Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions

Abstract

DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications.

Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring

“…The depth and accuracy of DNA metabarcoding‐based identifications are mainly dependent on the availability of reference libraries containing representative and accurate sequences for the targeted species. The existence of gaps and unequal representation of taxonomic groups in reference databases may compromise the accuracy of the DNA‐based biodiversity assessments (Ardura, 2019; Duarte et al., 2020; Leite et al., 2020; Weigand et al., 2019). Thus, assessing these gaps and the quality of sequence data in reference databases is mandatory for the successful implementation of DNA‐based tools in biodiversity assessments.…”

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

“…43% and 34% were covered by sequences, in BOLD and PR2 databases, respectively (Rey et al 2020). Very recently, Duarte et al (2020), found that from the total number of species included in the AquaNIS and EASIN databases, occurring in European coastal regions, approximately 65% and 55%, respectively, had at least one of the searched barcode markers (COI, 18S, rbcL and matK), in BOLD or GenBank. However, the values of missing barcodes clearly differed among taxonomic groups (i.e.…”

“…However, the values of missing barcodes clearly differed among taxonomic groups (i.e. Animalia, Chromista and Plantae) and the barcode markers searched (Duarte et al 2020). Definitely, expanding genetic databases with reference sequences is mandatory to make the most of the potential of the DNA metabarcoding approach in NIS surveillance in coastal ecosystems.…”

On the Diversity of Phyllodocida (Annelida: Errantia), with a Focus on Glyceridae, Goniadidae, Nephtyidae, Polynoidae, Sphaerodoridae, Syllidae, and the Holoplanktonic Families

“…We conducted a global gap-analysis by comparing the available barcoded species of Phyllodocida by 4 April 2020 and its congruence with the total number of valid species [24,59,60]. We compared the species list CL-MTVPP with all publicly available COI-5P sequence records using the BOLD checklist tool to obtain the percentage of barcoded species.…”

“…However, the number of studies dedicated to this annelid group and, consequently, that of the associated barcoding projects must also be taken into account [24]. For example, in the case of fishes, the amount of dedicated projects is significantly higher and, thus, the barcode library closer to completion [115][116][117], which is not the case for macroinvertebrate barcoding projects and the current state of its molecular libraries [60].…”