Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species

Abstract

This study presents a phylogenetic analysis of the selected representatives of the Triticeae tribe and the assessment of possibilities of species identification on the basis of sequence variation in the three regions from the chloroplast DNA (matK, rbcL and trnH-psbA). The analysis included diploid and polyploid species of the following genomic compositions: E b , E e , H, I, Ns, St, Ta, Xu, NsXm, XoXr, XuXu, E b E e , E b E b E e , E b E e St, StH, StStH. The obtained matK and rbcL sequences revealed three well-supported clades: (1) Elymus, Lopophyrum, Pseudoroegneria, Thinopyrum (genomes E b , E e , St, StH, E b E e , E b E b E e , E b E e St, StStH); (2) Leymus, Hordelymus, Psathyrostachys (genomes Ns, NsXm, XoXr); (3) Hordeum (genomes H, I, Xu). This results support the view that the analyzed Elymus species (E. caninus, E. repens) acquired the Pseudoroegneria St genome maternally. They also indicate that Hordelymus europaeus carries the Ns genome from Psathyrostachys and point at the maternal origin of this component. Moreover, the presented results confirm the contribution of Psathyrostachys in the origin of Leymus as well as indicate the maternal character of this input. Differentiation observed within the Hordeum clade aligns with the alleged genome composition of the analyzed species. The DNA barcoding potential of the analyzed sequences was low. Nevertheless, several informative polymorphisms were found like e.g. the matK substitution specific for Thinopyrum bessarabicum, the trnH-psbA substitution differentiating Leymus arenarius from Psathyrostachys juncea and the group of speciesspecific deletions within trnH-psbA. In the DNA barcoding context we have also demonstrated negative importance of the high frequency cpDNA inversion leading to intraspecific variation.

DNA barcoding and morpho-anatomical characters of two forms of <i>Convolvulus arvensis</i> L. (Convolvulaceae) grown in Asir region, Saudi Arabia

“…Therefore, all of these factors individually or altogether will lead to a consequence of mutations in the lineage of C. arvensis forms according the prevailing environmental conditions. Variation in the amount of GC content and other nucleotides A, T and C in the first, second and third position is same to that of some other plant groups, for example, Triticeae tribe (Bieniek et al, 2015) and Pisum sativum varieties (Moustafa et al, 2019).…”

Assessment of genetic diversity in germplasm of Guinea grass (Panicum maximum Jacq.)

“…In the recent years, DNA barcode markers like ITS, matK and trnHpsbA are popular in understanding the intraspecific diversities among the closely related plant groups. Nucleotide diversity, sequence variation and secondary structure variations from the barcode markers are carefully investigated to characterize the intra species variations (Jiang et al 2016;Li et al 2017;Bieniek et al 2015;Singh et al 2017). While discriminating very closely related taxa, it is equally important to consider the indels in the highly variable sequences.…”

“…Enormous information on the plant DNA barcodes like nrITS, matK, rbcL, trnHpsbA, and their utility in species identification and phylogeny analyses have been generated in the past two to three decades (Kress and Erickson 2008;Bieniek et al 2015;Singh et al 2017;CBOL Plant Working Group 2009). As defined by Kress and Erickson (2008), the key criteria of a DNA barcode marker is significant species level genetic variability and divergence.…”

Cacao biotechnology: current status and future prospects

“…In addition to markers based on nuclear genomic DNA, several loci of chloroplast DNA (cpDNA) such as matK , rbcL and trnH‐psbA can be used as markers in DNA barcoding (Bieniek et al ., ). Recently, sequence variation of the trnH‐psbA intergenic spacer has been analysed in 28 cacao accession obtained from different farms in southern Mexico (Gutiérrez‐López et al ., ).…”