The complete chloroplast genome of Abeliophyllum distichum Nakai (Oleaceae), cultivar Ok Hwang 1ho: insights of cultivar specific variations of A. distichum

Abstract

Abeliophyllum distichum Nakai is the only species in Abeliophyllum genus, which is Korean endemic. Ok Hwang 1ho, the first official cultivar of A. distichum., displays that colour of corolla is light yellow (8D and 9D). Here, we completed chloroplast genome of A. distichum cultivar Ok Hwang 1ho to understand genetic diversity of A. distichum cultivar. Its length is 156,008 bp long and has four subregions: 86,773 bp of large single copy (LSC) and 17,827 bp of small single copy (SSC) regions are separated by 25,704 bp of inverted repeat (IR) regions including 133 genes (88 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC contents of this chloroplast genome are 37.8% and in the LSC, SSC, and IR regions are 35.8%, 31.9%, and 43.2%, respectively. Ninety-three single nucleotide polymorphisms (SNPs) and 56 insertion and deletions (INDELs) are identified against previous A. distichum chloroplast genome. Phylogenetic trees show that A. distichum is clustered with two Forsythia species and many cultivars of Olea europaea subspecies present shorter branches than that of A. distichum. Our chloroplast genome will be a fundamental data to understand morphological diversity of A. distuichum.

Keywords:

• Abeliophyllum distichum
• chloroplast genome
• cultivar specific variation
• Ok Hwang 1ho
• Korea endemic

Abeliophyllum distichum Nakai belonging to Oleaceae is only species in Korean endemic genus, Abeliophyllum (Nakai 1919). Abeliophyllum distichum was firstly identified in Jincheon-gun, Chungcheongbuk province and six out of nine natural habitats have been designated as Korean National Monument (No. 14, 147, 221, 220, 364, and 370; Lee et al. 2014). However, Jincheon-gun habitat was unassigned due to destruction. Ok Hwang 1ho, the first official cultivar of A. distichum, displays that colour of corolla is light yellow (8D and 9D) in contrast to ivory colour of natural isolate.

To uncover cultivar specific variations on chloroplast genome with complete chloroplast genome from Jincheon-gun (Kim et al. 2016), total DNA of Ok Hwang 1ho collected in GoesanBunjae-Nongwon (Goesan-gun, Chungbuk Province, Republic of Korea, Voucher in InfoBoss Cyber Herbarium (IN); Y. Kim, IB-00589) was extracted from fresh leaves using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Genome was sequenced using HiSeqX at Macrogen Inc., Korea, and de novo assembly and sequence confirmation were done by Velvet 1.2.10 (Zerbino and Birney 2008), SOAPGapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.0.5 (Biomatters Ltd, Auckland, New Zealand) was used for chloroplast genome annotation based on A. distichum chloroplast complete genome (NC_031445; Kim et al. 2016).

The chloroplast genome of A. distichum (Genbank accession is MK616470) is 156,008 bp (GC ratio is 37.8%) and has four subregions: 86,773 bp of large single copy (LSC; 35.8%) and 17,827 bp of small single copy (SSC; 31.9%) regions are separated by 25,704 bp of inverted repeat (IR; 43.2%). It contains 133 genes (88 protein-coding genes, eight rRNAs, and 37 tRNAs); 19 genes (8 protein-coding genes, four rRNAs, and seven tRNAs) are duplicated in IR regions.

Based on alignment with the previously sequenced A. distichum chloroplast genome (NC_031445) isolated in Jincheon-gun, Korea (Kim et al. 2016), 93 single nucleotide polymorphisms (SNPs) and 56 insertion and deletions (INDELs) are identified, which is similar level to those of Illicium anisatum (Park, Kim, Xi 2019), Duchesnea chrysantha (Park, Kim, Lee 2019), and Eucommia ulmoides (Wang et al. 2016). Dioscorea polystachya (Cao et al. 2018) and Chenopodium quinoa (Maughan et al. 2019) present number of sequence variations among cultivars smaller than that of A. distichum, indirectly explaining morphological variations of A. distichum (e.g. different flower colours).

Thirty-five Oleaceae chloroplast genomes including two A. distichum chloroplasts (Kim et al. 2016) were used for constructing neighbor joining (bootstrap repeat is 10,000) and maximum likelihood phylogenic trees (bootstrap repeat is 1,000) using MEGA X (Kumar et al. 2018) and IQ-TREE (Nguyen et al. 2015), respectively, after aligning whole chloroplast genome sequences by MAFFT 7.388 (Katoh and Standley 2013). Phylogenetic trees show that A. distichum is clustered with two Forsythia species (Figure 1), of which morphology is similar. In addition, many cultivars of Olea europaea subspecies present shorter branches (Figure 1), indicating number of variations between two A. distichum may reflect its morphological variations. Our chloroplast genome will be a fundamental data to understand the morphological diversity of A. distuichum.

Figure 1. Neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1,000) phylogenetic trees of thirty-five Oleaceae chloroplast genomes: Abeliophyllum distichum (MK616470 in this study and NC_031445), Forsythia suspensa (NC_036367), Forsythia x intermedia (NC_036982), Fontanesia phillyreoides subsp. fortunei (MG255754), Olea woodiana subsp. woodiana (NC_015608), Olea exasperata voucher A. Costa 1 (NC_036985), Olea europaea subsp. maroccana (NC_015623), Olea europaea subsp. guanchica isolate La Gomera 10 (MG255764), Olea europaea cultivar Frantoio (GU931818), Olea europaea cultivar Bianchera (NC_013707), Olea europaea subsp. europaea cultivar Manzanilla (FN996972), Olea europaea subsp. europaea isolate Stavrovouni 11 (HF558645), Olea europaea subsp. laperrinei isolate Adjelella 10 (MG255765), Olea europaea subsp. europaea isolate Vallee du Fango 5 (MG255762), Olea europaea subsp. cuspidate (NC_015604), Hesperelaea palmeri (NC_025787), Chionanthus retusus (NC_035000), Olea europaea subsp. europaea isolate Oeiras 1 (MG255763), Schrebera arborea (NC_036986), Fraxinus excelsior (NC_037446), Syringa vulgaris (NC_036987), Noronhia lowryi (NC_036984), Fraxinus chiisanensis (MF980720), Chionanthus rupicola (NC_036980), Olea europaea subsp. cuspidate (FN996944), Olea europaea subsp. cuspidata isolate Menagesha Forest 14 (MG255760), Olea europaea subsp. cuspidata isolate Almihwit 5.1 (FN996943), Chionanthus parkinsonii (NC_036979), Syringa pinnatifolia (MG917095), Forestiera isabelae (NC_036981), Olea europaea subsp. europaea isolate Stavrovouni Monastery 11 (MG255761), Nestegis apetala (NC_036983), Ligustrum lucidum (MH394207), and Jasminum nudiflorum (NC_008407). Phylogenetic tree was drawn based on neighbor joining tree. The numbers above branches indicate bootstrap support values of maximum likelihood and neighbor joining phylogenetic trees, respectively.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education [NRF-2016R1D1A1B03934869].