Korean government, MSIP (NRF-2015M3A9A5030733).