Unique Bins Research Articles

Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding.

The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.

Barcoding Hymenoptera: 11 Malaise Traps in Three Thai Forests: The First 68 Trap Weeks and 15,338 Parasitoid Wasp Sequences

We report the results of DNA barcoding week-long Malaise trap catches from 11 sites in three Thai conservation areas, concentrating on the parasitoid Hymenoptera, particularly the superfamily Ichneumonoidea. From a total of 15,338 parasitoid wasp sequences, 13,473 were barcode compliant and could be assigned to a family based on morphology and sequence data. These collectively represented 4917 unique BINs (putative species) in 46 families, with the Scelionidae, Ichneumonidae, Eulophidae, Braconidae and Platygastridae being, by far, the most abundant. Spatial proximity had a strong positive effect on the numbers of BINs shared between traps.

Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning.

Metagenome binning is a key step, downstream of metagenome assembly, to group scaffolds by their genome of origin. Although accurate binning has been achieved on datasets containing multiple samples from the same community, the completeness of binning is often low in datasets with a small number of samples due to a lack of robust species co-abundance information. In this study, we exploited the chromatin conformation information obtained from Hi-C sequencing and developed a new reference-independent algorithm, Metagenome Binning with Abundance and Tetra-nucleotide frequencies-Long Range (metaBAT-LR), to improve the binning completeness of these datasets. This self-supervised algorithm builds a model from a set of high-quality genome bins to predict scaffold pairs that are likely to be derived from the same genome. Then, it applies these predictions to merge incomplete genome bins, as well as recruit unbinned scaffolds. We validated metaBAT-LR's ability to bin-merge and recruit scaffolds on both synthetic and real-world metagenome datasets of varying complexity. Benchmarking against similar software tools suggests that metaBAT-LR uncovers unique bins that were missed by all other methods. MetaBAT-LR is open-source and is available at https://bitbucket.org/project-metabat/metabat-lr.

Metagenomic binning with assembly graph embeddings.

MotivationDespite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are not optimized for long-read assemblies. Deep graph learning algorithms have been proposed in other fields to deal with complex graph data structures. The graph structure generated during the assembly process could be integrated with contig features to obtain better bins with deep learning.ResultsWe propose GraphMB, which uses graph neural networks to incorporate the assembly graph into the binning process. We test GraphMB on long-read datasets of different complexities, and compare the performance with other binners in terms of the number of High Quality (HQ) genome bins obtained. With our approach, we were able to obtain unique bins on all real datasets, and obtain more bins on most datasets. In particular, we obtained on average 17.5% more HQ bins when compared with state-of-the-art binners and 13.7% when aggregating the results of our binner with the others. These results indicate that a deep learning model can integrate contig-specific and graph-structure information to improve metagenomic binning.Availability and implementationGraphMB is available from https://github.com/MicrobialDarkMatter/GraphMB.Supplementary information Supplementary data are available at Bioinformatics online.

Rethinking Monocular Height Estimation From a Classification Task Perspective Leveraging the Vision Transformer

Height estimation from a single remote sensing image has great potential in generating digital surface models (DSM) efficiently for a quick earth surface reconstruction. Recently, convolutional neural networks (CNN) have emerged as a powerful method to deal with this ill-posed problem. Most existing methods formulate height estimation as a regression problem due to the continuity of object height. However, it is difficult for the model to regress the object heights exactly to the ground-truth values with a wide range. In this letter, we reformulate the height estimation task as a classification task to improve the model performance. Specifically, we discretize the continuous ground-truth height into bins and assign each pixel to a single label according to the bin subdivision. In addition, we propose to generate a unique bin subdivision for each input image adaptively by viewing the bin generation as a set-to-set problem. Compared with the fixed bin subdivision method, a specific bin subdivision for each input image makes the model adaptively focus on the height range that is more probable to occur in the scene of the input image. In our experiments, we qualitatively and quantitatively demonstrate that the proposed method outperforms the state-of-the-art approaches on both Vaihingen and Potsdam datasets.

A DNA barcode library for the water mites of Montenegro

Water mites (Acari, Hydrachnidia) are a significant component of freshwater ecosystems inhabiting a wide range of aquatic habitats. This study provides a first comprehensive DNA barcode library for the water mites of Montenegro. DNA barcodes were analysed from 233 specimens of water mites morphologically assigned to 86 species from 28 genera and 15 families. In the course of the study, four species, i.e. Lebertiareticulata (Koenike, 1919), Atractidesinflatipalpis K.Viets, 1950, A.latipes (Szalay, 1935) and Parabrachypodamontii (Maglio, 1924) were molecularly confirmed as new for Montenegro and three species, i.e. Protziaoctopora Lundblad, 1954, Pionalaminata (Thor, 1901) and Unionicolaypsilophora (Bonz, 1783) are new for the Balkan Peninsula. Results are analysed using the Barcode Index Number system (BIN) and the Refined Single Linkage (RESL) of BOLD. The BIN assigned sequences to 98 clusters, while the RESL reveal 103 operational taxonomic units (OTUs). Unique BINs were revealed for 72 species (83.7%), whereas twelve species (14%) were characterised by two BINs and two species (2.3%) with three BINs. Amongst the studied taxa, 14 species were found with a high intraspecific sequence divergences (˃ 2.2%), emphasising the need for additional comprehensive morphological and molecu­lar analysis of these species.

DNA barcode library revealed unknown diversity of chironomid midges in Montenegro

We present the first results of the study aiming to investigate the diversity of the non-biting midges (Diptera: Chironomidae) fauna of the Skadar Lake system (Montenegro and Albania), a well-known hotspot of freshwater biodiversity composed by the young lake Skadar (originated 1200 before present) and by its old system of springs (originated during Pliocene). During the study, 8,147 COI barcodes were obtained and revealed the presence of 474 BINs and 586 OTUs assigned to 148 species. Our results provide the first insight into the factual molecular diversity among chironomids inhabiting Skadar Lake basin and fill a significant gap in the knowledge of the biodiversity in the Balkan region. With 219 (46.2%) unique BINs from the Skadar Lake basin new for BOLD, we can expect that further development of barcode reference libraries will help to bind unidentified developmental stages with those identified based on morphology and will reveal hidden Chironomidae species diversity. Further studies should be focused on sampling developmental stages which provides the best species-level resolution, such as mature males. It will help to develop a reliable reference barcode library - fundamental during further assessments.

AquaBOL.SK - how far have we come with the Slovak reference barcode database since DNAqua-Net was launched?

Essential for implementation of molecular tools in bioassessments are comprehensive databases with high-quality reference DNA sequence data. A recent survey arising from the DNAqua-Net EU COST Action WG1 has revealed significant gaps in the barcode reference data of aquatic biota both on a taxonomic and a geographical level (Weigand 2019). Although reference barcode libraries of all main freshwater groups are continuously improved through a number of national DNA-barcoding campaigns, still little data is available from Central and Eastern Europe. In Slovakia, the barcode coverage of the aquatic biota was very low when DNAqua-Net started. At the end of 2016 only 165 public records (60 OTUs) were available in BOLD (< 3 % of aquatic macroinvertebrates reported from Slovakia), and most of them were mined from GenBank. This led us to launch the campaign “Barcoding aquatic biota of Slovakia” (www.AquaBOL.SK), aiming to improve this unpleasant state. Since many common species in Slovakia are covered by barcodes from other countries, initially we focused on least explored habitat types within Europe - alpine glacial lakes in Tatra Mts and karstic springs. Both are located in Western and Slovak part of Eastern Carpathians, which are considered one of the most valuable biodiversity centers in Europe. More than 2700 sequences of COI-5P (337 BINs), originating in Slovakia, are currently in our dataset. Mostly they represent aquatic insects (86 %) and crustaceans (12 %), followed by minor taxonomic groups. From insects, the best covered orders are Coleoptera (43 % of sequences, 21% of species), followed by Trichoptera (22 % of sequences, 24 % of species) and Ephemeroptera (18 % of sequences, 33 % of species). And even if other groups (Hemiptera, Plecoptera) represent only around 5 % of all sequences each, their species coverage is already 21 % or 28 %, respectively. Relatively high number of unique BINs (35 out of 337) from our area, and separate intraspecific lineages within BINs of many widespread species, supports the premise that the Western Carpathians belong to the most important biodiversity hotspots. Our local reference database, continuously updated, is useful for the analysis and interpretation of metabarcoding data - a prerequisite for effective and nondestructive monitoring of aquatic biotopes including vulnerable, threatened, and protected habitats. It is also beneficial for a number of other purposes such as taxonomic revisions and phylogenetic analyses. This contribution was partially supported by VEGA2/0030/17, VEGA2/0084/2021 and COST CA15219.

Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research.

SUMMARYThe limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1000–2000 genome‐wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay, BARCSoySNP6K, containing 6000 markers, which were carefully chosen from the SoySNP50K assay based on their position in the soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5000 single nucleotide polymorphisms (SNPs) from euchromatic and 1000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K versus BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays; however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARCSoySNP6K assay is proven as an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationships. The assay is commercialized by Illumina Inc. and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing.

DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity.

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae).

The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

BackgroundThe application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping.ResultsWe identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species.ConclusionsGBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2802-3) contains supplementary material, which is available to authorized users.

Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin.

Molecular identification through DNA barcoding has been proposed as a way to standardize a global biodiversity identification system using a partial sequence of the mitochondrial COI gene. We applied an integrative approach using DNA barcoding and traditional morphology-based bioassessment to identify fish from a neotropical region possessing low taxonomic knowledge: the Jequitinhonha River Basin (Southeastern Brazil). The Jequitinhonha River Basin (JRB) has a high rate of endemism and is considered an area of high priority for fish conservation, with estimates indicating the presence of around 110 native and non-indigenous species. DNA barcodes were obtained from 260 individuals belonging to 52 species distributed among 35 genera, 21 families and 6 orders, including threatened and rare species such as Rhamdia jequitinhonha and Steindachneridion amblyurum. The mean Kimura two-parameter genetic distances within species, genera and families were: 0.44, 12.16 and 20.58%, respectively. Mean intraspecific genetic variation ranged from 0 to 11.43%, and high values (>2%) were recovered for five species. Species with a deep intraspecific distance, possibly flagging overlooked taxa, were detected within the genus Pimelodella. Fifteen species, only identified to the genus level, had unique BINs, with a nearest neighbor distance over 2% and therefore, potential new candidate species supported by DNA barcoding. The integrative taxonomy approach using DNA barcoding and traditional taxonomy may be a remedy to taxonomy impediment, accelerating species identification by flagging potential new candidate species and to adequately conserve the megadiverse neotropical ichthyofauna.

Harmonising diverse 3D geometries in a hard rock environment for pre-stack imaging

Four 3D seismic surveys were acquired by HiSeis Pty Ltd over two years across an existing mining camp. The main objective of these seismic surveys was definition of structures which could assist characterization of mineralised zone that consists mainly of massive sulphides. Initial processing of seismic data started shortly after acquisition in 2011. Preliminary products have shown great promise in resolving complex structural environments and showed potential for direct targeting form seismic data. Our motive for reprocessing the dataset was in integration of all 2011 and 2012 seismic data in an amplitude consistent routine which could bring new value for amplitude based analysis of massive sulphide bodies. Conventional 3D deep-move out corrections (DMO), followed by a post-stack migration algorithm has not been successful in merging diverse datasets. Considerable improvement was achieved through the application of pre-stack time migration (PSTM) algorithm. This allowed us to use unique bin size for all merged seismic surveys. Successful imaging of merged datasets has been challenged. The main reason was that 3D seismic datasets had vastly diverse offset and azimuth distribution. Highly irregular migration fold coverage is an obvious problem which had to be overcome by exclusion of unsuccessful imaged events prior to stacking.

The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions.

During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.

A new genetic and deletion map of wheat chromosome 5A to detect candidate genes for quantitative traits

In the present study, a detailed deletion map for wheat chromosomes 5A and 5B is reported, as well as an integrated genetic linkage map of chromosome 5A enriched with single nucleotide polymorphism (SNP) markers, useful both for comparison studies with other existing maps and for mapping major genes and quantitative trait loci (QTLs). Physical mapping of 5,011 SNP markers was obtained using Chinese Spring bin deletion lines for the homoeologous chromosomes of group 5; 509 SNPs were also genetically mapped in a recombinant inbred line population segregating for chromosome 5A only, obtained by crossing the cultivar Chinese Spring and the disomic substitution line Chinese Spring-5A dicoccoides. The whole 5A genetic map, containing 572 markers, covered a total length of 248.7 cM distributed among three linkage groups of 83.5, 117.8 and 47.4, respectively. The majority of SNP markers physically mapped on 5A were mapped to a unique bin, while a small percentage was assigned a double location, suggesting the presence of a segment of 5A short arm which may have undergone a duplication followed by an insertion into the long arm of the same chromosome. A QTL analysis for yield components was performed, identifying a major QTL in the sub-telomeric region of chromosome 5A, corresponding to the 5AL15-0.67-0.78 bin; the chromosome segment was 23.5 cM long and included 111 markers. Candidate genes for yield components on chromosome 5A were identified through a syntenic genomic approach by comparison with genomes of model species. Putative function analysis revealed genes involved in basic metabolism and in stress condition responses, including heat shock proteins, chaperones, serine/threonine protein kinases and membrane transporters, located in the region of the QTL. This information represents an important step for map-based and candidate gene-based cloning of yield QTLs.