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

Abstract

DNA 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, and accD, sequenced, and submitted it to NCBI Genbank after verification. This study evaluated the significance of single (matK, rpoB, ndhJ, and accD) 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 for matK, rpoB, ndhJ, accD, ndhJ+matK, rpoB+matK, and accD+matK was 395 bp, 538 bp, 477 bp, 254 bp, 872 bp, 937 bp, and 649 bp, respectively. The highest substitution rate was recorded in the rpoB (18.47%), followed by ndhJ (17.38%), accD (14.00%), and matK (11.23%). The number of variable sites, segregating sites (S), nucleotide diversity (Pi), and mutations (Eta) were observed to be highest in the matK region. Evolutionary relationship based on the Neighbor-joining method demonstrated that candidate barcode sequences were competent for identifying Crinodendron, Elaeocarpus, Sloanea, and Vallea species. A significant barcoding gap was identified in two barcoding regions (matK and ndhJ+matK). The species-specific barcodes for the genus Elaeocarpus were 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.