Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa
https://doi.org/10.18699/VJ18.390
Abstract
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.
About the Authors
M. A. Filyushin
Federal Research Centre “Fundamentals of Biotechnology”, RAS, Institute of Bioengineering
Russian Federation
Moscow
Russian Federation
Moscow
A. M. Mazur
Federal Research Centre “Fundamentals of Biotechnology”, RAS, Institute of Bioengineering
Russian Federation
Moscow
Russian Federation
Moscow
A. V. Shchennikova
Federal Research Centre “Fundamentals of Biotechnology”, RAS, Institute of Bioengineering
Russian Federation
Moscow
Russian Federation
Moscow
Е. Z. Kochieva
Federal Research Centre “Fundamentals of Biotechnology”, RAS, Institute of Bioengineering
Russian Federation
Moscow
Russian Federation
Moscow
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