Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa
Sequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genus Allium L. (family Amaryllidaceae) incorporates more than 900 species, includes econom...
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| Format: | Article |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2018-08-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/1585 |
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| author | M. A. Filyushin A. M. Mazur A. V. Shchennikova Е. Z. Kochieva |
| author_facet | M. A. Filyushin A. M. Mazur A. V. Shchennikova Е. Z. Kochieva |
| author_sort | M. A. Filyushin |
| collection | DOAJ |
| description | Sequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genus Allium L. (family Amaryllidaceae) incorporates more than 900 species, includes economically significant vegetable crops such as garlic A. sativum, onion A. cepa, leek A. porrum, etc. In this work, the plastome of garlic A. sativum has been completely sequenced. The A. sativum plastome is 153172 bp in size. It consists of a large unique (LSC, 82035 bp) and small unique (SSC, 18015 bp) copies, separated by inverted repeats (IRa and IRb) of 26561 bp each. In the garlic plastome, 134 genes have been annotated: 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 6 pseudogenes. Comparative analysis of A. sativum and A. cepa plastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat boundaries. The total numbers of genes in A. sativum and A. cepa are the same, but the gene composition is different: the rpl22 gene is functional in A. sativum, being a pseudogene in A. cepa; conversely, the rps16 gene is a pseudogene in A. sativum and a protein-coding gene in A. cepa. In the A. sativum and A. cepa plastomes, 32 SSR sequences have been identified. More than half of them are dinucleotides, and the remaining are tetra-, penta-, and hexanucleotides at the same time, trinucleotides were absent. The compared plastomes differ in the numbers of certain SSRs, and some are present in only one of the species. |
| format | Article |
| id | doaj-art-2a20f1d710124808afbf689336291c81 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2018-08-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-2a20f1d710124808afbf689336291c812025-02-01T09:58:06ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592018-08-0122552453010.18699/VJ18.390787Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepaM. A. Filyushin0A. M. Mazur1A. V. Shchennikova2Е. Z. Kochieva3Federal Research Centre “Fundamentals of Biotechnology”, RAS, Institute of BioengineeringFederal Research Centre “Fundamentals of Biotechnology”, RAS, Institute of BioengineeringFederal Research Centre “Fundamentals of Biotechnology”, RAS, Institute of BioengineeringFederal Research Centre “Fundamentals of Biotechnology”, RAS, Institute of BioengineeringSequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genus Allium L. (family Amaryllidaceae) incorporates more than 900 species, includes economically significant vegetable crops such as garlic A. sativum, onion A. cepa, leek A. porrum, etc. In this work, the plastome of garlic A. sativum has been completely sequenced. The A. sativum plastome is 153172 bp in size. It consists of a large unique (LSC, 82035 bp) and small unique (SSC, 18015 bp) copies, separated by inverted repeats (IRa and IRb) of 26561 bp each. In the garlic plastome, 134 genes have been annotated: 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 6 pseudogenes. Comparative analysis of A. sativum and A. cepa plastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat boundaries. The total numbers of genes in A. sativum and A. cepa are the same, but the gene composition is different: the rpl22 gene is functional in A. sativum, being a pseudogene in A. cepa; conversely, the rps16 gene is a pseudogene in A. sativum and a protein-coding gene in A. cepa. In the A. sativum and A. cepa plastomes, 32 SSR sequences have been identified. More than half of them are dinucleotides, and the remaining are tetra-, penta-, and hexanucleotides at the same time, trinucleotides were absent. The compared plastomes differ in the numbers of certain SSRs, and some are present in only one of the species.https://vavilov.elpub.ru/jour/article/view/1585plastid genomegarlicallium sativumallium cepa |
| spellingShingle | M. A. Filyushin A. M. Mazur A. V. Shchennikova Е. Z. Kochieva Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa Вавиловский журнал генетики и селекции plastid genome garlic allium sativum allium cepa |
| title | Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa |
| title_full | Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa |
| title_fullStr | Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa |
| title_full_unstemmed | Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa |
| title_short | Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa |
| title_sort | comparative analysis of the complete plastomes of garlic allium sativum and bulb onion allium cepa |
| topic | plastid genome garlic allium sativum allium cepa |
| url | https://vavilov.elpub.ru/jour/article/view/1585 |
| work_keys_str_mv | AT mafilyushin comparativeanalysisofthecompleteplastomesofgarlicalliumsativumandbulbonionalliumcepa AT ammazur comparativeanalysisofthecompleteplastomesofgarlicalliumsativumandbulbonionalliumcepa AT avshchennikova comparativeanalysisofthecompleteplastomesofgarlicalliumsativumandbulbonionalliumcepa AT ezkochieva comparativeanalysisofthecompleteplastomesofgarlicalliumsativumandbulbonionalliumcepa |