The complete chloroplast genome sequence of strawberry (Fragaria X ananassa Duch.) and comparison with related species of Rosaceae

被引：65
|
作者：
Cheng, Hui [1 ]
Li, Jinfeng [2 ]
Zhang, Hong [1 ]
Cai, Binhus [1 ]
Gao, Zhihong [1 ]
Qiao, Yushan [1 ]
Mi, Lin [2 ]
机构：
[1] Nanjing Agr Univ, Lab Fruit Tree Biotechnol, Coll Agr, Nanjing, Jiangsu, Peoples R China
[2] Zhenjiang Inst Agr Sci Hilly Area Jiangsu Prov, Lab Fruit Tree, Jurong, Peoples R China
来源：
PEERJ | 2017年 / 5卷
关键词：
Fragaria x ananassa Duch; Benihoppe; Chloroplast genome; Comparative analysis; Chloroplast DNA markers; COMPLETE NUCLEOTIDE-SEQUENCE; COMPLETE PLASTID GENOME; PATERNAL INHERITANCE; NONCODING REGIONS; DNA; PHYLOGENY; GENES; TOLERANCE; GENETICS; NUCLEAR;
D O I：
10.7717/peerj.3919
中图分类号：
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
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. x ananassa 'Benihoppe' using the Mumma 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. x 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. x ananassa 'Benihoppe', F. chiloensis (GP33) and F. virginiana (O477). However, when the sequences of the coding and non-coding regions of F. x 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.
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页数：27
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