The complete chloroplast genome of ornamental coffee tree, Coffea arabica L. (Rubiaceae)

Abstract

Coffea arabica L. taking 70% of world coffee production is also used as an ornamental species. One imported coffee tree from Indonesia near to thirty years ago of which leaf is wrinkled (named as IN1) was chosen to know its genetic background. Here, we presented complete chloroplast genome of Coffea arabica IN1 which is 155,277 bp long and has four subregions: 85,248 bp of large single copy (LSC) and 18,137 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.4% and those in the LSC, SSC, and IR regions are 35.4%, 31.3%, and 43.0%, respectively. In comparison to three available coffee chloroplast genomes, 84 bp insertion on IN1 chloroplast genome is found, which is big differences in comparison to other available coffee chloroplast genomes. Even though relatively low number of sequence variations on coffee chloroplast genomes, these results can be used as a corner stone for establishing molecular markers to identify its origin or cultivars.

Keywords:

• Coffea arabica
• ornamental species
• wrinkled leaf
• Indonesia
• chloroplast genome

Coffea arabica L., has been cultivated world-wide along with ‘Bean belt’ (Bentley and Baker 2000), occupying 70% of world coffee production (Lashermes et al. 1999; O'brien and Kinnaird 2003). Several species in Coffea genus are used as ornamental species because of good-shape leaves, e.g., Coffea horsfieldiana has been used as ornamental species in Indonesia (Wellman 1961). There is one Korean gardener who imported coffee trees from Indonesia around 30 years ago for selling. Its leaf is more wrinkled than other cultivated coffee trees. To accumulate genetic diversity of coffee chloroplast genomes, we chose this wrinkled-leaf coffee tree for completing a third coffee chloroplast genomes.

Total DNA of IN1 coffee tree (Y. Kim, IB-00587 in InfoBoss Cyber Herbarium (IN)) was extracted from fresh leaves using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Genome sequencing was performed using HiSeq2000 at Macrogen Inc., Korea, de novo assembly and sequence confirmation were conducted 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 Coffea arabica chloroplast genome (NC_008535; Samson et al. 2007).

Chloroplast genome of IN1 (Genbank accession is MK353212) is 155,277 bp and has four subregions: 85,248 bp of large single copy (LSC) and 18,137 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR). It contains 131 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs); 19 genes (8 protein-coding genes, 4 rRNAs, and 7 tRNAs) are duplicated in IR regions. The overall GC content is 37.4% and in the LSC, SSC, and IR regions are 35.4%, 31.3%, and 43.0%, respectively.

Based on alignment with three C. arabica chloroplast genomes (NC_008535, MK342634, MK353209, named as CA, CH3, and HP1, respectively; Samson et al. 2007; Park et al. The complete chloroplast genome of cold hardiness individual of Coffea arabica L. (Rubiaceae), accepted; Park et al. The complete chloroplast genome of high production individual tree of Coffea arabica L. (Rubiaceae), accepted), one big insertion (84 bp) is found only on IN1 chloroplast genome, which is a big difference in comparison to sequence variations found in the other coffee chloroplast genomes (Park et al. The complete chloroplast genome of cold hardiness individual of Coffea arabica L. (Rubiaceae), accepted; Park et al. The complete chloroplast genome of high production individual tree of Coffea arabica L. (Rubiaceae), accepted). One deletion is CH3-specific, two deletions and two single nucleotide polymorphisms (SNPs) are CA-specific, and one 2-bp-deletion is identified in HP1. One SNP presents three different bases at 111,618 bp of CA chloroplast genome (Park et al. The complete chloroplast genome of cold hardiness individual of Coffea arabica L. (Rubiaceae), accepted). All these variations are in intergenic or intron areas on chloroplast genomes.

Six Coffea and four chloroplast genomes of Rubiaceae were used as outgroup species for constructing neighbor joining (bootstrap repeat is 10,000) and maximum-likelihood (bootstrap repeat is 1,000) trees using MEGA X (Kumar et al. 2018) based on the alignment by MAFFT 7.388 (Katoh and Standley 2013; Figure 1). Phylogenetic trees show that IN1 is clustered with other Coffea arabica chloroplast genomes. Even though relatively low number of sequence variations are observed on coffee chloroplast genomes, these results can be used as a corner stone for establishing molecular markers to identify its origin or cultivars.

Figure 1. (A) Neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1,000) phylogenetic trees of five Coffea and four Rubiaceae complete chloroplast genomes: five Coffea arabica (MK353212, in this study, NC_008535, KY085909, MK342634, and MK353209), Coffea canephora (NC_030053), Mitragyna speciosa (NC_034698), Dunnia sinensis (NC_039965), Emmenopterys henryi (NC_036300), and Gynochthodes nanlingensis (NC_028614). Phylogenetic tree was drawn based on neighbor joining tree. The numbers above branches indicate bootstrap support values of neighbor joining and maximum likelihood phylogenetic trees, respectively.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by InfoBoss Research Grant [IBG-0011].