The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of Rosaceae
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 chloroplas...
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PeerJ Inc.
2017-10-01
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| Online Access: | https://peerj.com/articles/3919.pdf |
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| author | Hui Cheng Jinfeng Li Hong Zhang Binhua Cai Zhihong Gao Yushan Qiao Lin Mi |
| author_facet | Hui Cheng Jinfeng Li Hong Zhang Binhua Cai Zhihong Gao Yushan Qiao Lin Mi |
| author_sort | Hui Cheng |
| collection | DOAJ |
| 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. |
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| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:31:07Z |
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| spelling | doaj.art-814d723f121846aaa7b7e7bf1159ff232023-12-03T11:05:49ZengPeerJ Inc.PeerJ2167-83592017-10-015e391910.7717/peerj.3919The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of RosaceaeHui Cheng0Jinfeng Li1Hong Zhang2Binhua Cai3Zhihong Gao4Yushan Qiao5Lin Mi6Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, ChinaLaboratory of Fruit Tree, Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, Jurong, ChinaLaboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, ChinaLaboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, ChinaLaboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, ChinaLaboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, ChinaLaboratory of Fruit Tree, Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, Jurong, ChinaCompared 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.https://peerj.com/articles/3919.pdfFragaria × ananassa Duch.BenihoppeChloroplast genomeComparative analysisChloroplast DNA markers |
| spellingShingle | Hui Cheng Jinfeng Li Hong Zhang Binhua Cai Zhihong Gao Yushan Qiao Lin Mi The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of Rosaceae PeerJ Fragaria × ananassa Duch. Benihoppe Chloroplast genome Comparative analysis Chloroplast DNA markers |
| title | The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of Rosaceae |
| title_full | The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of Rosaceae |
| title_fullStr | The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of Rosaceae |
| title_full_unstemmed | The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of Rosaceae |
| title_short | The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of Rosaceae |
| title_sort | complete chloroplast genome sequence of strawberry fragaria ananassa duch and comparison with related species of rosaceae |
| topic | Fragaria × ananassa Duch. Benihoppe Chloroplast genome Comparative analysis Chloroplast DNA markers |
| url | https://peerj.com/articles/3919.pdf |
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