Complete chloroplast genomes of ten species from subgenus Allium (Allium, Amaryllidaceae)
DOI:
https://doi.org/10.54981/PDCA/vol1_iss2/a3Keywords:
phylogeny, plastome, nucleotide polymorphism, pseudogeneAbstract
Subgenus Allium is the largest group within the genus Allium (Amaryllidaceae) which detailed phylogenetic classification is still missing despite intensive phylogenetic research. Reconstruction of the subgenus phylogeny is impossible without proper coverage of the subgenus members representing Central Asia, one of the centers of genus (and subgenus) diversity. We sequenced whole chloroplast genomes of 10 species from subgenus Allium, mainly from Central Asia, which, together with 7 species available at NCBI provided us with a representative subgenus sampling for making inferences about the whole plastome-based phylogeny of subgenus Allium. The phylogenetic relationships among the representatives of subgenus Allium in our phylogenetic tree not only contradicted the current sectional classification within a subgenus, but even doubted the validity of the current subgenera recognized in genus Allium. The detected numerous mismatches between the species positions in the phylogenetic tree and the current species taxonomic position may suggest that the importance of the morphological traits used previously for defining sections in subgenus Allium needs reconsideration. Analysis of single nucleotide polymorphism in the studied genomes identified the genes ycf1, ndhF, rpoC2, matK and ndhD as the most variable regions (number of SNPs ≥ 30).
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