The complete chloroplast genome of wild diploid potato species Solanum chacoense bitter

Abstract

Solanum chacoense is a wild tuber-bearing species and an important resource used as inbred line to improve common scab resistance in interspecies transfer to cultivated potato (S. tuberosum). In this study, we report the complete chloroplast genome sequence of S. chacoense using Illumina sequencing technology. The complete chloroplast genome was 155,528 bp in length and comprised a pair of inverted repeats (IR) regions of 25,592 bp separated by a large single-copy (LSC) region of 86,178 bp and a small single-copy (SSC) region of 18,586 bp. The GC content was 37.9% overall. The genome contained 132 genes including 87 protein-coding genes (PCGs), 37 tRNAs and 8 rRNAs. Phylogenetic analysis based on eight complete chloroplast genomes showed a sister-group relationship between S. chacoense and S. commersonii.

Keywords:

• Potato
• wild species
• Solanum chacoense
• chloroplast genome

Wild potatoes are broadly distributed in the America from the southwestern United States to the Southern Cone of South America (Spooner et al. 2014). They possess rich genetic variations which are readily available to potato breeder (Hawkes 1958; Hanneman 1989; Jansky et al. 2014). As a member of wild relative potato, Solanum chacoense, is identified to be high resistance to common scab, Colorado Potato Beetle, verticillium wilt, and an important source of potato breeding (Lynch et al. 1997; Ronning et al. 2000; Jansky et al. 2018b). A clone of S. chacoense, 524-8, was identified as highly resistant to common scab and used to create common scab resistant tetraploid potato clone (Jansky et al. 2018a). In addition, it was used to create self-compatible potato clone M6 which is a vigorous and fertile inbred line. M6 is a useful tool in diploid breeding, thus the whole genome of this clone was sequenced for effective utilization (Jansky et al. 2014; Leisner et al. 2018). In this study, we generated a chloroplast genome sequence, assembled, and characterized the complete nucleotide sequence of S. chacoense in chloroplast genome.

The S. chacoense (S-695) was provided by Huazhong Agricultural University, China. A pair-end library was constructed with total genomic DNA using NovaSeq platform (Illumina, San Diego, CA). Low-quality reads were filtered and about 4.0 Gb of clean reads were assembled using GetOrganelle pipeline (Jin et al. 2018). In this pipeline, chloroplast genome of S. stoloniferum was set as a reference sequence. Plastid-like reads were treated as ‘baits’ and Bowtie 2 (Langmead and Salzberg 2012) was used to map the baits sequence to the reference sequence. It got more plastid-like reads with multiple extension iterations until no more chloroplast reads can be extracted. Then, the total plastid-like reads were de novo assembled into a FASTA Graph (‘fastg’) using SPAdes (Bankevich et al. 2012). The complete circular chloroplast genome was finalized through a visual software, Bandage (Wick et al. 2015). The annotation of chloroplast genome was performed using a Perl script, PGA (https://github.com/quxiaojian/PGA). To determine the position of S. chacoense in section Petota, seven plastomes of Solanum was downloaded from GenBank including five wild potato relatives and two outgroups, S. lycopersicum and S. nigrum. Whole chloroplast genome sequences were aligned in MAFFT v. 7 (Katoh and Standley 2013). The phylogenetic relationship of eight solanum species was reconstructed using RAxML v.8.1.1179 (Stamatakis 2014) at the XSEDE Teragrid of CIPRES science Gateway and adopting 1000 replicates of rapid bootstrap with GTRGAMMA substitution model (Miller et al. 2010).

Figure 1. Maximum likelihood phylogenetic tree of S. chacoense based on eight complete chloroplast genome sequences using S. lycopersicum and S. nigrum as outgroups. Bootstrap values are given above branches based 1000 replicates.

The complete chloroplast genome of S. chacoense (GenBank accession no. MK398247) was 155,528 bp in length consisting of a pair of inverted repeats (IR) regions of 25,592 bp separated by a large single-copy (LSC) region of 86,178 bp and a small single-copy (SSC) region of 18,586 bp. The GC content was 37.9% overall. The complete chloroplast genome comprised 132 genes including 87 protein-coding genes (PCGs), 37 tRNAs, and 8 rRNAs. Furthermore, multiple copies of seven PCGs, four rRNAs and seven tRNAs genes were completely duplicated within IR. Within maximum likelihood phylogenetic tree, S. chacoense and S. commersonii formed a sister-group clade (Figure 1).

Acknowledgments

We appreciated the help of Li Zhong and Jian-Jun Jin on the bioinformatic analyses.

Disclosure statement

The author reports no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was financially supported by the National Natural Science Foundation of China [31760409]; National Key R & D Program of China [2017YFD0101906]; Yunnan Agricultural Foundation Projects [2017FG001 (-012)]; Project Science and Technology in the Universities of Inner Mongolia Autonomous Region [NJZY16214].