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1. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

Author

Magali Schweizer, Frederik Leliaert, Jan Pawlowski, Rodolphe Rougerie, Frédéric Rimet, Torbjørn Ekrem, Alexis Canino, Teofana Chonova, David G. Mann, Agnès Bouchez, Régis Lionel Vivien, Christian Chauvin, Chloé Goulon, Valentin Vasselon, Romain Gastineau, Rosa Trobajo, Christophe Laplace-Treyture, Jonas Zimmermann, Eva Aylagas, Wolf-Henning Kusber, Andrzej Witkowski, Vona Méléder, Frédéric Marchand, Sinziana F. Rivera, Maria Kahlert, Muriel Gugger, Filipe O. Costa, Maria Holzmann, Benoît J.D. Ferrari, Serena Rasconi, Alexander M. Weigand, Regine Jahn, Fedor Čiampor, Florian Leese, Ángel Borja, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdullah University of Science and Technology (KAUST), Basque Research and Technology Alliance (BRTA), King Abdulaziz University, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Slovak Academy of Science [Bratislava] (SAS), Universidade do Minho, Swiss Centre for Applied Ecotoxicology (Ecotox Center), Ecole Polytechnique Fédérale de Lausanne (EPFL), Technical university of Szczecin, Collection des Cyanobactéries, Institut Pasteur [Paris], University of Geneva [Switzerland], Freie Universität Berlin, Swedish University of Agricultural Sciences (SLU), Universitat Duisberg-Essen, Botanic Garden Meise, Institute of Agrifood Research and Technology [Sant Carles de la Ràpita] (IRTA), Institute of Agrifood Research and Technology (IRTA), Royal Botanic Garden Edinburgh, Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique - U3E (Rennes, France) (U3E ), Université de Nantes (UN), Polish Academy of Sciences (PAN), ID-Gene ecodiagnostics [Geneva], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire de Planétologie et Géodynamique [UMR 6112] (LPG), Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), SCIMABIO Interface SAS, Musée National d'Histoire Naturelle de Luxembourg (MNHN), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), This paper was written under COST Action DNAqua-Net. The European COST Action DNAqua-Net (CA 15219 collaborative network which gathers several hundreds of scientists and water managers, with the objective of developing new genetic tools for bioassessment and monitoring of aquatic ecosystems (Leese et al. 2016)., European Project, West Pomeranian University of Technology in Szczecin (ZUT), Universidade do Minho = University of Minho [Braga], Université de Genève = University of Geneva (UNIGE), Institut Pasteur [Paris] (IP), Meise Botanic Garden [Belgium] (Plantentuin), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Royal Botanic Garden [Edinburgh], Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Producció Animal, and Aigües Marines i Continentals

Subjects
0106 biological sciences, 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Ciências Biológicas [Ciências Naturais], computer.software_genre, Barcode, 01 natural sciences, DNA barcoding, law.invention, law, QH540-549.5, aquatic organisms, media_common, Database, Ecology, Quality, Voucher, Identification (information), Aquatic organisms, quality, Biologie, Traceability, media_common.quotation_subject, reference library, Engenharia e Tecnologia::Engenharia do Ambiente, 010603 evolutionary biology, 03 medical and health sciences, Genetics (medical genetics to be 30107 and agricultural genetics to be 40402), Genetics, Quality (business), Relevance (information retrieval), 14. Life underwater, Molecular Biology, Nature and Landscape Conservation, Engenharia do Ambiente [Engenharia e Tecnologia], Metadata, Ciências Naturais::Ciências Biológicas, metadata, barcode, Reference library, DNA, 030104 developmental biology, traceability, Animal Science and Zoology, computer
Abstract

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data, (undefined)

Published
2021

2. An rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria

Author

Simonetta Gribaldo, Virginie Gaget, Nicole Tandeau de Marsac, Collection des Cyanobactéries, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], We wish to thank the CAE (Centre d'Analyses Environnementales) of Veolia Environment, the Institut Pasteur and CNRS URA-2172 for funding this work. We are grateful to the CAE of Veolia Environment for providing a thesis fellowship to V. G., and to K. Delabre and F. Enguehard for constant support during this study. We express our gratitude to T. Rose for his advice on three-dimensional predictions and thank J. P. Rasmussen for helpful comments and his revision of the English during the preparation of this paper., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)

Subjects
DNA, Bacterial, NJ, [SDV]Life Sciences [q-bio], Biology, Cyanobacteria, Microbiology, MESH: Bacterial Typing Techniques, MESH: INDEL Mutation, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, INDEL Mutation, maximum-parsimony, RNA polymerase, Indel, Gene, MESH: Bacterial Proteins, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetics, 0303 health sciences, MESH: Molecular Typing, 030306 microbiology, MP, DNA-Directed RNA Polymerases, General Medicine, MESH: Cyanobacteria, rpoB, 16S ribosomal RNA, ML, neighbour-joining, MESH: DNA, Bacterial, Bacterial Typing Techniques, MESH: DNA-Directed RNA Polymerases, Molecular Typing, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Evolutionary biology, Metagenomics, maximum-likelihood, Subgenus, DNA
Abstract

The use of morphological characters for the classification of cyanobacteria has often led to ambiguous strain assignment. In the past two decades, the availability of sequences, such as those of the 16S rRNA,nif,cpcandrpoC1genes, and the use of metagenomics, has steadily increased and has made the reconstruction of evolutionary relationships of some cyanobacterial groups possible in addition to improving strain assignment. Conserved indels (insertions/deletions) are present in all cyanobacterial RpoB (βsubunit of RNA polymerase) sequences presently available in public databases. These indels are located in the Rpb2_6 domain of RpoB, which is involved in DNA binding and DNA-directed RNA polymerase activity. They are variable in length (6–44 aa) and sequence, and form part of what appears to be a longer signature sequence (43–81 aa). Indeed, a number of these sequences turn out to be distinctive among several strains of a given genus and even among strains of a given species. These signature sequences can thus be used to identify cyanobacteria at a subgenus level and can be useful molecular markers to establish the taxonomic positions of cyanobacterial isolates in laboratory cultures, and/or to assess cyanobacterial biodiversity in space and time in natural ecosystems.

Published
2011

3. Human mucin gene MUC5B, the 10.7-kb large central exon encodes various alternate subdomains resulting in a super-repeat. Structural evidence for a 11p15.5 gene family

Author

J L, Desseyn, V, Guyonnet-Dupérat, N, Porchet, J P, Aubert, A, Laine, Biologie et Physiopathologie des Cellules Mucipares (u377), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laboratoire de Biochimie [Hopital Huriez, Lille], Hôpital Claude Huriez [Lille], CHU Lille-CHU Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), This work was supported by 'La Ligue contre le Cancer,' 'l'Association de Recherche contre le Cancer,' and 'l'Association Française de Lutte contre la Mucoviscidose.' The costs of publication of this article were defrayed in part by the payment of page charges., The nucleotide sequence(s) reported in this paper has been submitted to the GenBank™/EMBL Data Bank with accession number(s) Z72496[GenBank] (HSMUC5BEX)., and Lille Inflammation Research International Center - U 995 [LIRIC]

Subjects
Base Sequence, Nucleic Acid, Amino Acid Sequence, Blotting, Southern, DNA, Exons, Humans, Molecular Sequence Data, Mucin-5B, Mucins, Peptide Mapping, Repetitive Sequences, Restriction Mapping, Sequence Alignment, [SDV]Life Sciences [q-bio], Blotting, Southern, Repetitive Sequences, Nucleic Acid
Abstract

The article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.; International audience; Human mucin gene MUC5B is mapped clustered with MUC6, MUC2, and MUC5AC on chromosome 11p15.5. We report here the isolation of three overlapping genomic clones of human MUC5B spanning approximately 40 kilobases. We have determined their partial restriction maps and the intron-exon boundaries of the central region encoding a single open reading frame. This coding region has been completely sequenced. Its length is 10,713 base pairs, and it encodes a 3570-amino acid peptide. Nineteen subdomains have been individualized. Some subdomains show similarity to each other, creating larger composite repeat units that we have called super-repeats. Four super-repeats of 528 amino acid residues are thus observed within the central exon. Each comprises (i) a subdomain composed of 11 repeats of the irregular repeat of 29 amino acid residues, (ii) a unique conserved subdomain with no typical repeat, and (iii) a cysteine-rich subdomain. This latter subdomain has high sequence similarity to the cysteine-rich domains described in MUC2 and MUC5AC. Sequence data of these three genes, together with their clustered organization, lead us to suggest that they may be a part of a multigene family. The super-repeat present in MUC5B is the largest ever determined in mucin genes and the central exon of this gene is, by far, the largest reported for a vertebrate gene.

Published
1997