Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa

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 genusAlliumL. (family Amaryllidaceae) incorporates more than 900 species, includes economically signifi­cant vegetable crops such as garlicA. sativum, onionA. cepa, leekA. porrum, etc. In this work, the plastome of garlicA. sativumhas been completely sequenced. TheA. sativumplastome 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 ofA. sativumandA. cepaplastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat bound­aries. The total numbers of genes inA. sativumandA. cepaare the same, but the gene composition is dif­ferent: therpl22gene is functional inA. sativum, being a pseudogene inA. cepa; conversely, therps16gene is a pseudogene inA. sativumand a protein-coding gene inA. cepa. In theA. sativumandA. cepaplastomes, 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.

Characterization of the complete chloroplast genome of leek Allium porrum L. (Amaryllidaceae)

“…The chloroplast genome A. porrum (cultivar ‘Premier’; seed from Federal Scientific Center of Vegetable Crops, Russia) was amplified via long range PCR using 11 pairs of primers developed on the basis of the Allium cepa plastid genome (Filyushin, Beletsky, et al. 2018 ), sequencing was conducted using the Illumina HiSeq 1500 Sequencing System with single-end 220 bp reads. Spades v.3.8 was used to assemble the high-quality short reads into contigs (Bankevich et al.…”

DNA profiling and assessment of genetic diversity of relict speciesAllium altaicumPall. on the territory of Altai

“…This is difficult and expensive work and is usually only requested for critical agricultural crops requiring these types of markers for identification of and genotyping selection lines. Sequencing the plastid genome of the bulb onion Allium cepa ( Filyushin et al, 2018 ; Huo et al, 2019 ) does not solve the problems of intraspecific diversity analysis. To study the intraspecific genetic polymorphism of the Allium wildlife relict species, it is preferable to use markers characterized by a wide distribution in a genome and, above all, the accessibility for any species including those that have not been studied.…”