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Samreen KB, Manzoor F. Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan. PeerJ 2024; 12:e17420. [PMID: 38832046 PMCID: PMC11146329 DOI: 10.7717/peerj.17420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/28/2024] [Indexed: 06/05/2024] Open
Abstract
Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore's Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research.
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Affiliation(s)
- Khush Bakhat Samreen
- Department of Zoology, Lahore College for Women University, Lahore, Lahore, Pakistan
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Yang L, Metzger GA, Padilla Del Valle R, Delgadillo Rubalcaba D, McLaughlin RN. Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome. EMBO J 2024; 43:112-131. [PMID: 38177314 PMCID: PMC10883270 DOI: 10.1038/s44318-023-00007-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/18/2023] [Accepted: 11/10/2023] [Indexed: 01/06/2024] Open
Abstract
Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.
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Affiliation(s)
- Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | - Ricky Padilla Del Valle
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Richard N McLaughlin
- Pacific Northwest Research Institute, Seattle, WA, USA.
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA.
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3
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Lszl GM, Volynkin AV. A new species of Karschiola Gaede from Mozambique and Zimbabwe (Lepidoptera: Erebidae: Arctiinae) with updated information on the distribution of the genus. Zootaxa 2023; 5375:214-226. [PMID: 38220826 DOI: 10.11646/zootaxa.5375.2.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Indexed: 01/16/2024]
Abstract
The present paper provides the description of a new species of the genus Karschiola Gaede, 1926 from central Mozambique and Zimbabwe: K. ndzou sp. n. The pairwise genetic distance between the two Karschiola species is calculated and a neighbour-joining tree based on DNA barcodes of two K. holoclera and five K. ndzou sp. n. specimens is provided. The paper is illustrated with eight colour photos of adults and 18 genitalia images, a distribution map and two habitat photos.
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Affiliation(s)
- Gyula M Lszl
- African Natural History Research Trust; Street Court; Kingsland; Leominster; HR6 9QA; United Kingdom.
| | - Anton V Volynkin
- Altai State University; Lenina Avenue 61; RF-656049; Barnaul; Russia.
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van Dijk EL, Naquin D, Gorrichon K, Jaszczyszyn Y, Ouazahrou R, Thermes C, Hernandez C. Genomics in the long-read sequencing era. Trends Genet 2023; 39:649-671. [PMID: 37230864 DOI: 10.1016/j.tig.2023.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.
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Affiliation(s)
- Erwin L van Dijk
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kévin Gorrichon
- National Center of Human Genomics Research (CNRGH), 91000 Évry-Courcouronnes, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Rania Ouazahrou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Céline Hernandez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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5
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Leroy BML, Rabl D, Püls M, Hochrein S, Bae S, Müller J, Hebert PDN, Kuzmina ML, Zakharov EV, Lemme H, Hahn WA, Hilmers T, Jacobs M, Kienlein S, Pretzsch H, Heidrich L, Seibold S, Roth N, Vogel S, Kriegel P, Weisser WW. Trait-mediated responses of caterpillar communities to spongy moth outbreaks and subsequent tebufenozide treatments. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2890. [PMID: 37212374 DOI: 10.1002/eap.2890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 03/14/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023]
Abstract
Outbreaks of the spongy moth Lymantria dispar can have devastating impacts on forest resources and ecosystems. Lepidoptera-specific insecticides, such as Bacillus thuringiensis var. kurstaki (BTK) and tebufenozide, are often deployed to prevent heavy defoliation of the forest canopy. While it has been suggested that using BTK poses less risk to non-target Lepidoptera than leaving an outbreak untreated, in situ testing of this assumption has been impeded by methodological challenges. The trade-offs between insecticide use and outbreaks have yet to be addressed for tebufenozide, which is believed to have stronger side effects than BTK. We investigated the short-term trade-offs between tebufenozide treatments and no-action strategies for the non-target herbivore community in forest canopies. Over 3 years, Lepidoptera and Symphyta larvae were sampled by canopy fogging in 48 oak stands in southeast Germany during and after a spongy moth outbreak. Half of the sites were treated with tebufenozide and changes in canopy cover were monitored. We contrasted the impacts of tebufenozide and defoliator outbreaks on the abundance, diversity, and functional structure of chewing herbivore communities. Tebufenozide treatments strongly reduced Lepidoptera up to 6 weeks after spraying. Populations gradually converged back to control levels after 2 years. Shelter-building species dominated caterpillar assemblages in treated plots in the post-spray weeks, while flight-dimorphic species were slow to recover and remained underrepresented in treated stands 2 years post-treatment. Spongy moth outbreaks had minor effects on leaf chewer communities. Summer Lepidoptera decreased only when severe defoliation occurred, whereas Symphyta declined 1 year after defoliation. Polyphagous species with only partial host plant overlap with the spongy moth were absent from heavily defoliated sites, suggesting greater sensitivity of generalists to defoliation-induced plant responses. These results demonstrate that both tebufenozide treatments and spongy moth outbreaks alter canopy herbivore communities. Tebufenozide had a stronger and longer lasting impact, but it was restricted to Lepidoptera, whereas the outbreak affected both Lepidoptera and Symphyta. These results are tied to the fact that only half of the outbreak sites experienced severe defoliation. This highlights the limited accuracy of current defoliation forecast methods, which are used as the basis for the decision to spray insecticides.
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Affiliation(s)
- Benjamin M L Leroy
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Dominik Rabl
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Marcel Püls
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sophia Hochrein
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Soyeon Bae
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
- Bavarian Forest National Park, Grafenau, Germany
| | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Maria L Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V Zakharov
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Hannes Lemme
- Department of Forest Protection, Bavarian State Institute of Forestry, Freising, Germany
| | - W Andreas Hahn
- Department of Forest Protection, Bavarian State Institute of Forestry, Freising, Germany
| | - Torben Hilmers
- Chair of Forest Growth and Yield Science, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Martin Jacobs
- Chair of Forest Growth and Yield Science, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Sebastian Kienlein
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Hans Pretzsch
- Chair of Forest Growth and Yield Science, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Lea Heidrich
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sebastian Seibold
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
- Ecosystem Dynamics and Forest Management Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
- Berchtesgaden National Park, Berchtesgaden, Germany
| | - Nicolas Roth
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sebastian Vogel
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Peter Kriegel
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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Fiebig R, Lszl GM, Volynkin AV, Taberer TR. Integrative taxonomic revision of the Metarctia Walker, 1855 subgenus HebenaWalker, 1856, with descriptions of six new species and one new subspecies(Lepidoptera: Erebidae: Arctiinae: Syntomini). Zootaxa 2023; 5339:301-354. [PMID: 38221049 DOI: 10.11646/zootaxa.5339.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Indexed: 01/16/2024]
Abstract
A revision of the subgenus Hebena Walker, 1856 of the syntomine genus Metarctia Walker, 1855 is given based on integrative taxonomic analyses. Six new species (Metarctia (Hebena) manfredi sp. n., M. (H.) elleni sp. n., M. (H.) brigitta sp. n., M. (H). lukaszi sp. n., M. (H.) smithi sp. n., and M. (H.) haraldsulaki sp.n.) and one new subspecies (M. (H.) smithi transvallesiana ssp. n.) are described. Metarctia (H.) kelleni (Snellen, 1886) stat. rev. is reinstated from synonymy with M. (H.) rubra (Walker, 1856) and Metarctia (H.) subincarnata Kiriakoff, 1954 syn. n. is synonymised with M. (H.) henrardi Kiriakoff, 1953 and Metarctia cinnamomea (Wallengren, 1860) syn. n. with M. (H.) rubra (Walker, 1856). DNA barcodes were obtained for 116 specimens representing 7 taxa, and genetic analyses were performed using Maximum Likelihood and Bayesian Inference approaches; a DNA barcode tree resulting from the latter is illustrated. Pairwise distances of barcodes between taxa are provided where available. The adults and genitalia of all taxa, their habitats and distribution are illustrated in 19 colour plates and 5 distribution maps.
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Affiliation(s)
- Ralf Fiebig
- Nordstrasse 30; Roleben-Wiehe; D-06571; Germany.
| | - Gyula M Lszl
- African Natural History Research Trust (ANHRT); Street Court; Leominster-Kingsland; HR6 9QA; United Kingdom.
| | - Anton V Volynkin
- African Natural History Research Trust (ANHRT); Street Court; Leominster-Kingsland; HR6 9QA; United Kingdom.
| | - Tabitha R Taberer
- African Natural History Research Trust (ANHRT); Street Court; Leominster-Kingsland; HR6 9QA; United Kingdom.
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8
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Liston A, Vikberg V, Mutanen M, Nyman T, Prous M. Palaearctic willow-catkin sawflies: a revision of the amentorum species group of Euura (Hymenoptera, Tenthredinidae). Zootaxa 2023; 5323:349-395. [PMID: 38220961 DOI: 10.11646/zootaxa.5323.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Indexed: 01/16/2024]
Abstract
The Euura amentorum species group is Holarctic, and in Europe it is most species-rich in the North. Their larvae develop entirely within the female catkins of Salix species: some species bore in the central stalk, whereas others live outside this and feed mainly on the developing seeds. Eight Palaearctic species are treated here as valid, and a key to these is provided. Males of five species are known. Two new species are described from northern Europe: Euura pohjola sp. n. and E. ursaminor sp. n. First records of E. itelmena (Malaise, 1931) from the West Palaearctic are presented. We propose seven new synonymies: Pontopristia montana Lindqvist, 1961 (junior secondary homonym in Euura) with Euura freyja (Liston, Taeger & Blank, 2009); Pontopristia brevilabris Malaise, 1921, Amauronematus fennicus Lindqvist, 1944, Pontopristia boreoalpina Lindqvist, 1961, Pontopristia punctulata Lindqvist, 1961, and Amauronematus pyrenaeus Lacourt, 1995 with Euura microphyes (Frster, 1854); and Pteronidea holmgreni Lindqvist, 1968 with Nematus umbratus Thomson, 1871. Lectotypes are designated for: Amauronematus fennicus Lindqvist, 1944, Nematus amentorum Frster, 1854, Nematus suavis Ruthe, 1859, Pontopristia brevilabris Malaise, 1921, Pontopristia itelmena Malaise, 1931, Pontopristia kamtchatica Malaise, 1931, Pontopristia lapponica Malaise, 1921, Pontopristia latiserra Malaise, 1921, Pontopristia romani Malaise, 1921, and Pristiphora amentorum var. nigripleuris Enslin, 1916. Many new host plant associations are recorded.
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Affiliation(s)
- Andrew Liston
- Senckenberg Deutsches Entomologisches Institut; Eberswalder Str. 90; 15374 Mncheberg; Germany.
| | - Veli Vikberg
- Liinalammintie 11 as. 6; 14200 Turenki; Finland.
| | - Marko Mutanen
- Ecology and Genetics Research Unit; PO Box 3000; 90014 University of Oulu; Finland.
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region; Norwegian Institute of Bioeconomy Research; Svanvik; Norway.
| | - Marko Prous
- Department of Zoology; Institute of Ecology and Earth Sciences; University of Tartu; Vanemuise 46; 51014 Tartu; Estonia.
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Huemer P, Aarvik L, Berggren K. A new species of Neurothaumasia Le Marchand (Lepidoptera, Tineidae) from Crete, Greece. Zootaxa 2023; 5318:401-410. [PMID: 37518374 DOI: 10.11646/zootaxa.5318.3.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Indexed: 08/01/2023]
Abstract
A new species of fungus moths (Tineidae), Neurothaumasia cretica sp. nov., is described from specimens collected on Crete isl. (Greece). It differs from congeneric taxa by the characteristic black and white forewing pattern which is only shared with N. fasciata Petersen, 1959 from the Middle East, and the widespread western Palaearctic N. ankerella (Mann, 1867). However, the new species differs strongly from the former by several characters of male and female genitalia, and from the latter species particularly from external appearance and by the highly divergent DNA barcode (cytochrome c-oxidase subunit 1) (unknown for N. fasciata). Adult and genitalia of N. cretica sp. nov. and the only similar European species N. ankerella are shown for comparison. Finally, a complete checklist of the genus is added.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H.; Natural History Collections; Krajnc-Str. 1; A-6060 Hall in Tirol; Austria.
| | - Leif Aarvik
- Natural History Museum; University of Oslo; P.O. Box 1172 Blindern; NO-0318 Oslo; Norway.
| | - Kai Berggren
- Bråvann terrasse 21; NO-4624 Kristiansand; Norway.
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László GM, Hausmann A, Karisch T. Integrative taxonomic revision of the African taxa of the Racotis Moore, 1887 generic complex (Lepidoptera, Geometridae, Ennominae, Boarmiini). Zootaxa 2023; 5308:1-109. [PMID: 37518660 DOI: 10.11646/zootaxa.5308.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Indexed: 08/01/2023]
Abstract
The Afrotropical taxa of the Racotis s.l. generic complex are revised utilising integrative taxonomical methods. Based on the evaluation of genital morphology and analyses of DNA barcodes, a new genus, Afroracotis gen. n. is established to include the Afrotropical "Racotis" species. The new genus is subdivided into 5 subgenera: Afroracotis subgen. n., Herbuloracotis subgen. n., Rwandaracotis subgen. n., Zebracotis subgen. n. and Sokokeracotis subgen. n.. A new monotypic genus is described to include Boarmia ugandaria Swinhoe, 1904 which was combined earlier with the genus Chorodna and recently with Racotis: Chorocotis gen. n.. Two species formerly assigned to Cleora are moved to Afroracotis: A. albitrigonis (Prout, 1927) comb. n., A. atriclava (Prout, 1926) comb. n.. Two species are transferred from Racotis to Colocleora: C. breijeri (Prout, 1922) comb. n., C. incauta (Prout, 1916) comb. n.. Seventeen new Afroracotis species (A. aliena, A. stadiei, A. violetteae, A. fiebigi, A. turlini, A. dargei, A. longicornuta, A. aristophanousi, A. muscivirens, A. chaineyi, A. lydiae, A. smithi, A. ochsei, A. milesi, A. helicalis, A. takanoi and A. staudei spp. n.) and 5 new subspecies (A. squalida thomensis, A. argillacea morettoi, A. longicornuta congolana, A. longicornuta ugandana and A. lydiae orientalis sspp. n.) are described, totalling 27 species and 8 subspecies contained in the genus Afroracotis. Adults and genitalia of all taxa are illustrated in 210 colour and 129 black and white figures demonstrating the intraspecific variability. The distribution of all taxa is illustrated in 6 dot maps. The results of the genetic analyses are figured in four phylograms.
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Affiliation(s)
- Gyula M László
- African Natural History Research Trust (ANHRT); Street Court; Leominster-Kingsland; HR6 9QA; United Kingdom.
| | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München; Münchhausenstr. 21; Munich; Germany.
| | - Timm Karisch
- Museum für Naturkunde und Vorgeschichte Dessau; Askanische Straße 32; D-06842; Dessau; Germany.
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Hebert PDN, Bock DG, Prosser SWJ. Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness. PLoS One 2023; 18:e0286620. [PMID: 37289794 PMCID: PMC10249859 DOI: 10.1371/journal.pone.0286620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.
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Affiliation(s)
- Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dan G. Bock
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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12
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Levesque-Beaudin V, Miller ME, Dikow T, Miller SE, Prosser SW, Zakharov EV, McKeown JT, Sones JE, Redmond NE, Coddington JA, Santos BF, Bird J, deWaard JR. A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections. Biodivers Data J 2023; 11:e100677. [PMID: 38327333 PMCID: PMC10848567 DOI: 10.3897/bdj.11.e100677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/20/2023] [Indexed: 02/09/2024] Open
Abstract
Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society - through, for example, digitisation or the construction of a validated, global DNA barcode library - is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging, tissue sampling, databasing and DNA barcoding. This approach was tested by harvesting and DNA barcoding 941 voucher specimens, representing 32 families, 819 genera and 695 identified species collected from 100 countries. We recovered 867 sequences (> 0 base pairs) with a sequencing success of 88.8% (727 of 819 sequenced genera gained a barcode > 300 base pairs). While Sanger-based methods were more effective for recently-collected specimens, the methods employing next-generation sequencing recovered barcodes for specimens over a century old. The utility of the newly-generated reference barcodes is demonstrated by the subsequent taxonomic assignment of nearly 5000 specimen records in the Barcode of Life Data Systems.
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Affiliation(s)
- Valerie Levesque-Beaudin
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Meredith E. Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Sean W.J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Jaclyn T.A. McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jayme E. Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Niamh E Redmond
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jonathan A. Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Bernardo F. Santos
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jessica Bird
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
- School of Environmental Sciences, University of Guelph, Guelph, CanadaSchool of Environmental Sciences, University of GuelphGuelphCanada
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13
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Karin BR, Arellano S, Wang L, Walzer K, Pomerantz A, Vasquez JM, Chatla K, Sudmant PH, Bach BH, Smith LL, McGuire JA. Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes. BMC Genomics 2023; 24:229. [PMID: 37131128 PMCID: PMC10155392 DOI: 10.1186/s12864-023-09277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/24/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods. RESULTS With the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80-90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes. CONCLUSIONS This method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.
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Affiliation(s)
- Benjamin R Karin
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA.
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.
| | - Selene Arellano
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Laura Wang
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Kayla Walzer
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Aaron Pomerantz
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Juan Manuel Vasquez
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Peter H Sudmant
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Lydia L Smith
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Jimmy A McGuire
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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14
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Jeon MS, Jeong DM, Doh H, Kang HA, Jung H, Eyun SI. A practical comparison of the next-generation sequencing platform and assemblers using yeast genome. Life Sci Alliance 2023; 6:e202201744. [PMID: 36746534 PMCID: PMC9902641 DOI: 10.26508/lsa.202201744] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
Assembling fragmented whole-genomic information from the sequencing data is an inevitable process for further genome-wide research. However, it is intricate to select the appropriate assembly pipeline for unknown species because of the species-specific genomic properties. Therefore, our study focused on relatively more static proclivities of sequencing platforms and assembly algorithms than the fickle genome sequences. A total of 212 draft and polished de novo assemblies were constructed under the different sequencing platforms and assembly algorithms with the repetitive yeast genome. Our comprehensive data indicated that sequencing reads from Oxford Nanopore with R7.3 flow cells generated more continuous assemblies than those derived from the PacBio Sequel, although the homopolymer-based assembly errors and chimeric contigs exist. In addition, the comparison between two second-generation sequencing platforms showed that Illumina NovaSeq 6000 provides more accurate and continuous assembly in the second-generation-sequencing-first pipeline, but MGI DNBSEQ-T7 provides a cheap and accurate read in the polishing process. Furthermore, our insight into the relationship among the computational time, read length, and coverage depth provided clues to the optimal pipelines of yeast assembly.
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Affiliation(s)
- Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Da Min Jeong
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Huijeong Doh
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyungtaek Jung
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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15
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Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R, Lawniczak MKN. Future of DNA-based insect monitoring. Trends Genet 2023:S0168-9525(23)00038-0. [PMID: 36907721 DOI: 10.1016/j.tig.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).
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Affiliation(s)
- Physilia Y S Chua
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Adenauerallee 127, 53113 Bonn, Germany
| | - Cameron Ferguson
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Petra Korlevic
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leia Zhao
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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16
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Phillips JD, Athey TB, McNicholas PD, Hanner RH. VLF: An R package for the analysis of very low frequency variants in DNA sequences. Biodivers Data J 2023; 11:e96480. [PMID: 38327328 PMCID: PMC10848336 DOI: 10.3897/bdj.11.e96480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/30/2022] [Indexed: 01/27/2023] Open
Abstract
Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer Science and Department of Integrative Biology, University of Guelph, Guelph, CanadaSchool of Computer Science and Department of Integrative Biology, University of GuelphGuelphCanada
| | - Taryn B.T. Athey
- Stollery Children's Hospital, Edmonton, CanadaStollery Children's HospitalEdmontonCanada
| | - Paul D. McNicholas
- Department of Mathematics and Statistics, McMaster University, Hamilton, CanadaDepartment of Mathematics and Statistics, McMaster UniversityHamiltonCanada
| | - Robert H. Hanner
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, CanadaBiodiversity Institute of Ontario and Department of Integrative Biology, University of GuelphGuelphCanada
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17
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Taberer TR, Fiebig R, Giusti A, László GM. Taxonomic revision of the genus Delorhachis Karsch 1896 (Lepidoptera: Limacodidae). J NAT HIST 2023. [DOI: 10.1080/00222933.2022.2157346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Tabitha R. Taberer
- The African Natural History Research Trust (ANHRT), Leominster-Kingsland, UK
- Department of Biology, University of Oxford, Oxford, UK
| | | | | | - Gyula M. László
- The African Natural History Research Trust (ANHRT), Leominster-Kingsland, UK
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18
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Li H, Zhang J, Zhao Y, Yang W. Predicting Corynebacterium glutamicum promoters based on novel feature descriptor and feature selection technique. Front Microbiol 2023; 14:1141227. [PMID: 36937275 PMCID: PMC10018189 DOI: 10.3389/fmicb.2023.1141227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
The promoter is an important noncoding DNA regulatory element, which combines with RNA polymerase to activate the expression of downstream genes. In industry, artificial arginine is mainly synthesized by Corynebacterium glutamicum. Replication of specific promoter regions can increase arginine production. Therefore, it is necessary to accurately locate the promoter in C. glutamicum. In the wet experiment, promoter identification depends on sigma factors and DNA splicing technology, this is a laborious job. To quickly and conveniently identify the promoters in C. glutamicum, we have developed a method based on novel feature representation and feature selection to complete this task, describing the DNA sequences through statistical parameters of multiple physicochemical properties, filtering redundant features by combining analysis of variance and hierarchical clustering, the prediction accuracy of the which is as high as 91.6%, the sensitivity of 91.9% can effectively identify promoters, and the specificity of 91.2% can accurately identify non-promoters. In addition, our model can correctly identify 181 promoters and 174 non-promoters among 400 independent samples, which proves that the developed prediction model has excellent robustness.
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Affiliation(s)
- HongFei Li
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Jingyu Zhang
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuming Zhao
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
- *Correspondence: Yuming Zhao, ; Wen Yang,
| | - Wen Yang
- International Medical Center, Shenzhen University General Hospital, Shenzhen, China
- *Correspondence: Yuming Zhao, ; Wen Yang,
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19
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Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome. Microbiol Spectr 2022; 10:e0251322. [PMID: 36409146 PMCID: PMC9769941 DOI: 10.1128/spectrum.02513-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The evolution of sequencing technology and multiplexing has rapidly expanded our ability to characterize fungal diversity in the environment. However, obtaining an unbiased assessment of the fungal community using ribosomal markers remains challenging. Longer amplicons were shown to improve taxonomic resolution and resolve ambiguities by reducing the risk of spurious operational taxonomic units. We examined the implications of barcoding strategies by amplifying and sequencing two ribosomal DNA fragments. We analyzed the performance of the full internal transcribed spacer (ITS) and a longer fragment including also a part of the 28S ribosomal subunit replicated on 60 grapevine trunk core samples. Grapevine trunks harbor highly diverse fungal communities with implications for disease development. Using identical handling, amplification, and sequencing procedures, we obtained higher sequencing depths for the shorter ITS amplicon. Despite the more limited access to polymorphism, the overall diversity in amplified sequence variants was higher for the shorter ITS amplicon. We detected no meaningful bias in the phylogenetic composition due to the amplicon choice across analyzed samples. Despite the increased resolution of the longer ITS-28S amplicon, the higher and more consistent yields of the shorter amplicons produced a clearer resolution of the fungal community of grapevine stem samples. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals. IMPORTANCE Surveying fungal communities is key to our understanding of ecological functions of diverse habitats. Fungal communities can inform about the resilience of agricultural ecosystems, risks to human health, and impacts of pathogens. Community compositions are typically analyzed using ribosomal DNA sequences. Due to technical limitations, most fungal community surveys were based on amplifying a short but highly variable fragment. Advances in sequencing technology enabled the use of longer fragments that can address some limitations of species identification. In this study, we examined the implications of choosing either a short or long ribosomal sequence fragment by replicating the analyses on 60 grapevine wood core samples. Using highly accurate long-read sequencing, we found that the shorter fragment produced substantially higher yields. The shorter fragment also revealed more sequence and species diversity. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.
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20
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Tadmor-Levi R, Cummings D, Borovski T, Shapira R, Marcos-Hadad E, David L. A method for quick and efficient identification of cichlid species by high resolution DNA melting analysis of minibarcodes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1010838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Freshwater bodies are key in supporting aquatic and terrestrial life. Ecological balance of freshwater habitats is very vulnerable, hence, often significantly disrupted by climatic changes and anthropogenic acts. In Israel, due to its relatively arid climate, many freshwater resources have been disrupted and still are under great pressure. The Sea of Galilee is the largest surface freshwater body in the Middle East and a habitat to unique populations of several fishes, including six cichlid species. Studies on the ecology of these fish and their conservation require effective monitoring tools. In this study, a simple and efficient molecular method was developed to identify the species of these lake cichlids using high resolution melting analysis of mini DNA barcodes. The species of an individual sample can be identified by a single tube PCR reaction. This assay successfully identified sequence differences both among and within species. Here, this method identified the species for 279 small cichlid fry that could not be morphologically identified, allowing to estimate relative species abundance and map their distribution in time and location. The results are key to understand not only the ecology of young stages but also their recruitment potential to adult fish populations and their sustainability. This method can be readily implemented in further ecological studies and surveys related to these species, in the lake and its surroundings, as a tool to enhance understanding and protection of these species.
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21
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Dong Y, He Y, Zhou X, Lv X, Huang J, Li Y, Qian X, Hu F, Zhu J. Diagnosis of Mycoplasma hominis Meningitis with Metagenomic Next-Generation Sequencing: A Case Report. Infect Drug Resist 2022; 15:4479-4486. [PMID: 35983300 PMCID: PMC9380824 DOI: 10.2147/idr.s371771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Background Mycoplasma hominis meningitis is a rare postoperative complication of neurosurgery. Accurate and early diagnosis of M. hominis remains challenging because of the limitations of traditional detection methods. Metagenomic next-generation sequencing (mNGS) is an advanced technique with high sensitivity and specificity for identifying infectious pathogens; however, its application in diagnosing M. hominis meningitis has not been widely studied. Case Presentation We report the case of a 61-year-old man who presented with fever and headache after neurosurgical treatment for a cerebral hemorrhage. Empiric antibiotic therapy was ineffective. Traditional culture of pathogens and serological testing yielded negative results, but M. hominis was detected in the cerebrospinal fluid by mNGS. After further verification by polymerase chain reaction (PCR), the patient's clinical treatment was adjusted accordingly. With targeted antibiotic intervention, the patient's symptoms were effectively alleviated, and clinical indicators returned to normal levels. Furthermore, the abundance of M. hominis decreased significantly compared to the initial mNGS reading after targeted treatment, indicating that the infection caused by M. hominis was effectively controlled. Conclusion Using mNGS, we found that M. hominis may be a candidate causative agent of meningitis. The technique also has the advantage of timeliness and accuracy that traditional cultures cannot achieve. A combination of mNGS with PCR is recommended to identify pathogens in the early stages of infectious diseases to administer targeted clinical medication.
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Affiliation(s)
- Yukang Dong
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Yingying He
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Xia Zhou
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Xia Lv
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Jia Huang
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Yaqi Li
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Xin Qian
- Department of Pharmacy, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Fangfang Hu
- Department of Clinical Laboratory, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Jiaying Zhu
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
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22
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QI LEI, HUANG JUNHAO, WU HONG, WANG QINGYUN. Two new species of Setostylus Matile, 1990 (Diptera: Keroplatidae) from China. Zootaxa 2022; 5165:443-450. [DOI: 10.11646/zootaxa.5165.3.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Indexed: 11/04/2022]
Abstract
In this study, two new species of Setostylus (Diptera: Keroplatidae: Keroplatinae), S. tridigitus sp. n. and S. triumphus sp. n. are described, with a key to all the species of the genus. Male habitus and images of diagnostic morphological characteristics are provided. Status of these two new species is also supported by the genetic distances and neighbor-joining (NJ) tree in the DNA barcode analysis.
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23
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Liu Y, Zhang Y, Wang J, Lu F. Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq. Nat Protoc 2022; 17:1980-2007. [PMID: 35831615 DOI: 10.1038/s41596-022-00704-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
Poly(A) tails are added to the 3' ends of most mRNAs in a non-templated manner and play essential roles in post-transcriptional regulation, including mRNA export, stability and translation. Measuring poly(A) tails is critical for understanding their regulatory roles in almost every aspect of biological and medical studies. Previous methods for analyzing poly(A) tails require large amounts of input RNA (microgram-level total RNA), which limits their application. We recently developed a poly(A) inclusive full-length RNA isoform-sequencing method (PAIso-seq) at single-oocyte-level sensitivity (a single mammalian oocyte contains ~0.5 ng of total RNA) based on PacBio sequencing that enabled accurate measurement of the poly(A) tail length and non-A residues within the body of poly(A) tails along with the full-length cDNA, providing the opportunity to study precious in vivo samples with very limited input material. Here, we describe a detailed protocol for PAIso-seq library preparation from single mouse oocytes or bulk oocyte samples. In addition, we provide a complete bioinformatic pipeline to perform the analysis from the raw data to downstream analysis. The minimum time required is ~14.5 h for PAIso-seq double-stranded cDNA preparation, 2 d for PacBio sequencing in HiFi mode and 8 h for the initial data analysis.
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Affiliation(s)
- Yusheng Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
| | - Yiwei Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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Goussarov G, Mysara M, Vandamme P, Van Houdt R. Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. Microbiologyopen 2022; 11:e1298. [PMID: 35765182 PMCID: PMC9179125 DOI: 10.1002/mbo3.1298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome‐assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation.
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Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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25
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Hartop E, Srivathsan A, Ronquist F, Meier R. Towards Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa. Syst Biol 2022; 71:1404-1422. [PMID: 35556139 PMCID: PMC9558837 DOI: 10.1093/sysbio/syac033] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa,” here defined as groups for which \documentclass[12pt]{minimal}
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}{}$\%$\end{document} of all species are described and the estimated diversity exceeds 1,000 species. Species delimitation for these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting multiple types of data risks impeding a discovery process that is already too slow. We here develop large-scale integrative taxonomy (LIT), an explicit method where preliminary species hypotheses are generated based on inexpensive data that can be obtained quickly and cost-effectively. These hypotheses are then evaluated based on a more expensive type of “validation data” that is only obtained for specimens selected based on objective criteria applied to the preliminary species hypotheses. We here use this approach to sort 18,000 scuttle flies (Diptera: Phoridae) into 315 preliminary species hypotheses based on next-generation sequencing barcode (313 bp) clusters (using objective clustering [OC] with a 3\documentclass[12pt]{minimal}
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}{}$\%$\end{document} threshold). These clusters are then evaluated with morphology as the validation data. We develop quantitative indicators for predicting which barcode clusters are likely to be incongruent with morphospecies by randomly selecting 100 clusters for in-depth validation with morphology. A linear model demonstrates that the best predictors for incongruence between barcode clusters and morphology are maximum p-distance within the cluster and a newly proposed index that measures cluster stability across different clustering thresholds. A test of these indicators using the 215 remaining clusters reveals that these predictors correctly identify all clusters that are incongruent with morphology. In our study, all morphospecies are true or disjoint subsets of the initial barcode clusters so that all incongruence can be eliminated by varying clustering thresholds. This leads to a discussion of when a third data source is needed to resolve incongruent grouping statements. The morphological validation step in our study involved 1,039 specimens (5.8\documentclass[12pt]{minimal}
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}{}$\%$\end{document} of the total). The formal LIT protocol we propose would only have required the study of 915 (5.1\documentclass[12pt]{minimal}
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}{}$\%$\end{document}: 2.5 specimens per species), as we show that clusters without signatures of incongruence can be validated by only studying two specimens representing the most divergent haplotypes. To test the generality of our results across different barcode clustering techniques, we establish that the levels of incongruence are similar across OC, Automatic Barcode Gap Discovery (ABGD), Poisson Tree Processes (PTP), and Refined Single Linkage (RESL) (used by Barcode of Life Data System to assign Barcode Index Numbers [BINs]). OC and ABGD achieved a maximum congruence score with the morphology of 89\documentclass[12pt]{minimal}
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}{}$\%$\end{document} while PTP was slightly less effective (84\documentclass[12pt]{minimal}
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}{}$\%$\end{document}). RESL could only be tested for a subset of the specimens because the algorithm is not public. BINs based on 277 of the original 1,714 haplotypes were 86\documentclass[12pt]{minimal}
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}{}$\%$\end{document} congruent with morphology while the values were 89\documentclass[12pt]{minimal}
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}{}$\%$\end{document} for OC, 74\documentclass[12pt]{minimal}
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}{}$\%$\end{document} for PTP, and 72\documentclass[12pt]{minimal}
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}{}$\%$\end{document} for ABGD. [Biodiversity discovery; dark taxa; DNA barcodes; integrative taxonomy.]
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Affiliation(s)
- Emily Hartop
- Zoology Department, Stockholm University, Stockholm, Sweden.,Station Linné, Öland, Sweden.,Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde, Berlin
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore.,Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde, Berlin
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore.,Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde, Berlin
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26
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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27
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Steinke D, deWaard SL, Sones JE, Ivanova NV, Prosser SWJ, Perez K, Braukmann TWA, Milton M, Zakharov EV, deWaard JR, Ratnasingham S, Hebert PDN. Message in a Bottle-Metabarcoding enables biodiversity comparisons across ecoregions. Gigascience 2022; 11:6575387. [PMID: 35482490 PMCID: PMC9049109 DOI: 10.1093/gigascience/giac040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/24/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022] Open
Abstract
Background Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study used DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning 3 Canadian ecoregions. Results This study revealed the presence of 26,263 arthropod species in the 3 ecoregions and indicated that at least another 3,000–5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall α-diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site, with turnover greater than nestedness, suggesting the presence of many transient species. Conclusions Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities.
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Affiliation(s)
- D Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S L deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - J E Sones
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - N V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - K Perez
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - T W A Braukmann
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - M Milton
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - E V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - J R deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S Ratnasingham
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - P D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
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28
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Ashfaq M, Khan AM, Rasool A, Akhtar S, Nazir N, Ahmed N, Manzoor F, Sones J, Perez K, Sarwar G, Khan AA, Akhter M, Saeed S, Sultana R, Tahir HM, Rafi MA, Iftikhar R, Naseem MT, Masood M, Tufail M, Kumar S, Afzal S, McKeown J, Samejo AA, Khaliq I, D’Souza ML, Mansoor S, Hebert PDN. A DNA barcode survey of insect biodiversity in Pakistan. PeerJ 2022; 10:e13267. [PMID: 35497186 PMCID: PMC9048642 DOI: 10.7717/peerj.13267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 01/15/2023] Open
Abstract
Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010-2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- Centre for Animal Sciences and Fisheries, University of Swat, Mingora, Pakistan
| | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Naila Nazir
- Department of Entomology, University of Poonch, Rawalakot, Azad Kashmir, Pakistan
| | - Nazeer Ahmed
- Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Farkhanda Manzoor
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Ghulam Sarwar
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Azhar A. Khan
- College of Agriculture, Bahauddin Zakariya University Bahadur Campus, Layyah, Pakistan
| | - Muhammad Akhter
- Pulses Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shafqat Saeed
- Faculty of Agriculture and Environmental Sciences, MNS University of Agriculture, Multan, Pakistan
| | - Riffat Sultana
- Department of Zoology, University of Sindh, Jamshoro, Pakistan
| | | | - Muhammad A. Rafi
- National Insect Museum, National Agricultural Research Center, Islamabad, Pakistan
| | - Romana Iftikhar
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | - Mariyam Masood
- Government College Women University Faisalabad, Faisalabad, Pakistan
| | | | - Santosh Kumar
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Sabila Afzal
- Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | | | | | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
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29
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Wang H, Gan C, Luo X, Dong C, Zhou S, Xiong Q, Weng Q, Hu X, Du X, Zhu B. Complete chloroplast genome features of the model heavy metal hyperaccumulator Arabis paniculata Franch and its phylogenetic relationships with other Brassicaceae species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:775-789. [PMID: 35592481 PMCID: PMC9110617 DOI: 10.1007/s12298-022-01151-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/28/2021] [Accepted: 02/17/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Arabis paniculata Franch (Brassicaceae) has been widely used for the phytoremediation of heavy mental, owing to its hyper tolerance of extreme Pb, Zn, and Cd concentrations. However, studies on its genome or plastid genome are scarce. In the present study, we obtained the complete chloroplast (cp) genome of A. paniculata via de novo assembly through the integration of Illumina reads and PacBio subreads. The cp genome presents a typical quadripartite cycle with a length of 153,541 bp, and contains 111 unigenes, with 79 protein-coding genes, 28 tRNAs and 4 rRNAs. Codon usage analysis showed that the codons for leucine were the most frequent codons and preferentially ended with A/U. Synonymous (Ks) and non-synonymous (Ka) substitution rate analysis indicated that the unigenes, ndhF and rpoC2, related to "NADH-dehydrogenase" and "RNA polymerase" respectively, underwent the lowest purifying selection pressure. Phylogenetic analysis demonstrated that Arabis flagellosa and A. hirsuta are more similar to each other than to A. paniculata, and Arabis is the closest relative of Draba among all Brassicaceae genera. These findings provide valuable information for the optimal exploitation of this model species as a heavy-metal hyperaccumulator. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01151-1.
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Affiliation(s)
- Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Chenchen Gan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Xi Luo
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Changyu Dong
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Shijun Zhou
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Qin Xiong
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin’an Hangzhou, People’s Republic of China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
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30
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Nitta JH, Chambers SM. Identifying cryptic fern gametophytes using DNA barcoding: A review. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11465. [PMID: 35495195 PMCID: PMC9039790 DOI: 10.1002/aps3.11465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 05/14/2023]
Abstract
Ferns and lycophytes are unique among land plants in having sporophyte (diploid) and gametophyte (haploid) generations that can grow independently of each other. While most studies of fern ecology focus on the more visible sporophytic stage, the gametophyte is critically important, as it is the sexual phase of the life cycle. Yet, fern gametophytes have long been neglected in field studies due to their small size and cryptic morphology. DNA barcoding is a powerful method that can be used to identify field-collected gametophytes to species and allow for detailed study of their ecology. Here, we review the state of DNA barcoding as applied to fern gametophytes. First, we trace the history of DNA barcoding and how it has come to be applied to fern gametophytes. Next, we summarize case studies that show how DNA barcoding has been used to better understand fern species distributions, gametophyte ecology, and community ecology. Finally, we propose avenues for future research using this powerful tool, including next-generation DNA sequencing for in-field identification of cryptic gametophytes.
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Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of ScienceThe University of Tokyo2‐11‐16 Yayoi, Bunkyo‐kuTokyo113‐0032Japan
| | - Sally M. Chambers
- Marie Selby Botanical GardensBotany DepartmentSarasotaFlorida34236USA
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31
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Wei W, Hu X, Yang S, Wang K, Zeng C, Hou Z, Cui H, Liu S, Zhu L. Denitrifying halophilic archaea derived from salt dominate the degradation of nitrite in salted radish during pickling. Food Res Int 2022; 152:110906. [DOI: 10.1016/j.foodres.2021.110906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/27/2021] [Accepted: 12/13/2021] [Indexed: 11/04/2022]
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32
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Young MR, Hebert PDN. Unearthing soil arthropod diversity through DNA metabarcoding. PeerJ 2022; 10:e12845. [PMID: 35178296 PMCID: PMC8815377 DOI: 10.7717/peerj.12845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.
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Affiliation(s)
- Monica R. Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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33
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Chimeno C, Hausmann A, Schmidt S, Raupach MJ, Doczkal D, Baranov V, Hübner J, Höcherl A, Albrecht R, Jaschhof M, Haszprunar G, Hebert PDN. Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany. INSECTS 2022; 13:insects13010082. [PMID: 35055925 PMCID: PMC8779287 DOI: 10.3390/insects13010082] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/16/2021] [Accepted: 01/05/2022] [Indexed: 02/01/2023]
Abstract
Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these “dark taxa” families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four “dark taxa” families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800–2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling.
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Affiliation(s)
- Caroline Chimeno
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
- Correspondence:
| | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Michael J. Raupach
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Dieter Doczkal
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Viktor Baranov
- Department Biology II, Ludwig-Maximilians-University of Munich (LMU), Großhaderner Str. 2, Martinsried, 82152 Planegg, Germany;
| | - Jeremy Hübner
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Amelie Höcherl
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Rosa Albrecht
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | | | - Gerhard Haszprunar
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
- Department Biology II, Ludwig-Maximilians-University of Munich (LMU), Großhaderner Str. 2, Martinsried, 82152 Planegg, Germany;
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada;
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Nazar N, Howard C, Slater A, Sgamma T. Challenges in Medicinal and Aromatic Plants DNA Barcoding-Lessons from the Lamiaceae. PLANTS (BASEL, SWITZERLAND) 2022; 11:137. [PMID: 35009140 PMCID: PMC8747715 DOI: 10.3390/plants11010137] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
The potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and regulatory authorities. The successes and limitations of conventional DNA barcoding are considered in relation to important members of the Lamiaceae. The mint family (Lamiaceae) contains over one thousand species recorded as having a medicinal use, with many more exploited in food and cosmetics for their aromatic properties. The family is characterized by a diversity of secondary products, most notably the essential oils (EOs) produced in external glandular structures on the aerial parts of the plant that typify well-known plants of the basil (Ocimum), lavender (Lavandula), mint (Mentha), thyme (Thymus), sage (Salvia) and related genera. This complex, species-rich family includes widely cultivated commercial hybrids and endangered wild-harvested traditional medicines, and examples of potential toxic adulterants within the family are explored in detail. The opportunities provided by next generation sequencing technologies to whole plastome barcoding and nuclear genome sequencing are also discussed with relevant examples.
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Affiliation(s)
- Nazia Nazar
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
| | - Caroline Howard
- Tree of Life Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK;
| | - Adrian Slater
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
| | - Tiziana Sgamma
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
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Cowart DA, Murphy KR, Cheng CHC. Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction. Methods Mol Biol 2022; 2498:225-251. [PMID: 35727547 DOI: 10.1007/978-1-0716-2313-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has emerged in recent years as a powerful tool for the detection, monitoring, and characterization of aquatic metazoan communities, including vulnerable species. The rapid rate of adopting the eDNA approach across diverse habitats and taxonomic groups attests to its value for a wide array of investigative goals, from understanding natural or changing biodiversity to informing on conservation efforts at local and global scales. Regardless of research objectives, eDNA workflows commonly include the following essential steps: environmental sample acquisition, processing and preservation of samples, and eDNA extraction, followed by eDNA sequencing library preparation, high-capacity sequencing and sequence data analysis, or other methods of genetic detection. In this chapter, we supply instructional details for the early steps in the workflow to facilitate researchers considering adopting eDNA analysis to address questions in marine environments. Specifically, we detail sampling, preservation, extraction, and quantification protocols for eDNA originating from marine water, shallow substrates, and deeper sediments. eDNA is prone to degradation and loss, and to contamination through improper handling; these factors crucially influence the outcome and validity of an eDNA study. Thus, we also provide guidance on avoiding these pitfalls. Following extraction, purified eDNA is often sequenced on massively parallel sequencing platforms for comprehensive faunal diversity assessment using a metabarcoding or metagenomic approach, or for the detection and quantification of specific taxa by qPCR methods. These components of the workflow are project-specific and thus not included in this chapter. Instead, we briefly touch on the preparation of eDNA libraries and discuss comparisons between sequencing approaches to aid considerations in project design.
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Affiliation(s)
- Dominique A Cowart
- Company for Open Ocean Observations and Logging (COOOL), Saint Leu, La Réunion, France
| | - Katherine R Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C-H Christina Cheng
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana - Champaign, Urbana, IL, USA.
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DNA barcoding of insects from India: Current status and future perspectives. Mol Biol Rep 2022; 49:10617-10626. [PMID: 35716293 PMCID: PMC9206398 DOI: 10.1007/s11033-022-07628-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/01/2022]
Abstract
Insect fauna occupy the largest proportion of animal biodiversity on earth, but the assessment or quantification in terms of species diversity is far from complete. Several recent studies have demonstrated the rapid pace at which insect population decline is occurring. There is an urgent need to document and quantify the diversity of insect fauna for a proper understanding of terrestrial ecosystems. This can be achieved by using modern technology to identify species much faster than relying on traditional methods alone. In line with this, the molecular approach through DNA barcoding coupled with morphological identification needs to be focused and accelerated. The present paper describes the current status of barcoding of insect species in India along with the gaps that need to be remedied. This analysis shows that barcoded specimens cover a very meagre proportion of less than 3.73% of the known taxa/described species and the most represented orders are Lepidoptera and Hemiptera followed by Diptera and Coleoptera. There is a need to expedite insect species discovery and documentation in a collaborative mode between traditional taxonomists and molecular biologists, to accomplish the DNA barcoding of all known insect taxa from India.
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Wührl L, Pylatiuk C, Giersch M, Lapp F, von Rintelen T, Balke M, Schmidt S, Cerretti P, Meier R. DiversityScanner: Robotic handling of small invertebrates with machine learning methods. Mol Ecol Resour 2021; 22:1626-1638. [PMID: 34863029 DOI: 10.1111/1755-0998.13567] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/20/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023]
Abstract
Invertebrate biodiversity remains poorly understood although it comprises much of the terrestrial animal biomass, most species and supplies many ecosystem services. The main obstacle is specimen-rich samples obtained with quantitative sampling techniques (e.g., Malaise trapping). Traditional sorting requires manual handling, while molecular techniques based on metabarcoding lose the association between individual specimens and sequences and thus struggle with obtaining precise abundance information. Here we present a sorting robot that prepares specimens from bulk samples for barcoding. It detects, images and measures individual specimens from a sample and then moves them into the wells of a 96-well microplate. We show that the images can be used to train convolutional neural networks (CNNs) that are capable of assigning the specimens to 14 insect taxa (usually families) that are particularly common in Malaise trap samples. The average assignment precision for all taxa is 91.4% (75%-100%). This ability of the robot to identify common taxa then allows for taxon-specific subsampling, because the robot can be instructed to only pick a prespecified number of specimens for abundant taxa. To obtain biomass information, the images are also used to measure specimen length and estimate body volume. We outline how the DiversityScanner can be a key component for tackling and monitoring invertebrate diversity by combining molecular and morphological tools: the images generated by the robot become training images for machine learning once they are labelled with taxonomic information from DNA barcodes. We suggest that a combination of automation, machine learning and DNA barcoding has the potential to tackle invertebrate diversity at an unprecedented scale.
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Affiliation(s)
- Lorenz Wührl
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Matthias Giersch
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Florian Lapp
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Michael Balke
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | - Stefan Schmidt
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | - Pierfilippo Cerretti
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
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Mei S, Zhao M, Liu Y, Zhao C, Xu H, Fang Y, Zhu B. Evaluations and comparisons of microbial diversities in four types of body fluids based on two 16S rRNA gene sequencing methods. Forensic Sci Int 2021; 331:111128. [PMID: 34959019 DOI: 10.1016/j.forsciint.2021.111128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Body fluids are one of the common biological traces at crime scenes. Understanding the types of these biological traces could provide key clues for the investigations of the forensic cases. In recent years, partial hypervariable regions of 16S rRNA gene sequencing and full-length 16S rRNA gene sequencing have attracted the interests of researchers and we intend to explore which method can be better applied to forensic researches. METHODS In this study, the 16S rRNA gene V3-V4 (short-read) sequencing based on next-generation sequencing and the full-length 16S rRNA gene sequencing based on single molecule real-time sequencing were used to classify microbes in saliva, peripheral blood, vaginal secretion and menstrual blood samples. RESULTS Alpha diversity metrics in short-read sequencing were larger than those of full-length sequencing. Phylum-level bacteria in four kinds of body fluids obtained from the two platforms were similar, while their abundances were different. The results of principal coordinates analysis and analysis of molecular variance indicated the microbial compositions of vaginal secretion and menstrual blood samples were similar, and the microbial compositions among saliva, peripheral blood, vaginal secretion or menstrual blood samples were significantly different. The linear discriminant analysis effect size showed the differential bacteria screened among the four kinds of body fluids were variant in two sequencing results. CONCLUSION Both sequencing methods could be used to detect bacterial diversities in four different types of body fluids and provide potential tools for microbes to identify the four kinds of body fluids in forensic investigation, in which full-length sequencing could provide more accurate taxonomy.
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Affiliation(s)
- Shuyan Mei
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Ming Zhao
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Yanfang Liu
- School of Nursing, Guangdong Medical University, Dongguan 523808, P. R. China
| | - Congying Zhao
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Hui Xu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Yating Fang
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China
| | - Bofeng Zhu
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, P. R. China.
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Briscoe AG, Nichols S, Hartikainen H, Knipe H, Foster R, Green AJ, Okamura B, Bass D. High-Throughput Sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds. Mol Ecol Resour 2021; 22:1303-1318. [PMID: 34758191 DOI: 10.1111/1755-0998.13548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.
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Affiliation(s)
- Andrew G Briscoe
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Core Research Laboratories, Natural History Museum, London, United Kingdom
| | - Sarah Nichols
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Hanna Hartikainen
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Eawag and Institute for Integrative Biology, Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland
| | - Hazel Knipe
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Rachel Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana, EBD-CSIC, 41092, Sevilla, Spain
| | - Beth Okamura
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Centre for Environment, Aquaculture and Fisheries Science (Cefas), Weymouth, UK
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40
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Srivathsan A, Lee L, Katoh K, Hartop E, Kutty SN, Wong J, Yeo D, Meier R. ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 2021; 19:217. [PMID: 34587965 PMCID: PMC8479912 DOI: 10.1186/s12915-021-01141-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer. RESULTS We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. CONCLUSIONS We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
| | - Emily Hartop
- Zoology Department, Stockholms Universitet, Stockholm, Sweden
- Station Linné, Öland, Sweden
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Johnathan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany.
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Paloi S, Mhuantong W, Luangsa-ard JJ, Kobmoo N. Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species. J Fungi (Basel) 2021; 7:767. [PMID: 34575804 PMCID: PMC8467230 DOI: 10.3390/jof7090767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1-D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species based on molecular phylogenies was also assessed. PacBio sequences within strains showed variable level of intragenomic variation among the studied Cordyceps species with C. blackwelliae showing greater variation than the others. Some variants from a mix of species clustered together outside their respective species of origin, indicative of intragenomic variation that escaped concerted evolution shared between species. Proper selection of consensus sequences from HT amplicon sequencing is a challenge for interpretation of correct species identification. PacBio consensus sequences with the highest number of reads represent the major variants within a genome and gave the best results in terms of species identification.
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Affiliation(s)
| | | | | | - Noppol Kobmoo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Development Agency (NSTDA), 113 Thailand Science Park, Phahonuyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (W.M.); (J.J.L.)
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Meier R, Blaimer BB, Buenaventura E, Hartop E, von Rintelen T, Srivathsan A, Yeo D. A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science. Cladistics 2021; 38:264-275. [PMID: 34487362 DOI: 10.1111/cla.12489] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.'s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.'s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.'s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.
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Affiliation(s)
- Rudolf Meier
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.,Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Bonnie B Blaimer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Eliana Buenaventura
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Emily Hartop
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
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Lin X, Jiang K, Liu W, Liu W, Bu W, Wang X, Mo L. Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956. Ecol Evol 2021; 11:12161-12172. [PMID: 34522368 PMCID: PMC8427567 DOI: 10.1002/ece3.7979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.
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Affiliation(s)
- Xiao‐Long Lin
- College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal DiversityTianjin Normal UniversityTianjinChina
| | - Wei Liu
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Jun Bu
- College of Life SciencesNankai UniversityTianjinChina
| | - Xin‐Hua Wang
- College of Life SciencesNankai UniversityTianjinChina
| | - Lidong Mo
- Crowther LabInstitute of Integrative BiologyETH Zurich (Swiss Federal Institute of Technology)ZurichSwitzerland
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44
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Tedersoo L, Albertsen M, Anslan S, Callahan B. Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology. Appl Environ Microbiol 2021; 87:e0062621. [PMID: 34132589 PMCID: PMC8357291 DOI: 10.1128/aem.00626-21] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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Manzanilla V, Teixidor-Toneu I, Martin GJ, Hollingsworth PM, de Boer HJ, Kool A. Using target capture to address conservation challenges: Population-level tracking of a globally-traded herbal medicine. Mol Ecol Resour 2021; 22:212-224. [PMID: 34270854 DOI: 10.1111/1755-0998.13472] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 05/27/2021] [Accepted: 07/06/2021] [Indexed: 12/01/2022]
Abstract
The promotion of responsible and sustainable trade in biological resources is widely proposed as one solution to mitigate current high levels of global biodiversity loss. Various molecular identification methods have been proposed as appropriate tools for monitoring global supply chains of commercialized animals and plants. Here, we demonstrate the efficacy of target capture genomic barcoding in identifying and establishing the geographic origin of samples traded as Anacyclus pyrethrum, a medicinal plant assessed as globally vulnerable in the IUCN Red List of Threatened Species. Samples collected from national and international supply chains were identified through target capture sequencing of 443 low-copy nuclear makers and compared to results derived from genome skimming of plastome and DNA barcoding of standard plastid regions and ITS. Both target capture and genome skimming provided approximately 3.4 million reads per sample, but target capture largely outperformed standard plant barcodes and entire plastid genome sequences. We were able to discern the geographical origin of Anacyclus samples collected in Moroccan, Indian and Sri Lankan markets, differentiating between plant materials originally harvested from diverse populations in Algeria and Morocco. Dropping costs of analysing samples enables the potential of target capture to routinely identify commercialized plant species and determine their geographic origin. It promises to play an important role in monitoring and regulation of plant species in trade, supporting biodiversity conservation efforts, and in ensuring that plant products are unadulterated, contributing to consumer protection.
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Affiliation(s)
| | | | | | | | - Hugo J de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Anneleen Kool
- Natural History Museum, University of Oslo, Oslo, Norway
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46
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Abstract
Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.
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Abstract
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
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48
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Honeycutt RL. Editorial: DNA Barcodes: Controversies, Mechanisms, and Future Applications. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.718865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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49
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van der Loos LM, Nijland R. Biases in bulk: DNA metabarcoding of marine communities and the methodology involved. Mol Ecol 2021; 30:3270-3288. [PMID: 32779312 PMCID: PMC8359149 DOI: 10.1111/mec.15592] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/28/2020] [Indexed: 12/22/2022]
Abstract
With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly being implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, preprocessing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of three PCR replicates, and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, if appropriate controls are included along the data generation process, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments.
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Affiliation(s)
- Luna M. van der Loos
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
- Present address:
Department of BiologyPhycology Research GroupGhent UniversityGhentBelgium
| | - Reindert Nijland
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
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50
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Javal M, Terblanche JS, Conlong DE, Delahaye N, Grobbelaar E, Benoit L, Lopez-Vaamonde C, Haran JM. DNA barcoding for bio-surveillance of emerging pests and species identification in Afrotropical Prioninae (Coleoptera, Cerambycidae). Biodivers Data J 2021; 9:e64499. [PMID: 33967581 PMCID: PMC8099841 DOI: 10.3897/bdj.9.e64499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/11/2021] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding has been succesfully used for bio-surveillance of forest and agricultural pests in temperate areas, but has few applications in the tropics and particulary in Africa. Cacoscelesnewmannii (Coleoptera: Cerambycidae) is a Prioninae species that is locally causing extensive damage in commercially-grown sugarcane in the KwaZulu-Natal Province in South Africa. Due to the risk of spread of this species to the rest of southern Africa and to other sugarcane growing regions, clear and easy identification of this pest is critical for monitoring and for phytosanitary services. The genus Cacosceles Newman, 1838 includes four species, most being very similar in morphology. The damaging stage of the species is the larva, which is inherently difficult to distinguish morphologically from other Cerambycidae species. A tool for rapid and reliable identification of this species was needed by plant protection and quarantine agencies to monitor its potential abundance and spread. Here, we provide newly-generated barcodes for C.newmannii that can be used to reliably identify any life stage, even by non-trained taxonomists. In addition, we compiled a curated DNA barcoding reference library for 70 specimens of 20 named species of Afrotropical Prioninae to evaluate DNA barcoding as a valid tool to identify them. We also assessed the level of deeply conspecific mitochondrial lineages. Sequences were assigned to 42 different Barcode Index Numbers (BINs), 28 of which were new to BOLD. Out of the 20 named species barcoded, 11 (52.4%) had their own unique Barcode Index Number (BIN). Eight species (38.1%) showed multiple BINs with no morphological differentiation. Amongst them, C.newmannii showed two highly divergent genetic clusters which co-occur sympatrically, but further investigation is required to test whether they could represent new cryptic species.
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Affiliation(s)
- Marion Javal
- Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University Stellenbosch South Africa
| | - John S Terblanche
- Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University Stellenbosch South Africa
| | - Desmond E Conlong
- South African Sugarcane Research Institute, Mount Edgecombe, South Africa South African Sugarcane Research Institute Mount Edgecombe South Africa.,Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University Stellenbosch South Africa
| | | | - Elizabeth Grobbelaar
- Biosystematics Division, ARC-Plant Protection Research Institute, Private Bag X134, Queenswood, Pretoria, South Africa Biosystematics Division, ARC-Plant Protection Research Institute, Private Bag X134, Queenswood Pretoria South Africa
| | - Laure Benoit
- CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier Montpellier France
| | - Carlos Lopez-Vaamonde
- INRAE, URZF, Orleans, France INRAE, URZF Orleans France.,IRBI, UMR 7261, CNRS-Université de Tours, Tours, France IRBI, UMR 7261, CNRS-Université de Tours Tours France
| | - Julien M Haran
- CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier Montpellier France
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