The first comprehensive DNA barcode reference library of Chinese Tanytarsus (Diptera: Chironomidae) for environmental DNA metabarcoding

Abstract

Aim Reliable DNA barcode reference libraries are critical for biodiversity monitoring based on Environmental DNA (eDNA). DNA barcoding has proven successful in species delimitation and association of life stages in many groups of animals, such as non‐biting midges (Chironomidae). We use the genus Tanytarsus van der Wulp, 1874, second largest genus of the family Chironomidae, to test whether DNA barcodes can be used to identify unknown and cryptic species. A comprehensive DNA barcode library will be built to facilitate further eDNA studies for biodiversity monitoring and conservation in freshwater ecosystems. Location Mainland China. Methods In this study, the cytochrome c oxidase subunit 1 (COI) DNA barcodes from 298 individuals, representing 56 morphospecies from China, were analysed, including 136 sequences from previous studies and 162 newly generated DNA barcodes. 298 COI barcodes were applied into the Automatic Barcode Gap Discovery (ABGD) to compare the operational taxonomic units (OTU) number resulting from the Barcode Index Number (BIN) based “Barcode Gap Analysis” and neighbour joining (NJ) tree. Results Total 298 barcode sequences were applied to 66 BINs, including 20 singleton BINs and 46 concordant BINs. ABGD yielded 55 OTUs with a prior intraspecific divergence of Pmax = 3.59%. By Integrating DNA barcodes with morphology, we revealed 21 putative species new to science and two unidentified species from the 56 well‐separated morphospecies. Besides, several cryptic species are uncovered using the NJ tree and TCS haplotype network based on COI DNA barcodes. Main conclusions Our results demonstrate that DNA barcodes enable the discovery and identification of Tanytarsus non‐biting midges. A comprehensive DNA barcode reference library could speed up accurate species delimitation and discovery by providing a reliable resource for taxonomic studies, and improve the application of eDNA metabarcoding in biomonitoring of freshwater ecosystems.

A New Species in Notobitiella Hsiao in China Confirmed by Morphological and Molecular Data (Hemiptera: Heteroptera: Coreidae)

“…The complete sequence of the COI gene for Cloresmus pulchellus and three outgroups Clavigralla tomentosicollis , Leptoglossus membranaceus, and Hydaropsis longirostris from Liu et al, 2019 [ 15 , 16 , 17 ] were also included in our analysis (GenBank Accession Number: NC_042806, KY274846, NC_042809, and EU427337). The genetic distance matrix estimations and neighbor-joining tree [ 18 ] based on COI datasets were calculated in MEGA X, using the Kimura 2-Parameter (K2P) substitution model [ 19 ], 1000 non-parametric bootstrap replicates [ 20 ], and the “pairwise deletion” option for missing data [ 21 ].…”

Recent advances in environmental DNA‐based biodiversity assessment and conservation

“…Lin et al. (2021) analysed the cytochrome c oxidase subunit 1 (COI) DNA barcodes from 298 individuals of Tanytarsus non‐biting midges, representing 56 morphospecies including several cryptic species from China. This study was an important step to build a comprehensive DNA barcode library for chironomids, which are an important group for biomonitoring.…”

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

“…Impacts of human-induced climate change, habitat fragmentation, and over-exploitation of natural resources have depleted global biodiversity, in particular in the marine environment ( Díaz et al, 2006 ; Butchart et al, 2010 ; Pinsky et al, 2019 ). Conservation efforts based on robust biomonitoring programs are necessary to identify and mitigate ecological issues ( Stat et al, 2017 ; Berry et al, 2019 ); therefore, preservation of diversity depends on species classification accuracy ( Thomsen and Willerslev, 2015 ; Lin et al, 2020 ). The species composition and distribution can act as an environmental indicator of human activity ( DiBattista et al, 2020 ).…”

“…( Shokralla et al, 2015 ; Collins et al, 2019 ). Despite the successful use of these markers in fish biodiversity assessment via metabarcoding ( Singer et al.,2019 ; McClenaghan et al, 2020 ; Russo et al, 2021 ), biodiversity assessments could be maximized by the use of regional-specific reference barcode libraries ( Lin et al, 2020 ).…”