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Skern-Mauritzen R, Malde K, Eichner C, Dondrup M, Furmanek T, Besnier F, Komisarczuk AZ, Nuhn M, Dalvin S, Edvardsen RB, Klages S, Huettel B, Stueber K, Grotmol S, Karlsbakk E, Kersey P, Leong JS, Glover KA, Reinhardt R, Lien S, Jonassen I, Koop BF, Nilsen F. The salmon louse genome: Copepod features and parasitic adaptations. Genomics 2021; 113:3666-3680. [PMID: 34403763 DOI: 10.1016/j.ygeno.2021.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13,081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including apparent downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite repeated development of resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.
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Affiliation(s)
| | - Ketil Malde
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Christiane Eichner
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Michael Dondrup
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlens Gate 55, 5008 Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Francois Besnier
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Anna Zofia Komisarczuk
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Michael Nuhn
- EMBL-The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Sussie Dalvin
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Rolf B Edvardsen
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Kurt Stueber
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Sindre Grotmol
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Egil Karlsbakk
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Paul Kersey
- EMBL-The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK; Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433 Ås, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlens Gate 55, 5008 Bergen, Norway
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Frank Nilsen
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway.
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da Silva KR, Mariotto S, Centofante L, Parise-Maltempi PP. Chromosome mapping of a Tc1-like transposon in species of the catfish Ancistrus. COMPARATIVE CYTOGENETICS 2017; 11:65-79. [PMID: 28919950 PMCID: PMC5599695 DOI: 10.3897/compcytogen.v11i1.10519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/28/2016] [Indexed: 06/07/2023]
Abstract
The Tc1 mariner element is widely distributed among organisms and have been already described in different species of fish. The genus Ancistrus (Kner, 1854) has 68 nominal species and is part of an interesting taxonomic and cytogenetic group, as well as presenting a variation of chromosome number, ranging from 2n=34 to 54 chromosomes, and the existence of simple and multiple sex chromosome system and the occurrence of chromosomal polymorphisms involving chromosomes that carry the nucleolus organizer region. In this study, a repetitive element by restriction enzyme, from Ancistrus sp.1 "Flecha" was isolated, which showed similarity with a transposable element Tc1-mariner. Its chromosomal location is distributed in heterochromatic regions and along the chromosomal arms of all specimens covered in this study, confirming the pattern dispersed of this element found in other studies carried out with other species. Thus, this result reinforces the hypothesis that the sequence AnDraI is really a dispersed element isolated. As this isolated sequence showed the same pattern in all species which have different sex chromosomes systems, including in all sex chromosomes, we could know that it is not involved in sex chromosome differentiation.
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Affiliation(s)
- Keteryne Rodrigues da Silva
- Laboratório de Citogenética Animal – Universidade Estadual Paulista “Júlio de Mesquita Filho” Campus de Rio Claro – Av 24A, 1515 Jardim Bela Vista- 13600-000- Rio Claro/SP, Brasil
| | - Sandra Mariotto
- Instituto Federal de Ciências e Tecnologia do Mato Grosso, campus de Cuiabá – Bela Vista, MT, Brasil
| | - Liano Centofante
- Instituto de Biociências, UFMT Universidade Federal de Mato Grosso, Cuiabá, MT, Brasil
| | - Patricia Pasquali Parise-Maltempi
- Laboratório de Citogenética Animal – Universidade Estadual Paulista “Júlio de Mesquita Filho” Campus de Rio Claro – Av 24A, 1515 Jardim Bela Vista- 13600-000- Rio Claro/SP, Brasil
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Tc1-like Transposase Thm3 of Silver Carp (Hypophthalmichthys molitrix) Can Mediate Gene Transposition in the Genome of Blunt Snout Bream (Megalobrama amblycephala). G3-GENES GENOMES GENETICS 2015; 5:2601-10. [PMID: 26438298 PMCID: PMC4683633 DOI: 10.1534/g3.115.020933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tc1-like transposons consist of an inverted repeat sequence flanking a transposase gene that exhibits similarity to the mobile DNA element, Tc1, of the nematode, Caenorhabditis elegans. They are widely distributed within vertebrate genomes including teleost fish; however, few active Tc1-like transposases have been discovered. In this study, 17 Tc1-like transposon sequences were isolated from 10 freshwater fish species belonging to the families Cyprinidae, Adrianichthyidae, Cichlidae, and Salmonidae. We conducted phylogenetic analyses of these sequences using previously isolated Tc1-like transposases and report that 16 of these elements comprise a new subfamily of Tc1-like transposons. In particular, we show that one transposon, Thm3 from silver carp (Hypophthalmichthys molitrix; Cyprinidae), can encode a 335-aa transposase with apparently intact domains, containing three to five copies in its genome. We then coinjected donor plasmids harboring 367 bp of the left end and 230 bp of the right end of the nonautonomous silver carp Thm1 cis-element along with capped Thm3 transposase RNA into the embryos of blunt snout bream (Megalobrama amblycephala; one- to two-cell embryos). This experiment revealed that the average integration rate could reach 50.6% in adult fish. Within the blunt snout bream genome, the TA dinucleotide direct repeat, which is the signature of Tc1-like family of transposons, was created adjacent to both ends of Thm1 at the integration sites. Our results indicate that the silver carp Thm3 transposase can mediate gene insertion by transposition within the genome of blunt snout bream genome, and that this occurs with a TA position preference.
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Kuraku S, Qiu H, Meyer A. Horizontal transfers of Tc1 elements between teleost fishes and their vertebrate parasites, lampreys. Genome Biol Evol 2012; 4:929-36. [PMID: 22887124 PMCID: PMC3516227 DOI: 10.1093/gbe/evs069] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Horizontal gene transfer (HGT) has been recognized to be an important mechanism that shaped the evolution and genomes of prokaryotes and unicellular eukaryotes. However, HGT is regarded to be exceedingly rare among eukaryotes. We discovered massive transfers of a DNA transposon, a Tc1 element encoding a transposase, between multiple teleost fishes and lampreys that last shared a common ancestor over 500 Ma. Members of this group of Tc1 elements were found to exhibit a mosaic phylogenetic distribution, yet their sequences were highly similar even between distantly related lineages (95%-99% identity). Our molecular phylogenetic analyses suggested that horizontal transfers of this element happened repeatedly, involving multiple teleost fishes that are phylogenetically only distantly related. Interestingly, almost all the affected teleost lineages are also known to be subject to lamprey parasitism, suggesting that the horizontal transfers between vertebrates might have occurred through parasite-host interaction. The genomes of several northern hemisphere lamprey species, including that of the sea lamprey (Petromyzon marinus), were found to contain thousands of copies of the foreign elements. Impact of this event is discussed in relation to other peculiar genomic features of lampreys.
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Poćwierz-Kotus A, Burzyński A, Wenne R. Identification of a Tc1-like transposon integration site in the genome of the flounder (Platichthys flesus): a novel use of an inverse PCR method. Mar Genomics 2010; 3:45-50. [PMID: 21798196 DOI: 10.1016/j.margen.2010.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/12/2010] [Accepted: 03/30/2010] [Indexed: 12/20/2022]
Abstract
The inverse PCR method has been developed and applied employed for the identification of the integration sites of the Tc1-like transposons in the genome of the flounder, Platichthys flesus. One Tc1-like insertion instance was recognized and characterized, demonstrating an efficiency of the method for determining of transposon integration sites. The similarity of the sequence flanking transposon (SFT) to reverse transcriptase sequences (RVT) was demonstrated. It is likely that the insertion took place within currently degenerated LINE (long interspersed nuclear elements) retrotransposon.
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Affiliation(s)
- Anita Poćwierz-Kotus
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy, Sopot, Poland.
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Clark KJ, Carlson DF, Leaver MJ, Foster LK, Fahrenkrug SC. Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells. Nucleic Acids Res 2009; 37:1239-47. [PMID: 19136468 PMCID: PMC2651795 DOI: 10.1093/nar/gkn1025] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Tc1/mariner family of DNA transposons is widespread across fungal, plant and animal kingdoms, and thought to contribute to the evolution of their host genomes. To date, an active Tc1 transposon has not been identified within the native genome of a vertebrate. We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells. In transposition assays, we found that the Passport transposon system improved stable cellular transgenesis by 40-fold, has an apparent preference for insertion into genes, and is subject to overproduction inhibition like other Tc1 elements. Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active. The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements.
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Affiliation(s)
- Karl J Clark
- Department of Animal Science, University of Minnesota, St Paul, MN 55108, USA
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