Character-based DNA barcoding for authentication and conservation of IUCN Red listed threatened species of genus Decalepis (Apocynaceae)

Abstract

The steno-endemic species of genus Decalepis are highly threatened by destructive wild harvesting. The medicinally important fleshy tuberous roots of Decalepis hamiltonii are traded as substitute, to meet the international market demand of Hemidesmus indicus. In addition, the tuberous roots of all three species of Decalepis possess similar exudates and texture, which challenges the ability of conventional techniques alone to perform accurate species authentication. This study was undertaken to generate DNA barcodes that could be utilized in monitoring and curtailing the illegal trade of these endangered species. The DNA barcode reference library was developed in BOLD database platform for candidate barcodes rbcL, matK, psbA-trnH, ITS and ITS2. The average intra-specific variations (0–0.27%) were less than the distance to nearest neighbour (0.4–11.67%) with matK and ITS. Anchoring the coding region rbcL in multigene tiered approach, the combination rbcL + matK + ITS yielded 100% species resolution, using the least number of loci combinations either with PAUP or BLOG methods to support a character-based approach. Species-specific SNP position (230 bp) in the matK region that is characteristic of D. hamiltonii could be used to design specific assays, enhancing its applicability for direct use in CITES enforcement for distinguishing it from H. indicus.

Genome skimming and NMR chemical fingerprinting provide quality assurance biotechnology to validate Sarsaparilla identity and purity

“…Resulting amplicon is sequenced to identify genetic differences and species are identified. Mishra et al 8 examined the efficacy of recommended barcode markers rbcL, matK, trnH-psbA, ITS and ITS2 in differentiating three congeneric species of the genus Decalepis. They also examined the ability of these markers to separate Decalepis spp.…”

First genomic insights into the Mandevilla genus

“…By reviewing the main DNA barcoding studies performed in this family, we found contrasting opinions on which region is the most recommended, as the type of analysis (intragenus vs. intergenera) seems to greatly influence the suitability of the barcoding region. However, several works recognized a higher efficiency in the combined use of plastidial and nuclear markers ( Selvaraj et al, 2015 ; Mishra et al, 2017 ; Lv et al, 2020 ). For this reason, we chose both the plastidial rbc L region – one of the two core barcodes established by the Consortium for Barcode of Life, (CBOL; CBOL Plant Working Group, 2009 ) – and ITS1, a supplementary nuclear barcode candidate suggested again by the CBOL.…”

Introducing anrbcL andtrnL reference library to aid in the metabarcoding analysis of foraged plants from semi-arid eastern South African savannas

“…This implies that reliable species differentiation would not be possible for24% of the species in the rbc L dataset and 32% in the trn L dataset. However, limitations have also been reported in other DNA-barcode studies such as [19, 48and 30]. Gill et al ., (2019) [19] reported a barcode gap for only 73% of the species investigated for the rbc L primer and 79% for the trn L-F primer in their barcode library for the semi-arid eastern South African Savanna plants.…”