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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [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] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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Hundsdoerfer AK, Schell T, Patzold F, Wright CJ, Yoshido A, Marec F, Daneck H, Winkler S, Greve C, Podsiadlowski L, Hiller M, Pippel M. High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae). BMC Genomics 2023; 24:443. [PMID: 37550607 PMCID: PMC10405479 DOI: 10.1186/s12864-023-09506-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/05/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics. RESULTS The genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function. CONCLUSIONS Our two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).
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Affiliation(s)
- Anna K Hundsdoerfer
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany.
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Franziska Patzold
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany
| | | | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Hana Daneck
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Carola Greve
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
| | - Michael Hiller
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, 751 23, Sweden
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Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J. The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. Zookeys 2023; 1146:1-42. [DOI: 10.3897/zookeys.1146.96099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/03/2023] [Indexed: 02/10/2023] Open
Abstract
In this study the aim was to resolve the taxonomy of several species of Argyria Hübner (Pyraloidea, Crambinae) with previously unrecognised morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, the aim was to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridisation capture protocol, the DNA barcode of the lectotype of Argyria lacteella (Fabricius, 1794) was partially recovered for comparison with the 229 DNA barcode sequences of Argyria specimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: the Argyria abronalis (Walker, 1859) holotype, thus confirming the synonymy of this name with A. lacteella, the holotype of A. lusella (Zeller, 1863), syn. rev., the holotype of A. multifacta Dyar, 1914, syn. nov. newly synonymised with A. lacteella, and a specimen of Argyria diplomochalis Dyar, 1913, collected in 1992. In addition, nine specimens of A. lacteella, A. diplomochalis, A. centrifugens Dyar, 1914 and A. gonogramma Dyar, 1915, from North to South America were sampled using classical COI amplification and Sanger sequencing. Argyria gonogramma Dyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified as A. lacteella. Following morphological study of its holotype, Argyria vestalis Butler, 1878, syn. nov. is also synonymised with A. lacteella. The name A. pusillalis Hübner, 1818, is considered a nomen dubium associated with A. gonogramma. The adult morphology is diagnosed and illustrated, and distributions are plotted for A. lacteella, A. diplomochalis, A. centrifugens, and A. gonogramma based on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the Antillean A. diplomochalis. This work provides a modified, improved protocol for the efficient hybrid capture enrichment of DNA barcodes from 18th and 19th century type specimens in order to solve taxonomic issues in Lepidoptera.
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Dong L, Zhang Z, Zhu B, Li S, He Y, Lou Y, Li P, Zheng H, Tian Z, Ma X. Research on safety and compliance of imported microbial inoculants using high-throughput sequencing. Front Med (Lausanne) 2022; 9:963988. [PMID: 36213630 PMCID: PMC9532531 DOI: 10.3389/fmed.2022.963988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/22/2022] [Indexed: 01/09/2023] Open
Abstract
Microbial inoculants are widely used in wastewater treatment, soil remediation, and biological control. Safety and compliance for active constituents are considered to be the most important measures of imported microbial inoculants. Microbial inoculants composition was commonly identified by phenotypic culture, which is time-consuming and labor intense with occasionally false negative results provided, and can only be tested for specific species. High-throughput sequencing (HTS), known for its non-targeted detection of unknown species composition in samples, is suitable for composition consistency identification and biosafety analysis of imported microbial inoculants. In this study, the application of HTS for microflora distribution and resistance gene was verified in microbial inoculants for environmental protection and then applicated in imported microbial inoculants. Both Illumina- and Nanopore-based HTS methods identified the same dominant bacterial species successfully in the imported microbial inoculants. The main component of bacterial species was Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis, and Enterococcus faecium, and further confirmed with traditional methods. The antibiotic resistance genes Bacillus subtilis mprF, bcrA, blt, lmrB, rphB, tet(L), tmrB, vmlR, ykkC, and ykkD were detected in all samples. Our results indicated that HTS processes the application potential to identify the active ingredients of microbial inoculants. Therefore, rapid and accurate identification of the microbial compositions in microbial formulation products is of high importance for port biosafety supervision.
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Affiliation(s)
- Lin Dong
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Zilong Zhang
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Biyun Zhu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Yan He
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Yating Lou
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Ping Li
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai, China
- *Correspondence: Zhengan Tian,
| | - Xia Ma
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
- Xia Ma,
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Novel Gene Rearrangements in the Mitochondrial Genomes of Cynipoid Wasps (Hymenoptera: Cynipoidea). Genes (Basel) 2022; 13:genes13050914. [PMID: 35627299 PMCID: PMC9140913 DOI: 10.3390/genes13050914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Cynipoidea is a medium-sized superfamily of Hymenoptera with diverse lifestyles. In this study, 16 mitochondrial genomes were newly sequenced, 11 of which were the first obtained mitochondrial genomes in the family Liopteridae and four subfamilies (Anacharitinae, Aspicerinae, Figitinae, and Parnipinae) of Figitidae. All of the newly sequenced mitogenomes have unique rearrangement types within Cynipoidea, whereas some gene patterns are conserved in several groups. nad5-nad4-nad4L-nad6-cytb was remotely inverted and two rRNA genes were translocated to nad3 downstream in Ibaliidae and three subfamilies (Anacharitinae, Eucoilinae, and Parnipinae within Figitidae); two rRNA genes in Aspicerinae, Figitinae, and Liopteridae were remotely inverted to the cytb-nad1 junction; rrnL-rrnS was translocated to the cytb-nad1 junction in Cynipidae. Phylogenetic inference suggested that Figitidae was a polyphyletic group, while the Ibaliidae nested deep within Cynipoidea and was a sister-group to the Figitidae. These results will improve our understanding of the gene rearrangement of the mitogenomes and the phylogenetic relationships in the Cynipoidea.
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Scarsbrook L, Verry AJF, Walton K, Hitchmough RA, Rawlence NJ. Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus
Hoplodactylus. Mol Ecol 2022; 32:2964-2984. [DOI: 10.1111/mec.16434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Lachie Scarsbrook
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Alexander J. F. Verry
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Kerry Walton
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | | | - Nicolas J. Rawlence
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
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Improving Taxonomic Practices and Enhancing Its Extensibility—An Example from Araneology. DIVERSITY 2021. [DOI: 10.3390/d14010005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely available, whether an explicit species hypothesis was stated, what types of media were used, the sample sizes, and the degree to which species constructs were integrative. The findings we report reveal that taxonomy remains largely descriptive, not integrative, and provides no explicit conceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-third of all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies made data freely available, and only ~14% of all newly described species employed more than one line of evidence, with molecular data used in ~6% of the studies. These same trends have been discovered in other animal groups, and therefore we find it logical that taxonomists face an uphill challenge when justifying the scientific rigor of their field and securing the needed resources. To move taxonomy forward, we make recommendations that, if implemented, will enhance its rigor, repeatability, and scientific standards.
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