Abstract
Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa ‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo 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 F. × ananassa ‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallest Fragaria 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 Fragaria, particularly among three octoploid strawberries which were F. × ananassa ‘Benihoppe’, F. chiloensis (GP33) and F. virginiana (O477). However, when the sequences of the coding and non-coding regions of F. × ananassa ‘Benihoppe’ were compared in detail with those of F. chiloensis (GP33) and F. virginiana (O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK, trnS-trnG, atpF-atpH, trnC-petN, trnT-psbD and trnP-psaJ) 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 Fragaria.
Highlights
The chloroplast, which is considered to have originated from free-living cyanobacteria through endosymbiosis, plays an essential role in photosynthesis and many biosynthetic activities (Keeling, 2004)
The F. × ananassa ‘Benihoppe’ chloroplast genome is a typical circular double-stranded DNA molecule with a quadripartite structure; it is 155,549 bp in size and consists of inverted repeats (IRs) (25,936 bp) regions separated by LSC (85,531 bp) and SSC (18,146 bp) regions (Fig. 1, Table 1)
This study provides the first report of the complete chloroplast genome sequence of F . × ananassa ‘Benihoppe’
Summary
The chloroplast, which is considered to have originated from free-living cyanobacteria through endosymbiosis, plays an essential role in photosynthesis and many biosynthetic activities (Keeling, 2004). Most chloroplast genomes of angiosperms exhibit a highly conserved organization with a typical quadripartite structure that includes two copies of inverted repeats (IRs), separated by large (LSC) and small (SSC) single-copy (SC) regions (Palmer, 1991; Jansen et al, 2005). The chloroplast genomes of angiosperms encode 110–130 genes with a size range of 120–160 kb (Palmer, 1985). Chloroplast transformation presents the advantages of producing high protein levels, site-specific integration of transgenes, and a lack of posttranscriptional gene silencing, making it an environmentally friendly strategy for plant genetic engineering (Daniell, Khan & Allison, 2002; Bock, 2014)
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