The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification

Abstract

Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.

The Complete Chloroplast Genomes of Bulbophyllum (Orchidaceae) Species: Insight into Genome Structure Divergence and Phylogenetic Analysis

“…Recently, the development of methods based on molecular diagnostic characters (MDCs) comes into view; the number of observed MDCs has a particularly large impact on the efficiency of species identification [68]. We conducted an MDC analysis of five datasets (complete cp genomes, five coding genes, six noncoding regions, ycf1, and rpl32-trnL UAG ); the results revealed that B. crassipes possessed the most abundant MDCs of the Bulbophyllum species, possibly related to the insertion observed in the genome structure (Figures 1 and 6).…”