DNA barcoding and species delimitation based on four Chloroplast loci to identify species within the Elaeocarpaceae family

Abstract

AbstractDNA barcoding is an indispensable taxonomic tool for plant species identification. The present research successfully amplified the four coding regions of plastid namely;matK,rpoB,ndhJ, andaccD, sequenced, and submitted it to NCBI Genbank after verification. This study evaluated the significance of single (matK,rpoB,ndhJ, andaccD) and two-locus plastid loci (rpoB+matK,ndhJ+matK,accD+matK) and examined their abilities for species identification and phylogenetic construction of Elaeocarpaceae plants. The average aligned length formatK,rpoB,ndhJ,accD,ndhJ+matK,rpoB+matK, andaccD+matKwas 395 bp, 538 bp, 477 bp, 254 bp, 872 bp, 937 bp, and 649 bp, respectively. The highest substitution rate was recorded in therpoB(18.47%), followed byndhJ(17.38%),accD(14.00%), andmatK(11.23%). The number of variable sites, segregating sites (S), nucleotide diversity (Pi), and mutations (Eta) were observed to be highest in thematKregion. Evolutionary relationship based on the Neighbor-joining method demonstrated that candidate barcode sequences were competent for identifyingCrinodendron,Elaeocarpus,Sloanea, andValleaspecies. A significant barcoding gap was identified in two barcoding regions (matKandndhJ+matK). The species-specific barcodes for the genusElaeocarpuswere generated based on Single Nucleotide Polymorphism (SNP) analysis. This study offers novel strategies for effectively identifying species within Elaeocarpaceae and lays the foundation for germplasm conservation and utilization.