Sequence diversification of 45S rRNA ITS, trnH-psbA spacer, and matK genic regions in several Allium species

Abstract

Allium is a very diverse genus with over 600 species distributed worldwide. Haplotype analyses of 45S rRNA ITS, trnH-psbA spacer, and matK gene sequences in 9 Allium species were carried out, subsequent to which phylogenetic relations of the nine species were also analyzed. Of the three genes, the nuclear 45S rRNA ITS sequences showed the highest variation with one haplotype in each species. The other two chloroplast genes revealed that more than one haplotype was present in each species, and each haplotype was present in several of the species. In the matK gene, EcoRI restriction revealed heteroplasmy in which the functional gene retains the EcoRI recognition site while the nonfunctional, pseudogene does not. Phylogenetic patterns were not consistent among the haplotypes of the 45 rRNA ITS, trnH-psbA spacer, and matK genic regions. This phylogenetic incongruency might be due to the presence of multiple haplotypes in each of the chloroplast genes. However, the inconsistency of the phylogenetic relationships, based on the 45S rRNA ITS sequences makes a strong case for further analysis.

Testing the utility of matK and ITS DNA regions for discrimination of Allium species

“…Genetic relationships among 9 Allium species were recently analyzed using the polymorphisms within the nucleotide sequences of trnH-psbA, ITS, and matK (Son et al, 2010). The authors reported the presence of more than 1 haplotype in both organellar and nuclear genomes in a single plant of the Allium species, which makes phylogenetic analysis and barcoding impossible using the nucleotide sequences of these DNA regions.…”

Origin of African Physacanthus (Acanthaceae) via Wide Hybridization

“…The fact that all three species of Physacanthus showed molecular evidence of the hypothesized wide hybridization event and that the three species in the genus are morphologically cohesive (i.e., they share the defining morphological feature of inflated calyces, Figures 2, S3) argues that the hybridization event occurred prior to speciation, giving rise to the common ancestor of the three species, Similar lines of evidence were used to argue that establishment of organellar heteroplasmy preceded species diversification in Allium [47]. The alternative hypothesis of re-establishing heteroplasmy every generation via hybridization seems extremely implausible (and would require that parental sources of both chloroplast lineages remain in sympatry), especially given that modern geographic ranges of the three species of Physacanthus are distinct.…”

Phylogenetic relationships of IranianAlliumspecies using thematK(cpDNA gene) region

“…In a previous study, the matk gene was proposed for resolving phylogenetic associations in plant species (Abugalieva et al 2017;İpek et al 2014İpek et al Ito et al 1999Kim et al 2018;Son et al 2010). The genes utilized for DNA barcoding in plant populations include matK, rpoC1, rpoB, trnH-PsbA, rbcL, atpF-atpH, psbK-psbI, and their combinations, of which, matK and rbcL were adopted as 2-locus DNA barcode by the CBOL Group (Hollingsworth et al 2009).…”

“…DNA sections were mostly discrete parts in Allium. Nevertheless, some species were not distinguishable from one another by the matK sites (Abugalieva et al 2017;Ince et al 2005;İpek et al 2014;Li et al 2011;Son et al 2010).…”

“…The length of matK nucleotide sequences varied between 540 bp in A. porrum and A. austroiranicum and 1023 bp in Allium sp. Genetic associations among Allium species were examined through the polymorphisms within the nucleotide sequences of trnH-psbA, ITS and matK in a recent report (İpek et al 2014;Son et al 2010). Over one haplotype in both organellar and nuclear genomes were present in a single plant of Allium species, making phylogeny analysis and barcoding implausible applying the nucleotide arrays of these DNA sites.…”