Abstract
Mangroves are salt-tolerant forest ecosystems of tropical and subtropical intertidal regions. They are among most productive, diverse, biologically important ecosystem and inclined toward threatened system. Identification of mangrove species is of critical importance in conserving and utilizing biodiversity, which apparently hindered by a lack of taxonomic expertise. In recent years, DNA barcoding using plastid markers rbcL and matK has been suggested as an effective method to enrich traditional taxonomic expertise for rapid species identification and biodiversity inventories. In the present study, we performed assessment of available 14 mangrove species of Goa, west coast India based on core DNA barcode markers, rbcL and matK. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in rbcL (97.7 %) and matK (95.5 %) region. The two candidate chloroplast barcoding regions (rbcL, matK) yielded barcode gaps. Our results clearly demonstrated that matK locus assigned highest correct identification rates (72.09 %) based on TaxonDNA Best Match criteria. The concatenated rbcL + matK loci were able to adequately discriminate all mangrove genera and species to some extent except those in Rhizophora, Sonneratia and Avicennia. Our study provides the first endorsement of the species resolution among mangroves using plastid genes with few exceptions. Our future work will be focused on evaluation of other barcode markers to delineate complete resolution of mangrove species and identification of putative hybrids.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3191-4) contains supplementary material, which is available to authorized users.
Highlights
Mangroves are unique ecosystem exist along the sheltered inter-tidal coastline, in the margin between the land and sea in tropical and subtropical areas
The sequences obtained using barcode markers: ribulose-bisphosphate carboxylase gene (rbcL) and maturase K (matK) were submitted to the NCBI GenBank (Accession numbers indicated in Table 1), and publicly accessible through the dataset of project DNA Barcoding of Indian Mangroves (Project code: IMDB) in Barcode of Life Data systems (BOLD) (Ratnasingham and Hebert 2007)
We acquired high quality DNA barcodes for 45 specimens belonging to 14 species, which were sequenced for rbcL and matK
Summary
Mangroves are unique ecosystem exist along the sheltered inter-tidal coastline, in the margin between the land and sea in tropical and subtropical areas. This ecosystem endowed with productive wetland having flora and fauna adapted to local environment such as fluctuated water level, salinity and anoxic condition (Tomlinson 1986; Hutchings and Saenger 1987). They are most productive and biologically important ecosystems of the world which provide goods and services to human society in coastal and marine systems (FAO 2007).
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