Comparative and bioinformatics analysis of the chloroplast genomes of three varieties of Strawberry: F.vesca, F.virginiana and F.chiloensis
Strawberry belongs to the genus Fragaria and family Rosaceae. Now days, the species Chiloensis, Virginia, and hybrid between them, namely, Ananasae, are cultivated. This perennial herb has a small genome that is prone to the transfer of Fragaria ananasae cultivated strawberry genes and other importa...
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University of Isfahan
2019-07-01
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| Series: | Zīst/shināsī-i Giyāhī-i Īrān |
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| Online Access: | http://ijpb.ui.ac.ir/article_23933_989f3a89a7fdd4338f589c902ead959d.pdf |
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| author | Farshid Talat Nesa Ghaffari Abolhasan Faraji Mehdi Badri Anarjan |
| author_facet | Farshid Talat Nesa Ghaffari Abolhasan Faraji Mehdi Badri Anarjan |
| author_sort | Farshid Talat |
| collection | DOAJ |
| description | Strawberry belongs to the genus Fragaria and family Rosaceae. Now days, the species Chiloensis, Virginia, and hybrid between them, namely, Ananasae, are cultivated. This perennial herb has a small genome that is prone to the transfer of Fragaria ananasae cultivated strawberry genes and other important economic plants from the Rosaceae family. Present study was conducted to study and compare the complete chloroplast sequence of Fragaria vesca, analyses of its genome structure, gene content and organization, repeated sequences, codon usage and comparison with two cultivated octaploid sequenced Fragaria species (F.chiloensis and F.virginiana). F.vesca chloroplast (cp) genome is 155691 bp in length with conserved quadripartite structure. Single copy region of cp genome is separated by the two inverted regions. The large single copy region is 85561 bp, and the small single copy region is 20204 bp whereas the inverted repeat is 24963 bp each. The plastidic genome has 130 single genes and 18 duplicated genes located in inverted repeats. The singletons encode 85 proteins, 8 ribosomal RNA genes and 37 transfer RNA genes. Amongst all plastidic genes only 18 genes appeared to have 1-2 introns and when compared with DNA of two cultivated octaploeids, rps18 was the only duplicated gene in F.vesca and rps 12, rpl 2 and trn I-GAU are genes which are located in inverted repeats. Despite the high level of conservation in chloroplast SSRs, these are useful in analysis of genetic diversity due to their greater efficiency as opposed to genomic SSRs. |
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| id | doaj.art-7ba7209b30a14e90b7f75265f22b192f |
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| language | fas |
| last_indexed | 2024-12-20T19:44:58Z |
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| spelling | doaj.art-7ba7209b30a14e90b7f75265f22b192f2022-12-21T19:28:26ZfasUniversity of IsfahanZīst/shināsī-i Giyāhī-i Īrān2008-82642322-22042019-07-01112637610.22108/ijpb.2019.113723.111823933Comparative and bioinformatics analysis of the chloroplast genomes of three varieties of Strawberry: F.vesca, F.virginiana and F.chiloensisFarshid Talat0Nesa Ghaffari1Abolhasan Faraji2Mehdi Badri Anarjan3Assistant Professor, Seed and Plant Improvement Research Department, West Azerbaijan Agricultural and Natural Resources Research and Education Center, AREEO, Urmia, IranMaster Graduate of Horticultural Biotechnology, Saba Institute of Education, Urmia, IranAssociated Professor, Saba Institute of Education, Urmia, IranMaster Graduate of Plant Breeding, Faculty of Agriculture, Urmia University, IranStrawberry belongs to the genus Fragaria and family Rosaceae. Now days, the species Chiloensis, Virginia, and hybrid between them, namely, Ananasae, are cultivated. This perennial herb has a small genome that is prone to the transfer of Fragaria ananasae cultivated strawberry genes and other important economic plants from the Rosaceae family. Present study was conducted to study and compare the complete chloroplast sequence of Fragaria vesca, analyses of its genome structure, gene content and organization, repeated sequences, codon usage and comparison with two cultivated octaploid sequenced Fragaria species (F.chiloensis and F.virginiana). F.vesca chloroplast (cp) genome is 155691 bp in length with conserved quadripartite structure. Single copy region of cp genome is separated by the two inverted regions. The large single copy region is 85561 bp, and the small single copy region is 20204 bp whereas the inverted repeat is 24963 bp each. The plastidic genome has 130 single genes and 18 duplicated genes located in inverted repeats. The singletons encode 85 proteins, 8 ribosomal RNA genes and 37 transfer RNA genes. Amongst all plastidic genes only 18 genes appeared to have 1-2 introns and when compared with DNA of two cultivated octaploeids, rps18 was the only duplicated gene in F.vesca and rps 12, rpl 2 and trn I-GAU are genes which are located in inverted repeats. Despite the high level of conservation in chloroplast SSRs, these are useful in analysis of genetic diversity due to their greater efficiency as opposed to genomic SSRs.http://ijpb.ui.ac.ir/article_23933_989f3a89a7fdd4338f589c902ead959d.pdfstructural analysisbioinformaticsstrawberry’s chloroplastgenome |
| spellingShingle | Farshid Talat Nesa Ghaffari Abolhasan Faraji Mehdi Badri Anarjan Comparative and bioinformatics analysis of the chloroplast genomes of three varieties of Strawberry: F.vesca, F.virginiana and F.chiloensis Zīst/shināsī-i Giyāhī-i Īrān structural analysis bioinformatics strawberry’s chloroplast genome |
| title | Comparative and bioinformatics analysis of the chloroplast genomes of three varieties of Strawberry: F.vesca, F.virginiana and F.chiloensis |
| title_full | Comparative and bioinformatics analysis of the chloroplast genomes of three varieties of Strawberry: F.vesca, F.virginiana and F.chiloensis |
| title_fullStr | Comparative and bioinformatics analysis of the chloroplast genomes of three varieties of Strawberry: F.vesca, F.virginiana and F.chiloensis |
| title_full_unstemmed | Comparative and bioinformatics analysis of the chloroplast genomes of three varieties of Strawberry: F.vesca, F.virginiana and F.chiloensis |
| title_short | Comparative and bioinformatics analysis of the chloroplast genomes of three varieties of Strawberry: F.vesca, F.virginiana and F.chiloensis |
| title_sort | comparative and bioinformatics analysis of the chloroplast genomes of three varieties of strawberry f vesca f virginiana and f chiloensis |
| topic | structural analysis bioinformatics strawberry’s chloroplast genome |
| url | http://ijpb.ui.ac.ir/article_23933_989f3a89a7fdd4338f589c902ead959d.pdf |
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