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The complete chloroplast genome sequence of Fragaria orientalis (Rosales: Rosaceae).

ABSTRACT: Fragaria orientalis (Rosales: Rosaceae) as drought-resisting plant is distributed throughout northeast and central Asia. The complete chloroplast genome sequence of Fragaria orientalis is reported and characterized in this study. The genome size of F. orientalis is 147,835 bp, containing a pair of inverted repeats (IR) regions of 51,216 bp, which were separated by a large single copy (LSC) region of 83,232 bp and a small single copy (SSC) region of 13,387 bp. The genome contains 128 genes, including 84 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. A total of 17 of these genes are duplicated in the IR regions, 16 genes contain one intron, and ycf3 has two introns. Maximum likelihood phylogenetic analysis based on chloroplast genome sequences indicates that F. orientalis is closely related to Fragaria chiloensis and Fragaria virginiana from the family Rosaceae.

SUBMITTER: Han Y

PROVIDER: S-EPMC7800701 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description: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.

Dataset Information

The complete chloroplast genome sequence of Fragaria orientalis (Rosales: Rosaceae).

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