The critical importance of vouchers in genomics

eLife, Год журнала: 2021, Номер 10

Опубликована: Июнь 1, 2021

A voucher is a permanently preserved specimen that maintained in an accessible collection. In genomics, vouchers serve as the physical evidence for taxonomic identification of genome assemblies. Unfortunately, vast majority vertebrate genomes stored GenBank database do not refer to specimens. Here, we urge researchers generating new assemblies deposit specimens accessible, permanent research collections, and link these publications, public databases, repositories. We also encourage scientists order recognize work local field biologists promote diverse inclusive knowledge base, recommend best practices deposition prevent errors ensure reproducibility legality genetic studies.

Язык: Английский

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Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom

Molecular Ecology Resources, Год журнала: 2021, Номер 21(6), С. 2050 - 2062

Опубликована: Март 22, 2021

Abstract DNA barcoding and metabarcoding provide new avenues for investigating biological systems. These techniques require well‐curated reference libraries with extensive coverage. Generating an exhaustive national barcode library can open up of research in ecology, evolution conservation, yet few studies to date have created such a resource. In plant barcoding, herbarium collections taxonomically robust material but also pose challenges lab processing. Here, we present resource covering all the native flowering plants conifers United Kingdom. This represents 1,482 species, majority specimens (81%) sourced from herbaria. Using Sanger sequencing markers, rbcL , matK ITS2, at least one was retrieved 98% UK flora. We sampled multiple individuals, resulting species coverage 96% (4,477 sequences), 90% (3,259 sequences) 75% ITS2 (2,585 sequences). Sequence recovery lower compared fresh collections, age specimen having significant effect on success sequence recovery. Species level discrimination highest however, ability successfully retrieve lowest this region. Analyses genetic distinctiveness across complete flora showed be informative most complex groups. The provides important many applications that identification DNA.

Язык: Английский

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A molecular‐based identification resource for the arthropods of Finland

Molecular Ecology Resources, Год журнала: 2021, Номер 22(2), С. 803 - 822

Опубликована: Сен. 25, 2021

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated Linnaean taxonomy. In this study, (1) report the creation of a comprehensive library DNA barcodes for arthropods an entire country (Finland), (2) publish library, and (3) deliver new identification tool insects spiders, as based on resource. The contains mtDNA COI 11,275 (43%) 26,437 arthropod species known from Finland, including 10,811 (45%) 23,956 insect species. quantify improvement in accuracy enabled current ran 1000 Finnish spider through Barcode Life Data system (BOLD) engine. Of these, 91% were correctly assigned unique when compared alone, 85% BOLD with material included, 75% excluded. capitalize resource, used train probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For full-length barcode region, assignments at level classes, orders, families, subfamilies, tribes, genera, reached 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, 88.5%, respectively. FinBOL FinPROTAX are available Biodiversity Information Facility (www.laji.fi) https://laji.fi/en/theme/protax. Overall, investment represents massive capacity-transfer community Finland all sectors society.

Язык: Английский

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The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

Fungal Diversity, Год журнала: 2021, Номер 109(1), С. 27 - 55

Опубликована: Июнь 26, 2021

Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic concept was utilized taking into consideration morphological aspects of colonies and cells, growth profiles. Later the biological added, which data from mating experiments. Biophysical measurements DNA similarity between isolates were an early measure that became more broadly with advent sequencing technology, leading sequence-based using comparisons parts ribosomal DNA. At present phylogenetic employ sequence rDNA other genes are universally in fungal taxonomy, including yeasts, because various studies revealed relatively good correlation divergence. The application genome information is becoming increasingly common, strongly recommend use complete, rather than draft genomes improve our understanding their genetic dynamics. Complete allow in-depth on evolvability and, consequently, they belong. Hybridization seems common phenomenon has observed all major lineages contain yeasts. Note hybrids may greatly differ post-hybridization development. Future studies, initially some model or complexes shift traditional as isolated clusters genetically compatible cohesive speciation network such interconnected by processes, hybridization.

Язык: Английский

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The Future of DNA Barcoding: Reflections from Early Career Researchers

Diversity, Год журнала: 2021, Номер 13(7), С. 313 - 313

Опубликована: Июль 9, 2021

Over the last two decades, use of DNA barcodes has transformed our ability to identify and assess life on planet. Both strengths weaknesses method have been exemplified through thousands peer-reviewed scientific articles. Given novel sequencing approaches, currently capable generating millions reads at low cost, we reflect questions: What will future bring for barcoding? Will identification species using short, standardized fragments stand test time? We present reflected opinions early career biodiversity researchers in form a SWOT analysis discuss answers these questions.

Язык: Английский

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BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries

Molecular Ecology Resources, Год журнала: 2020, Номер 21(2), С. 573 - 583

Опубликована: Окт. 1, 2020

Abstract Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species‐level assignment, consequent taxonomic coverage, relies on comprehensive barcode reference libraries. role these libraries is to support species identification, but accidental errors the generation barcodes may compromise their accuracy. Here, we present R‐based application, Barcode, Audit & Grade System (BAGS) ( https://github.com/tadeu95/BAGS ), that performs automated auditing annotation cytochrome c oxidase subunit I (COI) sequences libraries, for a given group animals, available Barcode Life Data (BOLD). This followed by implementing qualitative ranking system assigns one five grades (A E) each library, according attributes data congruency names with clustered index numbers (BINs). Our goal allow researchers obtain most useful reliable data, highlighting segregating records congruency. Different tests were performed perceive its usefulness limitations. BAGS fulfils significant gap current landscape barcoding research tools quickly screening gauge congruence status facilitate triage ambiguous posterior review. Thereby, has potential become valuable addition forthcoming metabarcoding studies, long term contributing globally improve quality reliability public

Язык: Английский

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DROP: Molecular voucher database for identification of Drosophila parasitoids

Molecular Ecology Resources, Год журнала: 2021, Номер 21(7), С. 2437 - 2454

Опубликована: Июнь 4, 2021

Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due lack sequenced voucher specimens by experts. Sometimes a large number sequences are available, but with too errors allow identification. Here, we address this problem for parasitoids Drosophila introducing curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying challenging poses major impediment realize the full potential model system in studies ranging from mechanisms food webs, biological control suzukii. In DROP, genetic data linked and, where possible, taxonomists vetted through direct comparison primary type material. To initiate 154 strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, six proteomes drawn total 183 operational taxonomic units (OTUs): 114 described parasitoid species 69 provisional species. We found richness heavily underestimated provide an updated catalogue community. offers accurate improves cross-referencing between individual that hope will catalyse research on diverse fascinating system. Our effort should also serve example researchers facing similar problems other organisms.

Язык: Английский

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Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding

Scientific Reports, Год журнала: 2022, Номер 12(1)

Опубликована: Сен. 29, 2022

Abstract Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional methods intrusive, time-consuming, substantially expensive, often provide only rough estimates in complex habitats. An advanced approach, environmental DNA (eDNA) metabarcoding, is promising, although few applications mangrove have been reported. In this study, we explore advantages limitations an eDNA metabarcoding survey on fish community Merbok Estuary (Peninsular Malaysia). COI 12S assays collectively detected 178 species from 127 genera, 68 families, 25 orders. Using significantly more over past decade (2010–2019) than conventional surveys, including several conservation importance. However, highlight three limitations: (1) absence a comprehensive reference database identities unresolved; (2) some previously documented specimen-based diversity was not captured by current method, perhaps consequence PCR primer specificity, (3) detection non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) marine coral reef holocentrids, syngnathids sharks), known to frequent estuaries, leading supposition that their drifted into estuary through water movements. The analysis revealed along homogenous, with upstream diverse further downstream. This could be due different landscapes or degree anthropogenic influences estuary. summary, demonstrated practicality assessing structure within rich environment short sampling period. need considered addressed fully exploit efficacy approach.

Язык: Английский

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Identification of eukaryotic microalgal strains

Journal of Applied Phycology, Год журнала: 2020, Номер 32(5), С. 2699 - 2709

Опубликована: Июль 15, 2020

Язык: Английский

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Animal Forensic Genetics

Genes, Год журнала: 2021, Номер 12(4), С. 515 - 515

Опубликована: Апрель 1, 2021

Animal forensic genetics, where the focus is on non-human species, broadly divided in two: domestic species and wildlife. When traces of a are relevant to investigation question identification less important, as material comes from either dog or cat for instance, but more may be actual pet. Identification specific animal draws similar methods those used human by using microsatellite markers. The use short tandem repeats link hair particular paved way dogs. Wildlife science becoming accepted recognised discipline. There growing acceptance that illegal trade wildlife having devasting effects numbers iconic species. Loci mitochondrial genome identify most likely present. Sequencing whole locus not needed if bases can targeted. benefits increased sensitivity loci testing, occasionally there an issue hybrids massively parallel DNA sequencing has role ingredients traditional medicines studies found protected present, potential future assignments. Non-human testing play key investigations provided it performed same standards all other profiling processes.

Язык: Английский

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