Initiating DNA barcoding of Eastern Mediterranean deep-sea biota

Abstract

Preliminary results of DNA barcoding survey of deep-sea mega-faunal biota are presented, collected by trawl and gillnet off the Israeli coast (SE Mediterranean, depths 700 to 1500 meters) during 2012-2013. 846 organisms were identified to 37 species, mainly fish and decapod crustaceans. The most abundant species were the blackmouth catshark Galeus melastomus, the cosmopolitan decapod Polycheles typhlops and the bivalve Abra longicallus. Two species were sampled for the first time from the southern Levant- the long armed chiroteuthid squid Chiroteuthis veranyi and the common mora, Mora moro. Four of the 18 fish species and two of the 10 crustacean species were abundant, representing 78% and 61%, respectively, of the organisms collected. Most other species are represented by fewer than 10 individuals. PCR products for the cytochrome c oxidase sub unit I (COI) gene for the 37 species were successfully sequenced. The identified and vouchered individuals are stored at the Steinhardt Museum of Natural History (Tel Aviv University, Israel) and their COI sequences were uploaded into the BoLD universal data center as part of the national marine barcoding project. The COI sequences of Acanthephyra eximia, Gryphus vitreus, Galeodea echinophora, Mesothuria intestinalis and Astropecten irregularis, constitute first records of these species in BoLD. When compared to the COI sequences in BoLD, the present results reveal some inconsistency in species identification, an outcome that should be taken into consideration primarily once the taxonomical verifications of collected taxa are elusive. This study is the first step in DNA barcoding of the Levant’s little-known benthic deep-sea fauna.

Gap-analysis of DNA barcoding reference libraries for two taxon inventories

“…Working on reference libraries of DNA barcodes of marine organisms (invertebrates and sh taxa), Weigand et al [5] recorded numerous identi cation errors, sequence contamination, incomplete reference (missing trace les or primer information) as inadequate data management. The results of the present study, as supported by other recent studies [2,5,17,28,30,32], reveal that we are still away from possessing decent representative reference libraries for important taxonomic groups. In addition, new DNA barcode data are continuously made available for the already barcoded and additional species from the reference libraries, including additional auditing and annotation processes, altogether helping in closing gap knowledge and purging accumulated erroneous data.…”

“…It is evident that the level of taxonomic detection and degree of accuracy is directly contingent on the newly developed molecular-biology depositories, the reference libraries completion and reliability of the DNA records [26][27][28][29]. Given our increased reliance on molecular taxonomy as a robust tool [4], strengthening the existing reference libraries is a necessitate for a wide range of scienti c and applied purposes, such as monitoring, eDNA and metabarcoding approaches, all targeting matched identi cations and the assessments of biodiversity and abundance [5,[14][15][16][17]29] .…”

“…Until recently, the standardized methodologies available for biological monitoring and management in the marine environments, primarily for practitioners, were restricted to traditional morphological taxonomy, tedious and time-consuming methodologies that require the involvement of expert taxonomists with skills that can only be attained via years of practice. This line of analyses is currently being replaced by molecular approaches such as DNA barcoding, environmental DNA (eDNA) and metabarcoding [5,[14][15][16][17]. For these approaches, it is of special interest to identify gaps in already existing or developing DNA barcode reference libraries, primarily those that are pertinent in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD).…”

Gap-analysis of DNA barcoding in ERMS reference libraries for ascidians and cnidarians

“…By working on reference libraries of DNA barcodes of marine organisms (invertebrates and sh taxa), Weigand et al [5] recorded numerous identi cation errors, sequence contamination, incomplete reference (missing trace les or primer information) as well as inadequate data management. The results of the present study, as supported by other recent studies [2,5,17,28,30,32], reveal that we are still away from holding representative and reliable reference libraries for important taxonomic groups, as those that were analysed in the current study. In addition, new DNA barcode data are continuously made available for the already barcoded and also for additional species from the reference libraries, including additional auditing and annotation processes, altogether helping in closing the gap knowledge and purging accumulated erroneous data.…”

Gap-analysis of DNA barcoding in ERMS reference libraries for ascidians and cnidarians

“…It is evident that the level of taxonomic detection and degree of accuracy by newly developed molecular tools is directly contingent on the reference libraries completion and reliability of the DNA records [26][27][28][29]. Given our increased reliance on molecular taxonomy as a robust tool [4], strengthening the existing reference libraries is a need for a wide range of scienti c and applied purposes, such as monitoring, eDNA and metabarcoding approaches, all targeting matched identi cations and for assessments of biodiversity and abundance [5,[14][15][16][17]29].…”