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  1. Article: The network structure of intertidal meiofaunal communities from environmental DNA metabarcoding surveys in Northwest Iberia

    Bellisario, Bruno / Fais, Maria / Duarte, Sofia / Vieira, Pedro E. / Canchaya, Carlos / Costa, Filipe O.

    Aquatic sciences. 2021 Oct., v. 83, no. 4

    2021  

    Abstract: The identification of patterns and mechanisms behind species’ distribution is one of the major challenges in ecology, having important outcomes for the conservation and management of ecosystems. This is especially true for those components of ... ...

    Abstract The identification of patterns and mechanisms behind species’ distribution is one of the major challenges in ecology, having important outcomes for the conservation and management of ecosystems. This is especially true for those components of biodiversity providing essential ecosystem functions and for which standard surveys may underestimate their real taxonomic diversity due to high degree of cryptic diversity and inherent diagnosis difficulties, such as meiofaunal communities. Within this context, environmental DNA (eDNA) metabarcoding may provide a fast and reliable way to refine and scale-up the characterization of biological diversity in complex environmental samples, allowing to bypass issues related to biodiversity estimation. Moreover, the possibility of integrating eDNA metabarcoding-derived data with tools and methods rooted in network theory would deepen the knowledge on the structuring processes of ecological communities in ways that cannot be predicted from studying individual species/communities in isolation. Here, a sediment eDNA metabarcoding of mitochondrial cytochrome c oxidase I (COI) and nuclear hypervariable V4 region of the 18S rDNA (18S) was used to reconstruct the bipartite networks linking intertidal meiofaunal OTUs and sampling stations from three estuaries of the North-Western Iberian Peninsula. Null models were used to identify the role of environmental and spatial constraints on the structure of COI- and 18S-derived networks and to characterize the macroecological features of surveyed phyla. Our results show the feasibility of eDNA metabarcoding to capture a fair amount of diversity hard to detect with standard survey procedures and to identify hierarchical spatial structures in intertidal meiofaunal assemblages, ultimately suggesting a restricted distributional range mostly driven by niche-based processes.
    Keywords DNA barcoding ; ecosystems ; environmental DNA ; littoral zone ; mitochondria ; network theory ; sediments ; species diversity ; surveys ; Iberian Peninsula
    Language English
    Dates of publication 2021-10
    Size p. 71.
    Publishing place Springer International Publishing
    Document type Article
    ZDB-ID 1464021-1
    ISSN 1420-9055 ; 1015-1621
    ISSN (online) 1420-9055
    ISSN 1015-1621
    DOI 10.1007/s00027-021-00828-1
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel.

    Ribeiro, Ângela M / Canchaya, Carlos A / Penaloza, Fernando / Galindo, Juan / da Fonseca, Rute R

    Marine genomics

    2018  Volume 45, Page(s) 11–15

    Abstract: Bivalve molluscs of the genus Mytilus are considered a model organism in ecotoxicology and are known to be well adapted to marine ecosystems affected by multiple anthropogenic factors, including pollution. In order to assess whether pollution interferes ... ...

    Abstract Bivalve molluscs of the genus Mytilus are considered a model organism in ecotoxicology and are known to be well adapted to marine ecosystems affected by multiple anthropogenic factors, including pollution. In order to assess whether pollution interferes with the reproductive success of Mytilus and affects the diversity within and between populations, we sequenced the transcriptomes of 72 individuals from 9 populations of Mytilus galloprovincialis collected along a ca. 130-km north-south transect on the Western coast of the Iberian Peninsula. We found that polluted areas are acting as a barrier to gene flow, potentially because of the detrimental effect of anthropogenic chemicals on larvae carried from more pristine environments. Furthermore, we observed an increase in genetic diversity in populations from polluted site, which could be indicative of higher mutagenicity driven by the environment. We propose that a microevolutionary perspective is essential for a full characterization of human activities on the dispersal of M. galloprovincialis and that it should be incorporated into management, and conservation plans and policies in the context of the effects of pollution on populations.
    MeSH term(s) Animals ; Genetic Variation/drug effects ; Metagenomics ; Mytilus/genetics ; Portugal ; Spain ; Transcriptome/drug effects ; Water Pollution, Chemical/adverse effects
    Language English
    Publishing date 2018-11-14
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2429626-0
    ISSN 1876-7478 ; 1874-7787
    ISSN (online) 1876-7478
    ISSN 1874-7787
    DOI 10.1016/j.margen.2018.10.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Correction: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis.

    Murgarella, Maria / Puiu, Daniela / Novoa, Beatriz / Figueras, Antonio / Posada, David / Canchaya, Carlos

    PloS one

    2016  Volume 11, Issue 7, Page(s) e0160081

    Abstract: This corrects the article DOI: 10.1371/journal.pone.0151561.]. ...

    Abstract [This corrects the article DOI: 10.1371/journal.pone.0151561.].
    Language English
    Publishing date 2016
    Publishing country United States
    Document type Published Erratum
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0160081
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis.

    Murgarella, Maria / Puiu, Daniela / Novoa, Beatriz / Figueras, Antonio / Posada, David / Canchaya, Carlos

    PloS one

    2016  Volume 11, Issue 3, Page(s) e0151561

    Abstract: Mussels belong to the phylum Mollusca, one of the largest and most diverse taxa in the animal kingdom. Despite their importance in aquaculture and in biology in general, genomic resources from mussels are still scarce. To broaden and increase the genomic ...

    Abstract Mussels belong to the phylum Mollusca, one of the largest and most diverse taxa in the animal kingdom. Despite their importance in aquaculture and in biology in general, genomic resources from mussels are still scarce. To broaden and increase the genomic knowledge in this family, we carried out a whole-genome sequencing study of the cosmopolitan Mediterranean mussel (Mytilus galloprovincialis). We sequenced its genome (32X depth of coverage) on the Illumina platform using three pair-end libraries with different insert sizes. The large number of contigs obtained pointed out a highly complex genome of 1.6 Gb where repeated elements seem to be widespread (~30% of the genome), a feature that is also shared with other marine molluscs. Notwithstanding the limitations of our genome sequencing, we were able to reconstruct two mitochondrial genomes and predict 10,891 putative genes. A comparative analysis with other molluscs revealed a gene enrichment of gene ontology categories related to multixenobiotic resistance, glutamate biosynthetic process, and the maintenance of ciliary structures.
    MeSH term(s) Adaptation, Biological/genetics ; Animals ; Computer Simulation ; Contig Mapping ; DNA, Mitochondrial/genetics ; Gene Library ; Gene Ontology ; Genome ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Models, Genetic ; Molecular Sequence Annotation ; Mollusca/genetics ; Mytilus/genetics ; Mytilus/physiology ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Species Specificity
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2016-03-15
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0151561
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.

    Moreira, Rebeca / Pereiro, Patricia / Canchaya, Carlos / Posada, David / Figueras, Antonio / Novoa, Beatriz

    BMC genomics

    2015  Volume 16, Page(s) 728

    Abstract: Background: The Mediterranean mussel (Mytilus galloprovincialis) is a cosmopolitan, cultured bivalve with worldwide commercial and ecological importance. However, there is a qualitative and quantitative lack of knowledge of the molecular mechanisms ... ...

    Abstract Background: The Mediterranean mussel (Mytilus galloprovincialis) is a cosmopolitan, cultured bivalve with worldwide commercial and ecological importance. However, there is a qualitative and quantitative lack of knowledge of the molecular mechanisms involved in the physiology and immune response of this mollusc. In order to start filling this gap, we have studied the transcriptome of mantle, muscle and gills from naïve Mediterranean mussels and hemocytes exposed to distinct stimuli.
    Results: A total of 393,316 million raw RNA-Seq reads were obtained and assembled into 151,320 non-redundant transcripts with an average length of 570 bp. Only 55 % of the transcripts were shared across all tissues. Hemocyte and gill transcriptomes shared 60 % of the transcripts while mantle and muscle transcriptomes were most similar, with 77 % shared transcripts. Stimulated hemocytes showed abundant defense and immune-related proteins, in particular, an extremely high amount of antimicrobial peptides. Gills expressed many transcripts assigned to both structure and recognition of non-self patterns, while in mantle many transcripts were related to reproduction and shell formation. Moreover, this tissue presented additional and interesting hematopoietic, antifungal and sensorial functions. Finally, muscle expressed many myofibril and calcium-related proteins and was found to be unexpectedly associated with defense functions. In addition, many metabolic routes related to cancer were represented.
    Conclusions: Our analyses indicate that whereas the transcriptomes of these four tissues have characteristic expression profiles in agreement with their biological structures and expected functions, tissue-specific transcriptomes reveal a complex and specialized functions.
    MeSH term(s) Animals ; Gene Expression Regulation ; Gills ; Hemocytes ; High-Throughput Nucleotide Sequencing/methods ; Mytilus/genetics ; Tissue Distribution/genetics ; Transcriptome/genetics
    Language English
    Publishing date 2015-09-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/s12864-015-1817-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel

    Ribeiro, Ângela M / Carlos A. Canchaya / Fernando Penaloza / Juan Galindo / Rute R. da Fonseca

    Marine genomics. 2019 June, v. 45

    2019  

    Abstract: Bivalve molluscs of the genus Mytilus are considered a model organism in ecotoxicology and are known to be well adapted to marine ecosystems affected by multiple anthropogenic factors, including pollution. In order to assess whether pollution interferes ... ...

    Abstract Bivalve molluscs of the genus Mytilus are considered a model organism in ecotoxicology and are known to be well adapted to marine ecosystems affected by multiple anthropogenic factors, including pollution. In order to assess whether pollution interferes with the reproductive success of Mytilus and affects the diversity within and between populations, we sequenced the transcriptomes of 72 individuals from 9 populations of Mytilus galloprovincialis collected along a ca. 130-km north-south transect on the Western coast of the Iberian Peninsula. We found that polluted areas are acting as a barrier to gene flow, potentially because of the detrimental effect of anthropogenic chemicals on larvae carried from more pristine environments. Furthermore, we observed an increase in genetic diversity in populations from polluted site, which could be indicative of higher mutagenicity driven by the environment. We propose that a microevolutionary perspective is essential for a full characterization of human activities on the dispersal of M. galloprovincialis and that it should be incorporated into management, and conservation plans and policies in the context of the effects of pollution on populations.
    Keywords Mytilus galloprovincialis ; coasts ; ecotoxicology ; gene flow ; genetic variation ; genomics ; issues and policy ; larvae ; marine ecosystems ; models ; mussels ; mutagenicity ; pollution ; reproductive success ; transcriptome ; Iberian Peninsula
    Language English
    Dates of publication 2019-06
    Size p. 11-15.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2429626-0
    ISSN 1876-7478 ; 1874-7787
    ISSN (online) 1876-7478
    ISSN 1874-7787
    DOI 10.1016/j.margen.2018.10.009
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Correction

    Maria Murgarella / Daniela Puiu / Beatriz Novoa / Antonio Figueras / David Posada / Carlos Canchaya

    PLoS ONE, Vol 11, Iss 7, p e

    A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis.

    2016  Volume 0160081

    Abstract: This corrects the article DOI:10.1371/journal.pone.0151561.]. ...

    Abstract [This corrects the article DOI:10.1371/journal.pone.0151561.].
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Book ; Online ; Thesis: The impact of phages on bacterial chromosomes: a genomic-based analysis

    Canchaya Sanchez, Carlos A

    2004  

    Author's details by Carlos A. Canchaya Sanchez
    Language English
    Size Online-Ressource (324 S), Ill
    Publishing place Zürich
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Diss., Naturwissenschaften, Eidgenössische Technische Hochschule ETH Zürich, Nr. 15651--Zürich, 1565
    Database Former special subject collection: coastal and deep sea fishing

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  9. Article ; Online: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis.

    Maria Murgarella / Daniela Puiu / Beatriz Novoa / Antonio Figueras / David Posada / Carlos Canchaya

    PLoS ONE, Vol 11, Iss 3, p e

    2016  Volume 0151561

    Abstract: Mussels belong to the phylum Mollusca, one of the largest and most diverse taxa in the animal kingdom. Despite their importance in aquaculture and in biology in general, genomic resources from mussels are still scarce. To broaden and increase the genomic ...

    Abstract Mussels belong to the phylum Mollusca, one of the largest and most diverse taxa in the animal kingdom. Despite their importance in aquaculture and in biology in general, genomic resources from mussels are still scarce. To broaden and increase the genomic knowledge in this family, we carried out a whole-genome sequencing study of the cosmopolitan Mediterranean mussel (Mytilus galloprovincialis). We sequenced its genome (32X depth of coverage) on the Illumina platform using three pair-end libraries with different insert sizes. The large number of contigs obtained pointed out a highly complex genome of 1.6 Gb where repeated elements seem to be widespread (~30% of the genome), a feature that is also shared with other marine molluscs. Notwithstanding the limitations of our genome sequencing, we were able to reconstruct two mitochondrial genomes and predict 10,891 putative genes. A comparative analysis with other molluscs revealed a gene enrichment of gene ontology categories related to multixenobiotic resistance, glutamate biosynthetic process, and the maintenance of ciliary structures.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Genome sequence of

    Ormeño-Orrillo, Ernesto / Rey, Luis / Durán, David / Canchaya, Carlos A / Zúñiga-Dávila, Doris / Imperial, Juan / Martínez-Romero, Esperanza / Ruiz-Argüeso, Tomás

    Genomics data

    2017  Volume 13, Page(s) 35–37

    Abstract: ... ...

    Abstract Bradyrhizobium
    Language English
    Publishing date 2017-06-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2751131-5
    ISSN 2213-5960
    ISSN 2213-5960
    DOI 10.1016/j.gdata.2017.06.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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