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Rodriguez-Pilco MA, Leśny P, Podsiadłowski L, Schubart CD, Baeza JA. Characterization of The Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae). Genes (Basel) 2022; 13:genes13020299. [PMID: 35205344 PMCID: PMC8872168 DOI: 10.3390/genes13020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Metopaulias depressus is a non-marine crab endemic to Jamaica that dwells in rainforest bromeliads and exhibits elaborate active parental care behavior. Current genomic resources on M. depressus are rare, limiting the understanding of its adaptation to terrestrial life in species that evolved from marine ancestors. This study reports the complete mitochondrial genome of M. depressus assembled using Sanger sequencing. The AT-rich mitochondrial genome of M. depressus is 15,765 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 691 bp-long intergenic space is assumed to be the control region (CR) or D-loop. A set of selective pressure analyses indicate that the entirety of the PCGs experience purifying selection. Cox1, cox2, nad5, cox3, and atp6 experience strong purifying selection, and atp8 experiences weak purifying selection compared to the rest of the PCGs. The secondary structures of most tRNA genes exhibit a standard ‘cloverleaf’ structure, with the exception of trnS1, which lacks the dihydroxyuridine (DHU) arm but not the loop, the trnH gene, which lacks the thymine pseudouracil cytosine (T) loop but not the arm, and trnM, which exhibits an overly developed T loop. A maximum likelihood phylogenetic analysis based on all PCGs indicated that M. depressus is more closely related to the genera Clistocoeloma, Nanosesarma, and Parasesarma than to Chiromantes, Geosesarma, and Orisarma. This study contributes to deciphering the phylogenetic relationships within the family Sesarmidae and represents a new genomic resource for this iconic crab species.
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Affiliation(s)
- Milena A. Rodriguez-Pilco
- Facultad de Ciencias Biológicas, Universidad Nacional de San Agustin, Av. Daniel Alcides Carreon s/n, Arequipa 04001, Peru;
| | - Peter Leśny
- Institute for Evolutionary Biology & Animal Ecology, University Bonn, 53121 Bonn, Germany;
| | - Lars Podsiadłowski
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), 53113 Bonn, Germany;
| | | | - Juan Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, Coquimbo 1281, Chile
- Correspondence:
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2
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Phylogenomics of the longitarsal Colossendeidae: The evolutionary history of an Antarctic sea spider radiation. Mol Phylogenet Evol 2019; 136:206-214. [PMID: 31002869 DOI: 10.1016/j.ympev.2019.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 11/20/2022]
Abstract
Sea spiders (Pycnogonida) constitute a group of marine benthic arthropods that has a particularly high species diversity in the Southern Ocean. The "longitarsal" group of the sea spider family Colossendeidae is especially abundant in this region. However, this group also includes some representatives from other oceans, which raises the question where the group originates from. Therefore, we here investigated the phylogeny of the group with a hybrid enrichment approach that yielded a dataset of 1607 genes and over one million base pairs. We obtained a well-resolved phylogeny of the group, which is mostly consistent with morphological data. The data support an Antarctic origin of the longitarsal Colossendeidae and multiple dispersal events to other regions, which occurred at different timescales. This scenario is consistent with evidence found in other groups of marine invertebrates and highlights the role of the Southern Ocean as a source for non-Antarctic biota, especially of the deep sea. Our results suggest an initially slow rate of diversification followed by a more rapid radiation possibly correlated with the mid-Miocene cooling of Antarctica, similar to what is found in other taxa.
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3
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Leydet KP, Grupstra CGB, Coma R, Ribes M, Hellberg ME. Host-targeted RAD-Seq reveals genetic changes in the coralOculina patagonicaassociated with range expansion along the Spanish Mediterranean coast. Mol Ecol 2018; 27:2529-2543. [DOI: 10.1111/mec.14702] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Karine Posbic Leydet
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
| | - Carsten G. B. Grupstra
- Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam The Netherlands
- Institut de Ciències del mar; Barcelona Spain
| | - Rafel Coma
- Centre d'Estudis Avançats de Blanes; Blanes Girona Spain
| | - Marta Ribes
- Institut de Ciències del mar; Barcelona Spain
| | - Michael E. Hellberg
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
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4
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Brand P, Lin W, Johnson BR. The Draft Genome of the Invasive Walking Stick, Medauroidea extradendata, Reveals Extensive Lineage-Specific Gene Family Expansions of Cell Wall Degrading Enzymes in Phasmatodea. G3 (BETHESDA, MD.) 2018; 8:1403-1408. [PMID: 29588379 PMCID: PMC5940134 DOI: 10.1534/g3.118.200204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
Abstract
Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata, an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components.
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Affiliation(s)
- Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, California 95619
| | - Wei Lin
- Department of Entomology and Nematology, University of California, Davis, California 95616
| | - Brian R Johnson
- Department of Entomology and Nematology, University of California, Davis, California 95616
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5
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The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma. G3-GENES GENOMES GENETICS 2017; 7:2891-2898. [PMID: 28701376 PMCID: PMC5592917 DOI: 10.1534/g3.117.043687] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bees provide indispensable pollination services to both agricultural crops and wild plant populations, and several species of bees have become important models for the study of learning and memory, plant–insect interactions, and social behavior. Orchid bees (Apidae: Euglossini) are especially important to the fields of pollination ecology, evolution, and species conservation. Here we report the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma Bembé & Eltz. E. dilemma was selected because it is widely distributed, highly abundant, and it was recently naturalized in the southeastern United States. We provide a high-quality assembly of the 3.3 Gb genome, and an official gene set of 15,904 gene annotations. We find high conservation of gene synteny with the honey bee throughout 80 MY of divergence time. This genomic resource represents the first draft genome of the orchid bee genus Euglossa, and the first draft orchid bee mitochondrial genome, thus representing a valuable resource to the research community.
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Dömel JS, Melzer RR, Harder AM, Mahon AR, Leese F. Nuclear and Mitochondrial Gene Data Support Recent Radiation within the Sea Spider Species Complex Pallenopsis patagonica. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2016.00139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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7
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Olsson S, Seoane-Zonjic P, Bautista R, Claros MG, González-Martínez SC, Scotti I, Scotti-Saintagne C, Hardy OJ, Heuertz M. Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers. Mol Ecol Resour 2016; 17:614-630. [PMID: 27718316 DOI: 10.1111/1755-0998.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain
| | - Pedro Seoane-Zonjic
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Rocío Bautista
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France
| | - Ivan Scotti
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Caroline Scotti-Saintagne
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Olivier J Hardy
- Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France.,Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
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8
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Frías-López C, Sánchez-Herrero JF, Guirao-Rico S, Mora E, Arnedo MA, Sánchez-Gracia A, Rozas J. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms. Bioinformatics 2016; 32:3753-3759. [DOI: 10.1093/bioinformatics/btw534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/07/2016] [Accepted: 08/09/2016] [Indexed: 11/13/2022] Open
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9
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Roterman CN, Copley JT, Linse KT, Tyler PA, Rogers AD. Connectivity in the cold: the comparative population genetics of vent-endemic fauna in the Scotia Sea, Southern Ocean. Mol Ecol 2016; 25:1073-88. [PMID: 26919308 DOI: 10.1111/mec.13541] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 12/19/2015] [Accepted: 12/24/2015] [Indexed: 01/18/2023]
Abstract
We report the first comparative population genetics study for vent fauna in the Southern Ocean using cytochrome C oxidase I and microsatellite markers. Three species are examined: the kiwaid squat lobster, Kiwa tyleri, the peltospirid gastropod, Gigantopelta chessoia, and a lepetodrilid limpet, Lepetodrilus sp., collected from vent fields 440 km apart on the East Scotia Ridge (ESR) and from the Kemp Caldera on the South Sandwich Island Arc, ~95 km eastwards. We report no differentiation for all species across the ESR, consistent with panmixia or recent range expansions. A lack of differentiation is notable for Kiwa tyleri, which exhibits extremely abbreviated lecithotrophic larval development, suggestive of a very limited dispersal range. Larval lifespans may, however, be extended by low temperature-induced metabolic rate reduction in the Southern Ocean, muting the impact of dispersal strategy on patterns of population structure. COI diversity patterns suggest all species experienced demographic bottlenecks or selective sweeps in the past million years and possibly at different times. ESR and Kemp limpets are divergent, although with evidence of very recent ESR-Kemp immigration. Their divergence, possibility indicative of incipient speciation, along with the absence of the other two species at Kemp, may be the consequence of differing dispersal capabilities across a ~1000 m depth range and/or different selective regimes between the two areas. Estimates of historic and recent limpet gene flow between the ESR and Kemp are consistent with predominantly easterly currents and potentially therefore, cross-axis currents on the ESR, with biogeographic implications for the region.
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Affiliation(s)
- C N Roterman
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - J T Copley
- Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, SO14 3ZH, UK
| | - K T Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - P A Tyler
- Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, SO14 3ZH, UK
| | - A D Rogers
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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10
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Heras S, Planella L, Caldarazzo I, Vera M, García-Marín JL, Roldán MI. Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus. PeerJ 2016; 4:e2200. [PMID: 27547526 PMCID: PMC4974933 DOI: 10.7717/peerj.2200] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
The blue and red shrimp, Aristeus antennatus, is a commercially important crustacean, in the Mediterranean Sea, which has been listed as a priority species for fishery management. Hypervariable microsatellite markers could be a useful tool to identify genetic stocks among geographically close fishing grounds. Potential microsatellite markers (97) identified from next-generation sequencing of an individual shrimp using a 454 GS Junior Pyrosequencer were tested on a preliminary panel of 15 individuals representing the four worldwide genetic stocks of the species from which 35 polymorphic loci were identified and used to characterize an additional 20 individuals from the Western Mediterranean Sea. In the Western Mediterranean sample, 32 out of 35 were polymorphic loci and the number of alleles per locus ranged from 2 to 14 and expected heterozygosity ranged from 0.050 to 0.968. No linkage disequilibrium was detected, indicating the independence of the loci. These novel microsatellites provide additional tools to address questions relating to genetic diversity, parentage studies and connectivity patterns of A. antennatus populations and help develop effective strategies to ensure long-term sustainability of this resource.
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Affiliation(s)
- Sandra Heras
- Biology Department, University of Girona, Girona, Spain
| | - Laia Planella
- Biology Department, University of Girona, Girona, Spain
| | | | - Manuel Vera
- Biology Department, University of Girona, Girona, Spain
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11
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Murgarella M, Puiu D, Novoa B, Figueras A, Posada D, Canchaya C. A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis. PLoS One 2016; 11:e0151561. [PMID: 26977809 PMCID: PMC4792442 DOI: 10.1371/journal.pone.0151561] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 03/01/2016] [Indexed: 02/06/2023] Open
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.
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Affiliation(s)
- Maria Murgarella
- Department of Biochemistry, Genetics and Immunology and Unidad Asociada CSIC, University of Vigo, Vigo, Spain
| | - Daniela Puiu
- Center for Computational Biology. McKusick-Nathans, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas, Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas, Vigo, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology and Unidad Asociada CSIC, University of Vigo, Vigo, Spain
| | - Carlos Canchaya
- Department of Biochemistry, Genetics and Immunology and Unidad Asociada CSIC, University of Vigo, Vigo, Spain
- * E-mail:
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13
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Deagle BE, Faux C, Kawaguchi S, Meyer B, Jarman SN. Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water. Mol Ecol 2015; 24:4943-59. [PMID: 26340718 DOI: 10.1111/mec.13370] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/23/2015] [Accepted: 09/01/2015] [Indexed: 12/18/2022]
Abstract
Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist.
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Affiliation(s)
- Bruce E Deagle
- Australian Antarctic Division, Kingston, Tasmania, Australia.,Antarctic Climate and Ecosystems Cooperative Research Centre, Hobart, Tasmania, Australia
| | - Cassandra Faux
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - So Kawaguchi
- Australian Antarctic Division, Kingston, Tasmania, Australia.,Antarctic Climate and Ecosystems Cooperative Research Centre, Hobart, Tasmania, Australia
| | - Bettina Meyer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Simon N Jarman
- Australian Antarctic Division, Kingston, Tasmania, Australia
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14
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Riesgo A, Taboada S, Avila C. Evolutionary patterns in Antarctic marine invertebrates: an update on molecular studies. Mar Genomics 2015; 23:1-13. [PMID: 26228311 DOI: 10.1016/j.margen.2015.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Ana Riesgo
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Sergi Taboada
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain
| | - Conxita Avila
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain
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15
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Rozenberg A, Brand P, Rivera N, Leese F, Schubart CD. Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans. BMC Evol Biol 2015; 15:142. [PMID: 26187050 PMCID: PMC4506587 DOI: 10.1186/s12862-015-0380-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 05/13/2015] [Indexed: 11/10/2022] Open
Abstract
Background The White Spot Syndrome Virus (WSSV) is an important pathogen that infects a variety of decapod species and causes a highly contagious disease in penaeid shrimps. Mass mortalities caused by WSSV have pronounced commercial impact on shrimp aquaculture. Until now WSSV is the only known member of the virus family Nimaviridae, a group with obscure phylogenetic affinities. Its isolated position makes WSSV studies challenging due to large number of genes without homology in other viruses or cellular organisms. Results Here we report the discovery of an unusually large amount of sequences with high similarity to WSSV in a genomic library from the Jamaican bromeliad crab Metopaulias depressus. De novo assembly of these sequences allowed for the partial reconstruction of the genome of this endogenized virus with total length of 200 kbp encompassed in three scaffolds. The genome includes at least 68 putative open reading frames with homology in WSSV, most of which are intact. Among these, twelve orthologs of WSSV genes coding for non-structural proteins and nine genes known to code for the major components of the WSSV virion were discovered. Together with reanalysis of two similar cases of WSSV-like sequences in penaeid shrimp genomic libraries, our data allowed comparison of gene composition and gene order between different lineages related to WSSV. Furthermore, screening of published sequence databases revealed sequences with highest similarity to WSSV and the newly described virus in genomic libraries of at least three further decapod species. Analysis of the viral sequences detected in decapods suggests that they are less a result of contemporary WSSV infection, but rather originate from ancestral infection events. Phylogenetic analyses suggest that genes were acquired repeatedly by divergent viruses or viral strains of the Nimaviridae. Conclusions Our results shed new light on the evolution of the Nimaviridae and point to a long association of this viral group with decapod crustaceans. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0380-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey Rozenberg
- Ruhr University Bochum, Department of Animal Ecology, Evolution and Biodiversity, Bochum, Germany.
| | - Philipp Brand
- Ruhr University Bochum, Department of Animal Ecology, Evolution and Biodiversity, Bochum, Germany. .,University of California, Davis, Department of Evolution and Ecology, Center for Population Biology, Davis, USA.
| | - Nicole Rivera
- University of Regensburg, Department of Zoology and Evolutionary Biology, Regensburg, Germany.
| | - Florian Leese
- Ruhr University Bochum, Department of Animal Ecology, Evolution and Biodiversity, Bochum, Germany.
| | - Christoph D Schubart
- University of Regensburg, Department of Zoology and Evolutionary Biology, Regensburg, Germany.
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Dietz L, Arango CP, Dömel JS, Halanych KM, Harder AM, Held C, Mahon AR, Mayer C, Melzer RR, Rouse GW, Weis A, Wilson NG, Leese F. Regional differentiation and extensive hybridization between mitochondrial clades of the Southern Ocean giant sea spider Colossendeis megalonyx. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140424. [PMID: 26587257 PMCID: PMC4632570 DOI: 10.1098/rsos.140424] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 06/29/2015] [Indexed: 05/13/2023]
Abstract
Assessing the enormous diversity of Southern Ocean benthic species and their evolutionary histories is a central task in the era of global climate change. Based on mitochondrial markers, it was recently suggested that the circumpolar giant sea spider Colossendeis megalonyx comprises a complex of at least six cryptic species with mostly small and non-overlapping distribution ranges. Here, we expand the sampling to include over 500 mitochondrial COI sequences of specimens from around the Antarctic. Using multiple species delimitation approaches, the number of distinct mitochondrial OTUs increased from six to 15-20 with our larger dataset. In contrast to earlier studies, many of these clades show almost circumpolar distributions. Additionally, analysis of the nuclear internal transcribed spacer region for a subset of these specimens showed incongruence between nuclear and mitochondrial results. These mito-nuclear discordances suggest that several of the divergent mitochondrial lineages can hybridize and should not be interpreted as cryptic species. Our results suggest survival of C. megalonyx during Pleistocene glaciations in multiple refugia, some of them probably located on the Antarctic shelf, and emphasize the importance of multi-gene datasets to detect the presence of cryptic species, rather than their inference based on mitochondrial data alone.
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Affiliation(s)
- Lars Dietz
- Faculty of Biology and Biotechnology, Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitaetsstrasse 150, Bochum 44801, Germany
| | - Claudia P. Arango
- Natural Environments Program, Queensland Museum, PO Box 3300, South Brisbane, Queensland 4101, Australia
| | - Jana S. Dömel
- Faculty of Biology and Biotechnology, Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitaetsstrasse 150, Bochum 44801, Germany
| | | | - Avril M. Harder
- Department of Biology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
| | - Christoph Held
- Alfred Wegener Institute, Helmholtz Center for Marine and Polar Biology, Am Alten Hafen 26, Bremerhaven 25768, Germany
| | - Andrew R. Mahon
- Department of Biology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
| | - Christoph Mayer
- Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn 53113, Germany
| | - Roland R. Melzer
- Bavarian State Collection of Zoology—SNSB, Münchhausenstraße 21, Munich 81247, Germany
- Department Biology II, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, Planegg-Martinsried 82152, Germany
- GeoBio-Center, Richard-Wagner-Straße 10, Munich 80333, Germany
| | - Greg W. Rouse
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla 92093-0202, CA, USA
| | - Andrea Weis
- Bavarian State Collection of Zoology—SNSB, Münchhausenstraße 21, Munich 81247, Germany
| | - Nerida G. Wilson
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla 92093-0202, CA, USA
- Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia
| | - Florian Leese
- Faculty of Biology and Biotechnology, Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitaetsstrasse 150, Bochum 44801, Germany
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Dietz L, Brand P, Eschner LM, Leese F. The mitochondrial genomes of the caddisflies Sericostoma personatum and Thremma gallicum (Insecta: Trichoptera). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3293-4. [PMID: 25714156 DOI: 10.3109/19401736.2015.1015009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial genomes of the caddisfly species Sericostoma personatum and Thremma gallicum were sequenced on a 454 FLX and Illumina MiSeq platform, respectively. Reads were assembled de novo and remaining gaps in the S. personatum mitogenome closed by Sanger sequencing. The lengths of the assembled mitogenomes were 15,260 bp and 15,343 bp for S. personatum and T. gallicum, respectively. Both mitogenomes contained all 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the control region. The mitochondrial gene order of both caddisflies is identical with the typical insect gene order. These are the third and fourth published mitogenomes of the order Trichoptera of two formerly unexplored families and thus will be useful in future phylogenetic analysis.
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Affiliation(s)
- Lars Dietz
- a Department of Animal Ecology , Evolution and Biodiversity, Ruhr University Bochum , Bochum , Germany and
| | - Philipp Brand
- a Department of Animal Ecology , Evolution and Biodiversity, Ruhr University Bochum , Bochum , Germany and.,b Department for Evolution and Ecology , Center for Population Biology, University of California Davis , Davis , CA , USA
| | - Lisa Marie Eschner
- a Department of Animal Ecology , Evolution and Biodiversity, Ruhr University Bochum , Bochum , Germany and
| | - Florian Leese
- a Department of Animal Ecology , Evolution and Biodiversity, Ruhr University Bochum , Bochum , Germany and
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Meglécz E, Pech N, Gilles A, Dubut V, Hingamp P, Trilles A, Grenier R, Martin JF. QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate. Mol Ecol Resour 2014; 14:1302-13. [PMID: 24785154 DOI: 10.1111/1755-0998.12271] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/21/2014] [Accepted: 04/25/2014] [Indexed: 11/30/2022]
Abstract
Microsatellite marker development has been greatly simplified by the use of high-throughput sequencing followed by in silico microsatellite detection and primer design. However, the selection of markers designed by the existing pipelines depends either on arbitrary criteria, or older studies on PCR success. Based on wet laboratory experiments, we have identified the following factors that are most likely to influence genotyping success rate: alignment score between the primers and the amplicon; the distance between primers and microsatellites; the length of the PCR product; target region complexity and the number of reads underlying the sequence. The QDD pipeline has been modified to include these most pertinent factors in the output to help the selection of markers. Furthermore, new features are also included in the present version: (i) not only raw sequencing reads are accepted as input, but also contigs, allowing the analysis of assembled high-coverage data; (ii) input data can be both in fasta and fastq format to facilitate the use of Illumina and IonTorrent reads; (iii) A comparison to known transposable elements allows their detection; (iv) A contamination check can be carried out by BLASTing potential markers against the nucleotide (nt) database of NCBI; (v) QDD3 is now also available imbedded into a virtual machine making installation easier and operating system independent. It can be used both on command-line version as well as integrated into a Galaxy server, providing a user-friendly interface, as well as the possibility to utilize a large variety of NGS tools.
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Affiliation(s)
- Emese Meglécz
- Aix-Marseille Université, CNRS, IRD, Univ. Avignon, UMR 7263 - IMBE, Equipe EGE, Centre Saint-Charles, Case 36, 3 Place Victor Hugo, 13331, Marseille Cedex 3, France
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19
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Zhou X, Rokas A. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Mol Ecol 2014; 23:1679-700. [DOI: 10.1111/mec.12680] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/17/2014] [Accepted: 01/22/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Xiaofan Zhou
- Department of Biological Sciences; Vanderbilt University; Nashville TN 37235 USA
| | - Antonis Rokas
- Department of Biological Sciences; Vanderbilt University; Nashville TN 37235 USA
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20
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Telomere-independent ageing in the longest-lived non-colonial animal, Arctica islandica. Exp Gerontol 2014; 51:38-45. [PMID: 24394156 DOI: 10.1016/j.exger.2013.12.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/19/2013] [Accepted: 12/25/2013] [Indexed: 02/08/2023]
Abstract
The shortening of telomeres as a causative factor in ageing is a widely discussed hypothesis in ageing research. The study of telomere length and its regenerating enzyme telomerase in the longest-lived non-colonial animal on earth, Arctica islandica, should inform whether the maintenance of telomere length plays a role in reaching the extreme maximum lifespan (MLSP) of >500years in this species. Since longitudinal measurements on living animals cannot be achieved, a cross-sectional analysis of a short-lived (MLSP 40years from the Baltic Sea) and a long-lived population (MLSP 226years Northeast of Iceland) and in different tissues of young and old animals from the Irish Sea was performed. A high heterogeneity of telomere length was observed in investigated A. islandica over a wide age range (10-36years for the Baltic Sea, 11-194years for Irish Sea, 6-226years for Iceland). Constant telomerase activity and telomere lengths were detected at any age and in different tissues; neither correlated with age or population habitat. Stable telomere maintenance might contribute to the long lifespan of A. islandica. Telomere dynamics are no explanation for the distinct MLSPs of the examined populations and thus the cause of it remains to be investigated.
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Ricci M, Luchetti A, Bonandin L, Mantovani B. Random DNA libraries from three species of the stick insect genus Bacillus (Insecta: Phasmida): repetitive DNA characterization and first observation of polyneopteran MITEs. Genome 2013; 56:729-35. [PMID: 24433208 DOI: 10.1139/gen-2013-0107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The repetitive DNA content of the stick insect species Bacillus rossius (facultative parthenogenetic), Bacillus grandii (gonochoric), and Bacillus atticus (obligate parthenogenetic) was analyzed through the survey of random genomic libraries roughly corresponding to 0.006% of the genome. By repeat masking, 19 families of transposable elements were identified (two LTR and six non-LTR retrotransposons; 11 DNA transposons). Moreover, a de novo analysis revealed, among the three libraries, the first MITE family observed in polyneopteran genomes. On the whole, transposable element abundance represented 23.3% of the genome in B. rossius, 22.9% in B. atticus, and 18% in B. grandii. Tandem repeat content in the three libraries is much lower: 1.32%, 0.64%, and 1.86% in B. rossius, B. grandii, and B. atticus, respectively. Microsatellites are the most abundant in all species. Minisatellites were only found in B. rossius and B. atticus, and five monomers belonging to the Bag320 satellite family were detected in B. atticus. Assuming the survey provides adequate representation of the relative genome, the obligate parthenogenetic species (B. atticus), compared with the other two species analyzed, does not show a lower transposable element content, as expected from some theoretical and empirical studies.
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Affiliation(s)
- Marco Ricci
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, via Selmi 3, 40126 Bologna, Italy
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Keith Barker F, Oyler-McCance S, Tomback DF. Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences. ACTA ACUST UNITED AC 2013; 26:384-8. [DOI: 10.3109/19401736.2013.840588] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Dambach J, Raupach MJ, Mayer C, Schwarzer J, Leese F. Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). BMC Res Notes 2013; 6:75. [PMID: 23448502 PMCID: PMC3629709 DOI: 10.1186/1756-0500-6-75] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/27/2013] [Indexed: 11/15/2022] Open
Abstract
Background The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. Findings We report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934. Conclusions The reported markers provide a novel tool to study genetic structure and diversity in Nematocarcinus lanceopes populations in the Southern Ocean and monitor effects of ongoing climate change in the region on the populations inhabiting these.
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