Evaluating the Utility of Single-Locus DNA Barcoding for the Identification of Ribbon Worms (Phylum Nemertea)

DNA barcoding of the genus Gampsocleis (Orthoptera, Tettigoniidae) from China

DNA barcoding is a useful addition to the traditional morphology-based taxonomy. A ca. 650 bp fragment of the 5' end of mitochondrial cytochrome c oxidase subunit I (hereafter COI-5P) DNA barcoding was sued as a practical tool for Gampsocleis species identification. DNA barcodes from 889 specimens belonging to 8 putative Gampsocleis species was analyzed, including 687 newly generated DNA barcodes. These barcode sequences were clustered/grouped into Operational Taxonomic Units (OTUs) using the criteria of five algorithms, namely Barcode Index Number (BIN) System, Assemble Species by Automatic Partitioning (ASAP), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP). The Taxon ID Tree grouped sequences of morphospecies and almost all MOTUs in distinct nonoverlapping clusters. Both long- and short-winged Gampsocleis species are reciprocally monophyletic in the Taxon ID Tree. In BOLD, 889 barcode sequences are assigned to 17 BINs. The algorithms ASAP, jMOTU, bPTP and GMYC clustered the barcode sequences into 6, 13, 10, and 23 MOTUs, respectively. BIN, ASAP, and bPTP algorithm placed three long-winged species, G. sedakovii, G. sinensis and G. ussuriensis within the same MOTU. All species delimitation algorithms split two short-winged species,G. fletcheri and G. gratiosa into at least two MOTUs each, except for ASAP algorithm. More detailed molecular and morphological integrative studies are required to clarify the status of these MOTUs in the future.

Seven new species of Tetranemertes Chernyshev, 1992 (Monostilifera, Hoplonemertea, Nemertea) from the Caribbean Sea, western Pacific, and Arabian Sea, and revision of the genus

The marine ribbon worm genus Tetranemertes Chernyshev, 1992 currently includes three species: the type species T.antonina (Quatrefages, 1846) from the Mediterranean Sea, T.rubrolineata (Kirsteuer, 1965) from Madagascar, and T.hermaphroditica (Gibson, 1982) from Australia. Seven new species are described: T.bifrostsp. nov., T.ocelatasp. nov., T.majinbuuisp. nov., and T.pastafariensissp. nov. from the Caribbean Sea (Panamá), and three species, T.unistriatasp. nov., T.paulayisp. nov., and T.arabicasp. nov., from the Indo-West Pacific (Japan and Oman). As a result, an amended morphological diagnosis of the genus is offered. To improve nomenclatural stability, a neotype of Tetranemertesantonina is designated from the Mediterranean. The newly described species, each characterized by features of external appearance and stylet apparatus, as well as by DNA-barcodes, form a well-supported clade with T.antonina on a molecular phylogeny of monostiliferan hoplonemerteans based on partial sequences of COI, 16S rRNA, 18S rRNA, and 28S rRNA. Six of the seven newly described species, as well as T.rubrolineata, possess the unusual character of having a central stylet basis slightly bilobed to deeply forked posteriorly in fully grown individuals, a possible morphological synapomorphy of the genus. In addition, an undescribed species of Tetranemertes is reported from the Eastern Tropical Pacific (Panamá), increasing the total number of known species in the genus to eleven.

Three new species in Tetrastemma Ehrenberg, 1828 (Nemertea, Monostilifera) from sublittoral to upper bathyal zones of the northwestern Pacific

Monostiliferous nemerteans in the genus Tetrastemma Ehrenberg, 1828 are generally characterized as having four eyes, and they occur worldwide, from the intertidal zone to the deep-sea bottom. Recent extensive sampling of Tetrastemma has explored the high species diversity, including many undescribed forms, but phylogenic analysis has revealed non-monophyly of the genus. We herein describe three new species of the genus (T. albumsp. nov., T. personasp. nov., and T. shohoensesp. nov.) from northwestern Pacific waters based on specimens collected by dredging or by use of a remotely operated vehicle at depths of 116–455 m. Since anatomical and histological characters traditionally used in systematics of the genus are sometimes interspecifically uniform, a histology-free approach is applied for the species descriptions in this study. To confirm the generic affiliation of the new species, a molecular phylogenetic analysis based on partial sequences of cytochrome c oxidase subunit I, 16S rRNA, 18S rRNA, 28S rRNA, and histone H3 genes was performed. Our result shows that all three new species are nested in a subclade formed by species from the North Pacific and American Atlantic, inferring that geographic distribution does not reflect the cladogenesis of Tetrastemma. Furthermore, two Tetrastemma species with a cylindrical stylet basis, T. freyaeChernyshev et al., 2020 from off the coast of India and Hawaii and T. shohoensesp. nov. from Shoho Seamount, Japan, constitute a clade in the resulting tree.

First eumonostiliferous nemertean from the Nishi-Shichito Ridge, Genrokunemertes obesa gen. et sp. nov. (Eumonostilifera, Nemertea)

Nemerteans are mostly marine, benthic invertebrates, inhabiting intertidal to hadal zones. Recently, they have been recognized from deep sea with environmental DNA (eDNA) metabarcoding of sediment samples whereas any records from the locations and/or the water depth have not been documented in nemertean taxonomic publications to date. It suggests that there are major gaps between deep-sea nemertean fauna observed with eDNA and taxonomic knowledge. During a research expedition in 2021, we obtained a single specimen of eumonostiliferous nemertean from the southern part of Genroku Seamount Chain, the Nishi-Shichito Ridge, where any nemertean species have never been reported. Subsequent morphological and molecular examination reveal that the species is placed in a new genus and herein described as Genrokunemertes obesa gen. et sp. nov. It resembles shallow-water-dwelling Kurilonemertes and Typhloerstedia, but differs from the former in lacking eyes and the latter in possessing well-developed cephalic glands and lacking accessory nerves of lateral nerve cords. In terms of genetic distances based on partial sequences of the cytochrome c oxidase subunit I gene, G. obesa gen. et sp. nov. is closest to Monostilifera sp. Owase collected from Japan, which is characterized by large four eyes; the COI distance is higher than commonly observed interspecific divergences in eumonostiliferans.

Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda

Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.

Singleton molecular species delimitation based on COI-5P barcode sequences revealed high cryptic/undescribed diversity for Chinese katydids (Orthoptera: Tettigoniidae)

Background

DNA barcoding has been developed as a useful tool for species discrimination. Several sequence-based species delimitation methods, such as Barcode Index Number (BIN), REfined Single Linkage (RESL), Automatic Barcode Gap Discovery (ABGD), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP), were used. Our aim was to estimate Chinese katydid biodiversity using standard DNA barcode cytochrome c oxidase subunit I (COI-5P) sequences.

Results

Detection of a barcoding gap by similarity-based analyses and clustering-base analyses indicated that 131 identified morphological species (morphospecies) were assigned to 196 BINs and were divided into four categories: (i) MATCH (83/131 = 64.89%), morphospecies were a perfect match between morphospecies and BINs (including 61 concordant BINs and 22 singleton BINs); (ii) MERGE (14/131 = 10.69%), morphospecies shared its unique BIN with other species; (iii) SPLIT (33/131 = 25.19%, when 22 singleton species were excluded, it rose to 33/109 = 30.28%), morphospecies were placed in more than one BIN; (iv) MIXTURE (4/131 = 5.34%), morphospecies showed a more complex partition involving both a merge and a split. Neighbor-joining (NJ) analyses showed that nearly all BINs and most morphospecies formed monophyletic cluster with little variation. The molecular operational taxonomic units (MOTUs) were defined considering only the more inclusive clades found by at least four of seven species delimitation methods. Our results robustly supported 61 of 109 (55.96%) morphospecies represented by more than one specimen, 159 of 213 (74.65%) concordant BINs, and 3 of 8 (37.5%) discordant BINs.

Conclusions

Molecular species delimitation analyses generated a larger number of MOTUs compared with morphospecies. If these MOTU splits are proven to be true, Chinese katydids probably contain a seemingly large proportion of cryptic/undescribed taxa. Future amplification of additional molecular markers, particularly from the nuclear DNA, may be especially useful for specimens that were identified here as problematic taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1404-5) contains supplementary material, which is available to authorized users.

Assessment of three plastid DNA barcode markers for identification of Clinacanthus nutans (Acanthaceae)

This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C. nutans was carried out using NCBI's Basic Local Alignment Search Tool (BLAST). The rbcL and trnH-psbA regions successfully identified C. nutans with sequencing rates of 100% through BLAST identification. Molecular Evolutionary Genetics Analysis (MEGA) 6.0 was used to analyze interspecific and intraspecific divergence of plastid DNA sequences. rbcL and matK exhibited the lowest average interspecific distance (0.0487 and 0.0963, respectively), whereas trnH-psbA exhibited the highest average interspecific distance (0.2029). The R package Spider revealed that trnH-psbA correctly identified Barcode of Life Data System (BOLD) 96%, best close match 79%, and near neighbor 100% of the species, compared to matK (BOLD 72%; best close match 64%; near neighbor 78%) and rbcL (BOLD 77%; best close match 62%; near neighbor 88%). These results indicate that trnH-psbA is very effective at identifying C. nutans, as it performed well in discriminating species in Acanthaceae.

Nipponnemertes incainca sp. n. Adoption of the new taxonomic proposal for nemerteans (Nemertea, Cratenemertidae)

A new species Nipponemertesincainca is described from the intertidal zone of Santa Marta, Colombia. A new recent approach based on both morphological and molecular characters is applied for the description. The main characteristics of the species are: red color, head shield-shaped with a mid-dorsal cephalic ridge, furrows pre-cerebral inconspicuous with few faint ridges orthogonal to furrow axis, two irregular groups of eyespots situated at lateral margins in precerebral cephalic region, proboscis provided with papillae and 12 nerves, stylet smooth supported on an oval basis, and two pouches containing 3–4 accessory stylets each. The sequence of the COI gene was analyzed as an additional support for the new species.

Cytochrome c oxidase subunit 1 gene as a DNA barcode for discriminating Trypanosoma cruzi DTUs and closely related species

BACKGROUND

The DNA barcoding system using the cytochrome c oxidase subunit 1 mitochondrial gene (cox1 or COI) is highly efficient for discriminating vertebrate and invertebrate species. In the present study, we examined the suitability of cox1 as a marker for Trypanosoma cruzi identification from other closely related species. Additionally, we combined the sequences of cox1 and the nuclear gene glucose-6-phosphate isomerase (GPI) to evaluate the occurrence of mitochondrial introgression and the presence of hybrid genotypes.

METHODS

Sixty-two isolates of Trypanosoma spp. obtained from five of the six Brazilian biomes (Amazon Forest, Atlantic Forest, Caatinga, Cerrado and Pantanal) were sequenced for cox1 and GPI gene fragments. Phylogenetic trees were reconstructed using neighbor-joining, maximum likelihood, parsimony and Bayesian inference methods. Molecular species delimitation was evaluated through pairwise intraspecific and interspecific distances, Automatic Barcode Gap Discovery, single-rate Poisson Tree Processes and multi-rate Poisson Tree Processes.

RESULTS

Both cox1 and GPI genes recognized and differentiated T. cruzi, Trypanosoma cruzi marinkellei, Trypanosoma dionisii and Trypanosoma rangeli. Cox1 discriminated Tcbat, TcI, TcII, TcIII and TcIV. Additionally, TcV and TcVI were identified as a single group. Cox1 also demonstrated diversity in the discrete typing units (DTUs) TcI, TcII and TcIII and in T. c. marinkellei and T. rangeli. Cox1 and GPI demonstrated TcI and TcII as the most genetically distant branches, and the position of the other T. cruzi DTUs differed according to the molecular marker. The tree reconstructed with concatenated cox1 and GPI sequences confirmed the separation of the subgenus Trypanosoma (Schizotrypanum) sp. and the T. cruzi DTUs TcI, TcII, TcIII and TcIV. The evaluation of single nucleotide polymorphisms (SNPs) was informative for DTU differentiation using both genes. In the cox1 analysis, one SNP differentiated heterozygous hybrids from TcIV sequences. In the GPI analysis one SNP discriminated Tcbat from TcI, while another SNP distinguished TcI from TcIII.

CONCLUSIONS

DNA barcoding using the cox1 gene is a reliable tool to distinguish T. cruzi from T. c. marinkellei, T. dionisii and T. rangeli and identify the main T. cruzi genotypes.

Estimating the barcoding gap in a global dataset of cox1 sequences for Odonata: close, but no cigar

We evaluated the extent of intraspecific and interspecific genetic distances for two highly diverse infraorders of Odonata: Anisoptera and Zygoptera. All cytochrome c oxidase subunit I sequences (cox1), the region chosen for zoological DNA barcoding, present in GenBank for each infraorder were downloaded and curated. For Anisoptera, the final dataset consisted of 2,961 individual cox1 sequences for 536 species and the equivalent numbers for Zygoptera were 2,477 sequences for 497 species. More than 7 million individual genetic comparisons were made and the results indicated that there is a tendency towards a barcoding gap, but that the size of the gap may not be sufficient to robustly infer identities for some taxa. DNA barcoding may be of less use for some odonate taxa, perhaps pertaining to misidentifications in global databases. However, at local scales or with more confined taxonomical sampling, this tool may yet be beneficial in identifying these charismatic organisms.