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Cunha RL, Nicastro KR, Zardi GI, Madeira C, McQuaid CD, Cox CJ, Castilho R. Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus. PeerJ 2022; 10:e13953. [PMID: 36187748 PMCID: PMC9521344 DOI: 10.7717/peerj.13953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Background The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the "primer-walking" method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.
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Affiliation(s)
- Regina L. Cunha
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal
| | - Katy R. Nicastro
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal,CNRS, Univ. Littoral Côte d’Opale, UMR 8187 – LOG – Laboratoire d’Océanologie et de Géosciences, Université de Lille, Lille, France,Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Gerardo I. Zardi
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Celine Madeira
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal
| | | | - Cymon J. Cox
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal
| | - Rita Castilho
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal
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2
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Lubośny M, Śmietanka B, Arculeo M, Burzyński A. No evidence of DUI in the Mediterranean alien species Brachidontes pharaonis (P. Fisher, 1870) despite mitochondrial heteroplasmy. Sci Rep 2022; 12:8569. [PMID: 35595866 PMCID: PMC9122905 DOI: 10.1038/s41598-022-12606-6] [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: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 01/05/2023] Open
Abstract
Two genetically different mitochondrial haplogroups of Brachidontes pharaonis (p-distance 6.8%) have been identified in the Mediterranean Sea. This hinted at a possible presence of doubly uniparental inheritance in this species. To ascertain this possibility, we sequenced two complete mitogenomes of Brachidontes pharaonis mussels and performed a qPCR analysis to measure the relative mitogenome copy numbers of both mtDNAs. Despite the presence of two very similar regions composed entirely of repetitive sequences in the two haplogroups, no recombination between mitogenomes was detected. In heteroplasmic individuals, both mitogenomes were present in the generative tissues of both sexes, which argues against the presence of doubly uniparental inheritance in this species.
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marco Arculeo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot JF, Allam B. Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. BMC Genomics 2022; 23:192. [PMID: 35260071 PMCID: PMC8905726 DOI: 10.1186/s12864-021-08262-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significant mortality events have been reported in the species throughout its native range as a result of diseases (microbial infections, leukemia) and acute environmental stress. In this context, the characterization of the hard clam genome can provide highly needed resources to enable basic (e.g., oncogenesis and cancer transmission, adaptation biology) and applied (clam stock enhancement, genomic selection) sciences. RESULTS Using a combination of long and short-read sequencing technologies, a 1.86 Gb chromosome-level assembly of the clam genome was generated. The assembly was scaffolded into 19 chromosomes, with an N50 of 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than the few other members of the Venerida sequenced so far, with coding regions representing only 2% of the assembly. Indeed, more than half of the genome is composed of repeated elements, including transposable elements. Major chromosome rearrangements were detected between this assembly and another recent assembly derived from a genetically segregated clam stock. Comparative analysis of the clam genome allowed the identification of a marked diversification in immune-related proteins, particularly extensive tandem duplications and expansions in tumor necrosis factors (TNFs) and C1q domain-containing proteins, some of which were previously shown to play a role in clam interactions with infectious microbes. The study also generated a comparative repertoire highlighting the diversity and, in some instances, the specificity of LTR-retrotransposons elements, particularly Steamer elements in bivalves. CONCLUSIONS The diversity of immune molecules in M. mercenaria may allow this species to cope with varying and complex microbial and environmental landscapes. The repertoire of transposable elements identified in this study, particularly Steamer elements, should be a prime target for the investigation of cancer cell development and transmission among bivalve mollusks.
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Affiliation(s)
- Sarah Farhat
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Eric Bonnivard
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Emmanuelle Pales Espinosa
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Arnaud Tanguy
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Isabelle Boutet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Nadège Guiglielmoni
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)2, B-1050, Brussels, Belgium
| | - Bassem Allam
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
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Al-Saad A, Khatir Z, Al-Maslamani I, Leitão A. Cytogenetic Characterization of Three Arabian Gulf Bivalve Species. MALACOLOGIA 2020. [DOI: 10.4002/040.063.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Aysha Al-Saad
- Environmental Science Center (ESC), Qatar University, P. O. Box 2713, Doha, Qatar
| | - Zenaba Khatir
- Environmental Science Center (ESC), Qatar University, P. O. Box 2713, Doha, Qatar
| | - Ibrahim Al-Maslamani
- Environmental Science Center (ESC), Qatar University, P. O. Box 2713, Doha, Qatar
| | - Alexandra Leitão
- Environmental Science Center (ESC), Qatar University, P. O. Box 2713, Doha, Qatar
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Gerdol M, Fujii Y, Pallavicini A, Ozeki Y. Response to the editorial "Fake news" (Feb. 2018) by Prof. Brian Morton. MARINE POLLUTION BULLETIN 2019; 141:363-365. [PMID: 30955745 DOI: 10.1016/j.marpolbul.2019.02.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Marco Gerdol
- Dept. of Life Sciences, Univ. of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy.
| | - Yuki Fujii
- Dept. of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International Univ., 2825-7 Huis Ten Bosch, Sasebo, Nagasaki 859-3298, Japan
| | - Alberto Pallavicini
- Dept. of Life Sciences, Univ. of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Yasuhiro Ozeki
- Dept. of Life and Environmental System Science, Graduate School of NanoBio Sciences, Yokohama City Univ., 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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Lukhtanov VA, Iashenkova Y. Linking karyotypes with DNA barcodes: proposal for a new standard in chromosomal analysis with an example based on the study of Neotropical Nymphalidae (Lepidoptera). COMPARATIVE CYTOGENETICS 2019; 13:435-449. [PMID: 31886776 PMCID: PMC6930310 DOI: 10.3897/compcytogen.v13i4.48368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/04/2019] [Indexed: 05/12/2023]
Abstract
Chromosomal data are important for taxonomists, cytogeneticists and evolutionary biologists; however, the value of these data decreases sharply if they are obtained for individuals with inaccurate species identification or unclear species identity. To avoid this problem, here we suggest linking each karyotyped sample with its DNA barcode, photograph and precise geographic data, providing an opportunity for unambiguous identification of described taxa and for delimitation of undescribed species. Using this approach, we present new data on chromosome number diversity in neotropical butterflies of the subfamily Biblidinae (genus Vila Kirby, 1871) and the tribe Ithomiini (genera Oleria Hübner, 1816, Ithomia Hübner, 1816, Godyris Boisduval, 1870, Hypothyris Hübner, 1821, Napeogenes Bates, 1862, Pseudoscada Godman et Salvin, 1879 and Hyposcada Godman et Salvin, 1879). Combining new and previously published data we show that the species complex Oleria onega (Hewitson, [1852]) includes three discrete chromosomal clusters (with haploid chromosome numbers n = 15, n = 22 and n = 30) and at least four DNA barcode clusters. Then we discuss how the incomplete connection between these chromosomal and molecular data (karyotypes and DNA barcodes were obtained for different sets of individuals) complicates the taxonomic interpretation of the discovered clusters.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, Russia
- Department of Entomology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg 199034, Russia
| | - Yaroslavna Iashenkova
- Department of Entomology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg 199034, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg 199034, Russia
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García-Souto D, Alonso-Rubido S, Costa D, Eirín-López JM, Rolán-Álvarez E, Faria R, Galindo J, Pasantes JJ. Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae). Genes (Basel) 2018; 9:E517. [PMID: 30360559 PMCID: PMC6266005 DOI: 10.3390/genes9110517] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/12/2018] [Accepted: 10/19/2018] [Indexed: 01/08/2023] Open
Abstract
Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Littorina arcana, L. saxatilis, and L. compressa, the flat periwinkles L. obtusata and L. fabalis, the common periwinkle L. littorea, the mangrove periwinkle Littoraria angulifera, the beaded periwinkle Cenchritis muricatus, and the small periwinkle Melarhaphe neritoides was performed. All species showed diploid chromosome numbers of 2n = 34, and karyotypes were mostly composed of metacentric and submetacentric chromosome pairs. None of the periwinkle species showed chromosomal differences between male and female specimens. The chromosomal mapping of major and minor rDNA and H3 histone gene clusters by fluorescent in situ hybridization demonstrated that the patterns of distribution of these DNA sequences were conserved among closely related species and differed among less related ones. All signals occupied separated loci on different chromosome pairs without any evidence of co-localization in any of the species.
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Affiliation(s)
- Daniel García-Souto
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
- CIMUS Biomedical Research Institute, University of Santiago de Compostela, E-15706 Santiago de Compostela, Spain.
| | - Sandra Alonso-Rubido
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
- Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC-Institute of Catalysis and Petrochemistry, C/Marie Curie 2, E-28049 Madrid, Spain.
| | - Diana Costa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
| | - José M Eirín-López
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA.
| | - Emilio Rolán-Álvarez
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
- CIM-UVIGO, Centro de Investigación Mariña, Universidade de Vigo, E-36331 Vigo, Spain.
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
| | - Juan Galindo
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
- CIM-UVIGO, Centro de Investigación Mariña, Universidade de Vigo, E-36331 Vigo, Spain.
| | - Juan J Pasantes
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
- CIM-UVIGO, Centro de Investigación Mariña, Universidade de Vigo, E-36331 Vigo, Spain.
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Cytogenetics in Arctica islandica (Bivalvia, Arctidae): the Longest Lived Non-Colonial Metazoan. Genes (Basel) 2018; 9:genes9060299. [PMID: 29899300 PMCID: PMC6027238 DOI: 10.3390/genes9060299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022] Open
Abstract
Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic aspects but nothing is known about their chromosomes. In this work, the chromosomes of the ocean quahog Arctica islandica were analysed by means of 4′,6-diamidino-2-phenylindole (DAPI)/propidium iodide (PI) staining and fluorescent in situ hybridization (FISH) with rDNA, histone gene and telomeric probes. Whilst both 5S rDNA and 45S rDNA were clustered at single subcentromeric locations on the long arms of chromosome pairs 2 and 12, respectively, histone gene clusters located on the short arms of chromosome pairs 7, 10 and 17. As happens with most bivalves, the location of the vertebrate type telomeric sequence clusters was restricted to chromosome ends. The knowledge of the karyotype can facilitate the anchoring of genomic sequences to specific chromosome pairs in this species.
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