The complete chloroplast genomes of two cold hardness coffee trees, Coffea arabica L. (Rubiaceae)

Abstract

We presented two complete chloroplast genomes of cold resistance coffee trees (Coffea arabica L.), named as CH1 and CH2 cultivated in Jeju island, Korea. Their length is 155,187 bp long (GC ratio is 37.4%) and has four subregions: 85,160 bp of large single copy (LSC; 35.4%) and 18,135 bp of small single copy (SSC; 31.3%) regions are separated by 25,946 bp of inverted repeat (IR; 43.0%) regions including 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). Like sequenced coffee chloroplast genomes, number of sequence variations of CH1 and CH2 against TY1 chloroplast genomes are zero and two, respectively.

Keywords:

• Coffea arabica
• Cold resistance
• Jeju island chloroplast genome low-level sequence variations

Coffea arabica L. is one of the major economical plants occupying 70% of world coffee production (Lashermes et al. 1999; O’brien and Kinnaird 2003). Seven coffee chloroplast genomes are available presenting low level of intraspecies variations (Samson et al. 2007; Min, Kim et al. 2019; Park, Kim, Xi, Heo 2019a, 2019b; Park, Kim, Xi, Nho et al. 2019; Park, Xi, Kim, Heo, et al. 2019). Cold resistance feature of coffee tree can expand cultivation area beyond ‘Bean Belt’ (Bentley and Baker 2000). Here, chloroplast genomes of two cold resistance coffee trees (CH1 and CH2) which can survive until –2 °C in Jeju island, Korea, without greenhouse were sequenced.

Total DNA of coffee trees (CH1 and CH2; J. Park, IBS-00013 and IBS-00014, respectively, InfoBoss Cyber Herbarium (IN); 33.239325 N, 126.287332E) was extracted from fresh leaves by using DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Sequencing was performed using HiSeq2000 at Macrogen Inc., Korea. Filtered raw reads by Trimmomatic 0.33 (Bolger et al. 2014) were subjected to de novo assembly and sequence confirmation processes conducted with 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 with C. arabica TY1 chloroplast (MK862266; Min, Kim et al. 2019).

Both chloroplast genomes of CH1 and CH2 (GenBank accessions are MN894550 and MN894551, respectively) are identical: its length is 155,189 bp long (GC ratio is 37.4%) and has four subregions: 85,160 bp of large single copy (35.4%) and 18,135 bp of small single copy (31.3%) regions are separated by 25,946 bp of inverted repeat (IR; 43.0%). It contains 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs); 19 genes (8 protein-coding genes, 4 rRNAs, and 7 tRNAs) are duplicated in IR regions.

CH1 and CH2 chloroplast genomes have six insertions and deletions (INDELs) against CH3, another cold hardness coffee (Park, Kim Xi, Kim 2019b) and two INDELs against TY1 chloroplast. It is similar to those of Camellia japonica (Park, Kim, Xi, Oh, et al. 2019b), Cucumis melo (Zhu et al. 2016), Chenopodium quinoa (Maughan et al. 2019), Abeliophyllum distichum (Park, Kim, Xi, Jang et al. 2019), Salix koriyanagi (Park, Kim, Xi, Kwon et al. 2019), Populus alba x Populus glandulosa (Park, Kim, Xi, Kwon et al. 2019), and Marchantia polymorpha (4 SNPs; Kwon et al. 2019) and smaller than those of other chloroplasts of Pyrus ussuriensis (Cho et al. 2019), Pseudostellaria palibiniana (Kim, Heo et al. 2019), Aconitum coreanum (Kim, Yi, et al. 2019), Artemisia fukudo (Min, Park et al. 2019), Goodyera schlechtendaliana (Oh et al. 2019), Dysphania pumilio (Park and Kim 2019), Nymphaea alba (Park, Kim, Kwon, Nam, et al. 2019), Liriodendron tulifipera (Park, Kim, Kwon, Xi, et al. 2019), Duchesnea chrysantha (Park, Kim, Lee 2019), Illicium anisatum (Park, Kim, Xi 2019a), Salix koriyanagi (Park, Kim, Xi 2019b), Viburnum erosum (Choi et al., 2020), Abeliophyllum distichum ( Min et al., 2019; Park et al., 2019), and Camellia japonica (Park, Kim, Xi, Oh et al. 2019a).

Ten Coffea and four chloroplast genomes of Rubiaceae as outgroup species were used for constructing bootstrapped neighbor joining and maximum likelihood trees using MEGA X (Kumar et al. 2018) after multiple sequence alignment by MAFFT 7.450 (Katoh and Standley 2013). Phylogenetic trees show that CH1 and CH2 are clustered in the C. arabica clade (Figure 1).

Figure 1 Neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1,000) phylogenetic trees of six Coffea and four Rubiaceae complete chloroplast genomes: nine Coffea arabica (MN894550 and MN894551 in this study, MK875244, MK862266, MK353212, 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 maximum likelihood tree. The numbers above branches indicate bootstrap support values of maximum likelihood and neighbor joining phylogenetic trees, respectively.

Disclosure statement

The authors declare that they have no competing interests.

Additional information

Funding

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