The complete chloroplast genome sequence of strawberry ( <i>Fragaria</i> × <i>ananassa</i> Duch.) and comparison with related species of Rosaceae

Abstract

Compared with other members of the family Rosaceae, the chloroplast genomes of <i>Fragaria</i> species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of <i>Fragaria</i> species is needed. In this study, we sequenced the complete chloroplast genome of <i>F</i>. × <i>ananassa</i> 'Benihoppe' using the Illumina HiSeq 2500-PE150 platform and then performed a combination of <i>de novo</i> assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of the <i>F</i>. × <i>ananassa</i> 'Benihoppe' chloroplast genome is 155,549 bp, representing the smallest <i>Fragaria</i> chloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content in <i>Fragaria</i>, particularly among three octoploid strawberries which were <i>F</i>. × <i>ananassa</i> 'Benihoppe', <i>F</i>. <i>chiloensis</i> (GP33) and <i>F</i>. <i>virginiana</i> (O477). However, when the sequences of the coding and non-coding regions of <i>F</i>. × <i>ananassa</i> 'Benihoppe' were compared in detail with those of <i>F</i>. <i>chiloensis</i> (GP33) and <i>F</i>. <i>virginiana</i> (O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (<i>trnK</i>-<i>matK</i>, <i>trnS</i>-<i>trnG</i>, <i>atpF</i>-<i>atpH</i>, <i>trnC</i>-<i>petN</i>, <i>trnT</i>-<i>psbD</i> and <i>trnP</i>-<i>psaJ</i>) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genus <i>Fragaria</i>.