1
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Angeloni A, Fissette S, Kaya D, Hammond JM, Gamaarachchi H, Deveson IW, Klose RJ, Li W, Zhang X, Bogdanovic O. Extensive DNA methylome rearrangement during early lamprey embryogenesis. Nat Commun 2024; 15:1977. [PMID: 38438347 PMCID: PMC10912607 DOI: 10.1038/s41467-024-46085-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
DNA methylation (5mC) is a repressive gene regulatory mark widespread in vertebrate genomes, yet the developmental dynamics in which 5mC patterns are established vary across species. While mammals undergo two rounds of global 5mC erasure, teleosts, for example, exhibit localized maternal-to-paternal 5mC remodeling. Here, we studied 5mC dynamics during the embryonic development of sea lamprey, a jawless vertebrate which occupies a critical phylogenetic position as the sister group of the jawed vertebrates. We employed 5mC quantification in lamprey embryos and tissues, and discovered large-scale maternal-to-paternal epigenome remodeling that affects ~30% of the embryonic genome and is predominantly associated with partially methylated domains. We further demonstrate that sequences eliminated during programmed genome rearrangement (PGR), are hypermethylated in sperm prior to the onset of PGR. Our study thus unveils important insights into the evolutionary origins of vertebrate 5mC reprogramming, and how this process might participate in diverse developmental strategies.
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Affiliation(s)
- Allegra Angeloni
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Skye Fissette
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Deniz Kaya
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jillian M Hammond
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, NSW, Australia
| | - Hasindu Gamaarachchi
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, NSW, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Ira W Deveson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Xiaotian Zhang
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, USA
- University of Texas Health Science Center, Houston, TX, USA
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.
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2
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Smith B, Walling A, Schwartz R. Phylogenomic investigation of lampreys (Petromyzontiformes). Mol Phylogenet Evol 2023; 189:107942. [PMID: 37804959 DOI: 10.1016/j.ympev.2023.107942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
The history of lamprey evolution has been contentious due to limited morphological differentiation and limited genetic data. Available data has produced inconsistent results, including in the relationship among northern and southern species and the monophyly of putative clades. Here we use whole genome sequence data sourced from a public database to identify orthologs for 11 lamprey species from across the globe and build phylogenies. The phylogeny showed a clear separation between northern and southern lamprey species, which contrasts with some prior work. We also find that the phylogenetic relationships of our samples of two genera, Lethenteron and Eudontomyzon, deviate from the taxonomic classification of these species, suggesting that they require reclassification.
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Affiliation(s)
- Brianna Smith
- Department of Biological Sciences, College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, United States
| | - Alexandra Walling
- Department of Biological Sciences, College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, United States
| | - Rachel Schwartz
- Department of Biological Sciences, College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, United States.
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3
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Novel selectively amplified DNA sequences in the germline genome of the Japanese hagfish, Eptatretus burgeri. Sci Rep 2022; 12:21373. [PMID: 36494570 PMCID: PMC9734144 DOI: 10.1038/s41598-022-26007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
In the Japanese hagfish Eptatretus burgeri, 16 chromosomes (eliminated [E]-chromosomes) have been lost in somatic cells (2n = 36), which is equivalent to approx. 21% of the genomic DNA in germ cells (2n = 52). At least seven of the 12 eliminated repetitive DNA families isolated in eight hagfish species were selectively amplified in the germline genome of this species. One of them, EEEb1 (eliminated element of E. burgeri 1) is exclusively localized on all E-chromosomes. Herein, we identified four novel eliminated repetitive DNA families (named EEEb3-6) through PCR amplification and suppressive subtractive hybridization (SSH) combined with Southern-blot hybridization. EEEb3 was mosaic for 5S rDNA and SINE elements. EEEb4 was GC-rich repeats and has one pair of direct and inverted repeats, whereas EEEb5 and EEEb6 were AT-rich repeats with one pair and two pairs of sub-repeats, respectively. Interestingly, all repeat classes except EEEb3 were transcribed in the testes, although no open reading frames (ORF) were identified. We conducted fluorescence in situ hybridization (FISH) to examine the chromosomal localizations of EEEb3-6 and EEEb2, which was previously isolated from the germline genome of E. burgeri. All sequences were only found on all EEEb1-positive E-chromosomes. Copy number estimation of the repeated elements by slot-blot hybridization revealed that (i) the EEEb1-6 family members occupied 39.9% of the total eliminated DNA, and (ii) a small number of repeats were retained in somatic cells, suggesting that there is incomplete elimination of the repeated elements. These results provide new insights into the mechanisms involved in the chromosome elimination and the evolution of E-chromosomes.
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4
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Kloc M, Kubiak JZ, Ghobrial RM. Natural genetic engineering: A programmed chromosome/DNA elimination. Dev Biol 2022; 486:15-25. [DOI: 10.1016/j.ydbio.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/16/2022] [Accepted: 03/17/2022] [Indexed: 11/03/2022]
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5
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Drotos KH, Zagoskin MV, Kess T, Gregory TR, Wyngaard GA. Throwing away DNA: programmed downsizing in somatic nuclei. Trends Genet 2022; 38:483-500. [DOI: 10.1016/j.tig.2022.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
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6
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Srikulnath K, Ahmad SF, Singchat W, Panthum T. Why Do Some Vertebrates Have Microchromosomes? Cells 2021; 10:2182. [PMID: 34571831 PMCID: PMC8466491 DOI: 10.3390/cells10092182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022] Open
Abstract
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.
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Affiliation(s)
- Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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7
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Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution. Nat Commun 2021; 12:4489. [PMID: 34301952 PMCID: PMC8302630 DOI: 10.1038/s41467-021-24573-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.
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8
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Abstract
Over the last few decades, an increasing number of vertebrate taxa have been identified that undergo programmed genome rearrangement, or programmed DNA loss, during development. In these organisms, the genome of germ cells is often reproducibly different from the genome of all other cells within the body. Although we clearly have not identified all vertebrate taxa that undergo programmed genome loss, the list of species known to undergo loss now represents ∼10% of vertebrate species, including several basally diverging lineages. Recent studies have shed new light on the targets and mechanisms of DNA loss and their association with canonical modes of DNA silencing. Ultimately, expansion of these studies into a larger collection of taxa will aid in reconstructing patterns of shared/independent ancestry of programmed DNA loss in the vertebrate lineage, as well as more recent evolutionary events that have shaped the structure and content of eliminated DNA.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; , ,
| | | | - Cody Saraceno
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; , ,
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9
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Bista I, McCarthy SA, Wood J, Ning Z, Detrich III HW, Desvignes T, Postlethwait J, Chow W, Howe K, Torrance J, Smith M, Oliver K, Miska EA, Durbin R. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861). Wellcome Open Res 2020; 5:148. [PMID: 33195818 PMCID: PMC7649722 DOI: 10.12688/wellcomeopenres.16012.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2020] [Indexed: 01/06/2023] Open
Abstract
We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is 609 megabases, with the majority of the assembly scaffolded into 24 chromosomal pseudomolecules. Gene annotation on Ensembl of this assembly has identified 21,662 coding genes.
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Affiliation(s)
- Iliana Bista
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Shane A. McCarthy
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | | | - Zemin Ning
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - H. William Detrich III
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Massachusetts, MA 01908, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - William Chow
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | | | | | - Karen Oliver
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Vertebrate Genomes Project Consortium
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Massachusetts, MA 01908, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Eric A. Miska
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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10
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Timoshevskiy VA, Timoshevskaya NY, Smith JJ. Germline-Specific Repetitive Elements in Programmatically Eliminated Chromosomes of the Sea Lamprey ( Petromyzon marinus). Genes (Basel) 2019; 10:E832. [PMID: 31652530 PMCID: PMC6826781 DOI: 10.3390/genes10100832] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/17/2019] [Accepted: 10/19/2019] [Indexed: 12/26/2022] Open
Abstract
The sea lamprey (Petromyzon marinus) is one of few vertebrate species known to reproducibly eliminate large fractions of its genome during normal embryonic development. This germline-specific DNA is lost in the form of large fragments, including entire chromosomes, and available evidence suggests that DNA elimination acts as a permanent silencing mechanism that prevents the somatic expression of a specific subset of "germline" genes. However, reconstruction of eliminated regions has proven to be challenging due to the complexity of the lamprey karyotype. We applied an integrative approach aimed at further characterization of the large-scale structure of eliminated segments, including: (1) in silico identification of germline-enriched repeats; (2) mapping the chromosomal location of specific repetitive sequences in germline metaphases; and (3) 3D DNA/DNA-hybridization to embryonic lagging anaphases, which permitted us to both verify the specificity of elements to physically eliminated chromosomes and characterize the subcellular organization of these elements during elimination. This approach resulted in the discovery of several repetitive elements that are found exclusively on the eliminated chromosomes, which subsequently permitted the identification of 12 individual chromosomes that are programmatically eliminated during early embryogenesis. The fidelity and specificity of these highly abundant sequences, their distinctive patterning in eliminated chromosomes, and subcellular localization in elimination anaphases suggest that these sequences might contribute to the specific targeting of chromosomes for elimination or possibly in molecular interactions that mediate their decelerated poleward movement in chromosome elimination anaphases, isolation into micronuclei and eventual degradation.
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Affiliation(s)
| | | | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA.
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11
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Sousa RPCD, Furo IDO, O'Brien PCM, Oliveira-Filho AB, Vallinoto M, de Oliveira EH, Silva-Oliveira GC. Genomic Organization of the Repetitive Sequences in Centropomus undecimalis (Perciformes, Centropomidae): Implications for Hybridization and Aquaculture Programs. Zebrafish 2019; 16:415-420. [PMID: 31188085 DOI: 10.1089/zeb.2018.1724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The family Centropomidae includes a number of fish species of high commercial value. One of these species, Centropomus undecimalis, is a target of artisanal, industrial, and sports fisheries and has also considerable potential for captive breeding, which has led to its inclusion in several aquaculture programs. While the biology and ecology of C. undecimalis are relatively well documented, few karyological data are available on this species, and they are still scarce for other centropomids. The few chromosomal data available on this family indicate a conserved karyotype 2n = 48, but it is unclear whether the chromosome microstructure is also conserved. In this study, new cytogenetic data are presented on C. undecimalis from the Amazon coastal zone, including C-banding, Ag-NOR, in situ hybridization with repetitive DNA probes (5S and 18S ribosomal genes), and telomeric (TTAGGG)n sequences. The diploid number of the species was 2n = 48, with heterochromatic blocks in the centromeric and pericentromeric regions, as well as distal signals; the nucleolus organizer regions (NORs) were associated with the heterochromatic region. The 18S and 5S recombinant DNA (rDNA) clusters were located in the distal region of chromosome pairs 1 and 11, respectively. The similarities of the karyotype macrostructure found among the centropomid species reinforce their exceptional chromosomal stability. However, the presence of heterochromatic blocks and location of NORs suggest the occurrence of structural rearrangements, which indicates that evolutionary dynamics at the microstructural level in this group may be relatively complex and should be evaluated carefully in any study that targets the production of hybrids for aquaculture.
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Affiliation(s)
- Rodrigo P C de Sousa
- 1Faculty of Natural Sciences, Institute of Coastal Studies, Federal University of Pará. Bragança PA, Brazil
| | - Ivanete de O Furo
- 2Faculty of Natural Sciences, Institute of Exact and Natural Sciences, Federal University of Pará. Belém PA, Brazil.,3Tissue Culture Laboratory, Environment Section, Evandro Chagas Institute, Ananindeua PA, Brazil
| | | | - Aldemir B Oliveira-Filho
- 1Faculty of Natural Sciences, Institute of Coastal Studies, Federal University of Pará. Bragança PA, Brazil
| | - Marcelo Vallinoto
- 1Faculty of Natural Sciences, Institute of Coastal Studies, Federal University of Pará. Bragança PA, Brazil.,5Associated Laboratory, Center for Research in Biodiversity and Genetic Resources, Agrarian Campus of Vairão, University of Porto, Vairão, Portugal
| | - Edivaldo H de Oliveira
- 2Faculty of Natural Sciences, Institute of Exact and Natural Sciences, Federal University of Pará. Belém PA, Brazil.,3Tissue Culture Laboratory, Environment Section, Evandro Chagas Institute, Ananindeua PA, Brazil
| | - Gláucia C Silva-Oliveira
- 1Faculty of Natural Sciences, Institute of Coastal Studies, Federal University of Pará. Bragança PA, Brazil
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12
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The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nat Genet 2018; 50:270-277. [PMID: 29358652 PMCID: PMC5805609 DOI: 10.1038/s41588-017-0036-1] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/15/2017] [Indexed: 12/24/2022]
Abstract
The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary datasets. Analysis of this highly contiguous (chromosome-scale) assembly reveals that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by Polycomb Repressive Complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and repressive/bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys’ unique biology and evolutionary/comparative perspective.
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13
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Ishijima J, Uno Y, Nunome M, Nishida C, Kuraku S, Matsuda Y. Molecular cytogenetic characterization of chromosome site-specific repetitive sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae). DNA Res 2017; 24:93-101. [PMID: 28025319 PMCID: PMC5381345 DOI: 10.1093/dnares/dsw053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 11/02/2016] [Indexed: 12/19/2022] Open
Abstract
All extant lamprey karyotypes are characterized by almost all dot-shaped microchromosomes. To understand the molecular basis of chromosome structure in lampreys, we performed chromosome C-banding and silver staining and chromosome mapping of the 18S–28S and 5S ribosomal RNA (rRNA) genes and telomeric TTAGGG repeats in the Arctic lamprey (Lethenteron camtschaticum). In addition, we cloned chromosome site-specific repetitive DNA sequences and characterized them by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. Three types of repetitive sequences were detected; a 200-bp AT-rich repetitive sequence, LCA-EcoRIa that co-localized with the 18S–28S rRNA gene clusters of 3 chromosomal pairs; a 364-bp AT-rich LCA-EcoRIb sequence that showed homology to the EcoRI sequence family from the sea lamprey (Petromyzon marinus), which contains short repeats as centromeric motifs; and a GC-rich 702-bp LCA-ApaI sequence that was distributed on nearly all chromosomes and showed significant homology with the integrase-coding region of a Ty3/Gypsy family long terminal repeat (LTR) retrotransposon. All three repetitive sequences are highly conserved within the Petromyzontidae or within Petromyzontidae and Mordaciidae. Molecular cytogenetic characterization of these site-specific repeats showed that they may be correlated with programed genome rearrangement (LCA-EcoRIa), centromere structure and function (LCA-EcoRIb), and site-specific amplification of LTR retroelements through homogenization between non-homologous chromosomes (LCA-ApaI).
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Affiliation(s)
- Junko Ishijima
- Laboratory of Animal Cytogenetics, Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoshinobu Uno
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Chizuko Nishida
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe 650-0047, Japan
| | - Yoichi Matsuda
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- To whom correspondence should be addressed. Tel. +81 52 789 4100. Fax. +81 52 789 4099.
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14
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Eslami Rasekh M, Chiatante G, Miroballo M, Tang J, Ventura M, Amemiya CT, Eichler EE, Antonacci F, Alkan C. Discovery of large genomic inversions using long range information. BMC Genomics 2017; 18:65. [PMID: 28073353 PMCID: PMC5223412 DOI: 10.1186/s12864-016-3444-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly due to the fact that breakpoints of such events typically lie within segmental duplications or common repeats, which reduces the mappability of short reads. The algorithms developed within the 1000 Genomes Project to identify inversions are limited to relatively short inversions, and there are currently no available algorithms to discover large inversions using high throughput sequencing technologies. RESULTS Here we propose a novel algorithm, VALOR, to discover large inversions using new sequencing methods that provide long range information such as 10X Genomics linked-read sequencing, pooled clone sequencing, or other similar technologies that we commonly refer to as long range sequencing. We demonstrate the utility of VALOR using both pooled clone sequencing and 10X Genomics linked-read sequencing generated from the genome of an individual from the HapMap project (NA12878). We also provide a comprehensive comparison of VALOR against several state-of-the-art structural variation discovery algorithms that use whole genome shotgun sequencing data. CONCLUSIONS In this paper, we show that VALOR is able to accurately discover all previously identified and experimentally validated large inversions in the same genome with a low false discovery rate. Using VALOR, we also predicted a novel inversion, which we validated using fluorescent in situ hybridization. VALOR is available at https://github.com/BilkentCompGen/VALOR.
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Affiliation(s)
- Marzieh Eslami Rasekh
- Department of Computer Engineering, Bilkent University, Bilkent, 06800, Ankara, Turkey
| | - Giorgia Chiatante
- Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Mattia Miroballo
- Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Joyce Tang
- Benaroya Research Institute, 1201 Ninth Avenue, 98101, Seattle, WA, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Chris T Amemiya
- Benaroya Research Institute, 1201 Ninth Avenue, 98101, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, 98195, Seattle, WA, USA
| | - Francesca Antonacci
- Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy.
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Bilkent, 06800, Ankara, Turkey.
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15
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Abstract
The germ track is the cellular path by which genes are transmitted to future generations whereas somatic cells die with their body and do not leave direct descendants. Transposable elements (TEs) evolve to be silent in somatic cells but active in the germ track. Thus, the performance of most bodily functions by a sequestered soma reduces organismal costs of TEs. Flexible forms of gene regulation are permissible in the soma because of the self-imposed silence of TEs, but strict licensing of transcription and translation is maintained in the germ track to control proliferation of TEs. Delayed zygotic genome activation (ZGA) and maternally inherited germ granules are adaptations that enhance germ-track security. Mammalian embryos exhibit very early ZGA associated with extensive mobilization of retroelements. This window of vulnerability to retrotransposition in early embryos is an indirect consequence of evolutionary conflicts within the mammalian genome over postzygotic maternal provisioning.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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16
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Yan X, Meng W, Wu F, Xu A, Chen S, Huang S. The Nuclear DNA Content and Genetic Diversity of Lampetra morii. PLoS One 2016; 11:e0157494. [PMID: 27388621 PMCID: PMC4936738 DOI: 10.1371/journal.pone.0157494] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/30/2016] [Indexed: 12/14/2022] Open
Abstract
We investigated the nuclear DNA content and genetic diversity of a river lamprey, the Korean lamprey Lampetra morii, which is distributed in the northeast of China. L. morii spends its whole life cycle in fresh water, and its adult size is relatively small (~160 mm long) compared with that of other lampreys. The haploid nuclear DNA content of L. morii is 1.618 pg (approximately 1.582 Gb) in germline cells, and there is ~15% germline DNA loss in somatic cells. These values are significantly smaller than those of Petromyzon marinus, a lamprey with a published draft genome. The chromosomes of L. morii are small and acrocentric, with a diploid modal number of 2n = 132, lower than some other lampreys. Sequence and AFLP analyses suggest that the allelic polymorphism rate (~0.14% based on examined nuclear and mitochondrial DNA sequences) of L. morii is much lower than that (~2%) of P. marinus. Phylogenetic analysis based on a mitochondrial DNA fragment confirms that L. morii belongs to the genus Lampetra, which, together with the genus Lethenteron, forms a sister group to P. marinus. These genetic background data are valuable for subsequent genetic and genomic research on L. morii.
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Affiliation(s)
- Xinyu Yan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Wenbin Meng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Fenfang Wu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- * E-mail:
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17
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Timoshevskiy VA, Herdy JR, Keinath MC, Smith JJ. Cellular and Molecular Features of Developmentally Programmed Genome Rearrangement in a Vertebrate (Sea Lamprey: Petromyzon marinus). PLoS Genet 2016; 12:e1006103. [PMID: 27341395 PMCID: PMC4920378 DOI: 10.1371/journal.pgen.1006103] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/13/2016] [Indexed: 11/21/2022] Open
Abstract
The sea lamprey (Petromyzon marinus) represents one of the few vertebrate species known to undergo large-scale programmatic elimination of genomic DNA over the course of its normal development. Programmed genome rearrangements (PGRs) result in the reproducible loss of ~20% of the genome from somatic cell lineages during early embryogenesis. Studies of PGR hold the potential to provide novel insights related to the maintenance of genome stability during the cell cycle and coordination between mechanisms responsible for the accurate distribution of chromosomes into daughter cells, yet little is known regarding the mechanistic basis or cellular context of PGR in this or any other vertebrate lineage. Here we identify epigenetic silencing events that are associated with the programmed elimination of DNA and describe the spatiotemporal dynamics of PGR during lamprey embryogenesis. In situ analyses reveal that the earliest DNA methylation (and to some extent H3K9 trimethylation) events are limited to specific extranuclear structures (micronuclei) containing eliminated DNA. During early embryogenesis a majority of micronuclei (~60%) show strong enrichment for repressive chromatin modifications (H3K9me3 and 5meC). These analyses also led to the discovery that eliminated DNA is packaged into chromatin that does not migrate with somatically retained chromosomes during anaphase, a condition that is superficially similar to lagging chromosomes observed in some cancer subtypes. Closer examination of “lagging” chromatin revealed distributions of repetitive elements, cytoskeletal contacts and chromatin contacts that provide new insights into the cellular mechanisms underlying the programmed loss of these segments. Our analyses provide additional perspective on the cellular and molecular context of PGR, identify new structures associated with elimination of DNA and reveal that PGR is completed over the course of several successive cell divisions. Lampreys possess a fascinating genome biology wherein large portions of the genome, including large numbers of genes, are programmatically deleted during development. The lamprey therefore represents a uniquely informative system with respect to several broad areas of biology, including genome stability/rearrangement, epigenetic silencing, and the establishment and maintenance of pluripotency. However, little is known regarding the cellular context or mechanism of deletion, partly due to the challenges of observing rearrangements in situ. Here we present analyses and new techniques that significantly advance our understanding of the subcellular context of programmed rearrangements and interactions between programmed deletion and canonical DNA silencing mechanisms. These analyses demonstrate that DNA elimination occurs earlier in embryogenesis than was previously recognized and reveal several new cellular and molecular aspects of programmed DNA loss. Specifically we show that eliminated DNA exhibits a unique migration pattern during cell division, is packaged into discreet subcellular structures later in the cell cycle, and undergoes epigenetic silencing through DNA and histone methylation. These observations provide new insight into the mechanisms underlying programmed DNA loss and suggest a functional link between programmed DNA loss and other, more conserved gene silencing pathways.
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Affiliation(s)
| | - Joseph R. Herdy
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America
- Laboratory of Genetics, The Salk Institute, La Jolla, California, United States of America
| | - Melissa C. Keinath
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jeramiah J. Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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18
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Bryant SA, Herdy JR, Amemiya CT, Smith JJ. Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus). Mol Biol Evol 2016; 33:2337-44. [PMID: 27288344 DOI: 10.1093/molbev/msw104] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The sea lamprey (Petromyzon marinus) is a basal vertebrate that undergoes developmentally programmed genome rearrangements (PGRs) during early development. These events facilitate the elimination of ∼20% of the genome from the somatic cell lineage, resulting in distinct somatic and germline genomes. Thus far only a handful of germline-specific genes have been definitively identified within the estimated 500 Mb of DNA that is deleted during PGR, although a few thousand germline-specific genes are thought to exist. To improve our understanding of the evolutionary/developmental logic of PGR, we generated computational predictions to identify candidate germline-specific genes within a new transcriptomic dataset derived from adult germline and the early embryonic stages during which PGR occurs. Follow-up validation studies identified 44 germline-specific genes and further characterized patterns of transcription and DNA loss during early embryogenesis. Expression analyses reveal that many of these genes are differentially expressed during early embryogenesis and presumably function in the early development of the germline. Ontology analyses indicate that many of these germline-specific genes play known roles in germline development, pluripotency, and oncogenesis (when misexpressed). These studies provide support for the theory that PGR serves to segregate molecular functions related to germline development/pluripotency in order to prevent their potential misexpression in somatic cells. This larger set of eliminated genes also allows us to extend the evolutionary/developmental breadth of this theory, as some deleted genes (or their gnathostome homologs) appear to be associated with the early development of somatic lineages, perhaps through the evolution of novel functions within gnathostome lineages.
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Affiliation(s)
| | | | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle Department of Biology, University of Washington, Seattle
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19
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Abstract
Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome.
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Affiliation(s)
- David W McCauley
- David W. McCauley ( ) is affiliated with the Department of Biology at the University of Oklahoma, in Norman. Margaret F. Docker and Steve Whyard are affiliated with the Department of Biological Sciences at the University of Manitoba, in Winnipeg, Canada. Weiming Li is affiliated with the Department of Fisheries and Wildlife at Michigan State University, in East Lansing
| | - Margaret F Docker
- David W. McCauley ( ) is affiliated with the Department of Biology at the University of Oklahoma, in Norman. Margaret F. Docker and Steve Whyard are affiliated with the Department of Biological Sciences at the University of Manitoba, in Winnipeg, Canada. Weiming Li is affiliated with the Department of Fisheries and Wildlife at Michigan State University, in East Lansing
| | - Steve Whyard
- David W. McCauley ( ) is affiliated with the Department of Biology at the University of Oklahoma, in Norman. Margaret F. Docker and Steve Whyard are affiliated with the Department of Biological Sciences at the University of Manitoba, in Winnipeg, Canada. Weiming Li is affiliated with the Department of Fisheries and Wildlife at Michigan State University, in East Lansing
| | - Weiming Li
- David W. McCauley ( ) is affiliated with the Department of Biology at the University of Oklahoma, in Norman. Margaret F. Docker and Steve Whyard are affiliated with the Department of Biological Sciences at the University of Manitoba, in Winnipeg, Canada. Weiming Li is affiliated with the Department of Fisheries and Wildlife at Michigan State University, in East Lansing
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20
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Smith JJ, Keinath MC. The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications. Genome Res 2015; 25:1081-90. [PMID: 26048246 PMCID: PMC4509993 DOI: 10.1101/gr.184135.114] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 06/03/2015] [Indexed: 01/17/2023]
Abstract
It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ∼550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ∼ 99), spanning a total of 5570.25 cM. Comparative mapping data yield strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionarily independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations of vertebrate evolution.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Melissa C Keinath
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
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21
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Ren J, Chung-Davidson YW, Yeh CY, Scott C, Brown T, Li W. Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey. BMC Genomics 2015; 16:436. [PMID: 26047617 PMCID: PMC4458048 DOI: 10.1186/s12864-015-1677-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 06/01/2015] [Indexed: 11/26/2022] Open
Abstract
Background Lampreys are extant representatives of the jawless vertebrate lineage that diverged from jawed vertebrates around 500 million years ago. Lamprey genomes contain information crucial for understanding the evolution of gene families in vertebrates. The ATP-binding cassette (ABC) gene family is found from prokaryotes to eukaryotes. The recent availability of two lamprey draft genomes from sea lamprey Petromyzon marinus and Japanese lamprey Lethenteron japonicum presents an opportunity to infer early evolutionary events of ABC genes in vertebrates. Results We conducted a genome-wide survey of the ABC gene family in two lamprey draft genomes. A total of 37 ABC transporters were identified and classified into seven subfamilies; namely seven ABCA genes, 10 ABCB genes, 10 ABCC genes, three ABCD genes, one ABCE gene, three ABCF genes, and three ABCG genes. The ABCA subfamily has expanded from three genes in sea squirts, seven and nine in lampreys and zebrafish, to 13 and 16 in human and mouse. Conversely, the multiple copies of ABCB1-, ABCG1-, and ABCG2-like genes found in sea squirts have contracted in the other species examined. ABCB2 and ABCB3 seem to be new additions in gnathostomes (not in sea squirts or lampreys), which coincides with the emergence of the gnathostome-specific adaptive immune system. All the genes in the ABCD, ABCE and ABCF subfamilies were conserved and had undergone limited duplication and loss events. In the sea lamprey transcriptomes, the ABCE and ABCF gene subfamilies were ubiquitously and highly expressed in all tissues while the members in other gene subfamilies were differentially expressed. Conclusions Thirteen more lamprey ABC transporter genes were identified in this study compared with a previous study. By concatenating the same gene sequences from the two lampreys, more full length sequences were obtained, which significantly improved both the assignment of gene names and the phylogenetic trees compared with a previous analysis using partial sequences. The ABC gene subfamilies in chordates have undergone obvious expansion or contraction. The ABCA subfamily showed the highest gene expansion rate during chordate evolution. The evolution of ABC transporters in lampreys requires further evaluation because the present results are based on a draft genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1677-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianfeng Ren
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA.
| | - Chu-Yin Yeh
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA.
| | - Camille Scott
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
| | - Titus Brown
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - Weiming Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China. .,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA.
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22
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Cytogenetic evidences of genome rearrangement and differential epigenetic chromatin modification in the sea lamprey (Petromyzon marinus). Genetica 2014; 142:545-54. [PMID: 25432678 DOI: 10.1007/s10709-014-9802-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/22/2014] [Indexed: 10/24/2022]
Abstract
This work explores both the chromatin loss and the differential genome methylation in the sea lamprey (Petromyzon marinus) from a molecular cytogenetic point of view. Fluorescent in situ hybridization experiments on meiotic bivalents and mitotic chromosomes corroborate the chromatin loss previously observed during the development of the sea lamprey and demonstrate that the elimination affects not only to Germ1 sequences but also to the rpt200 satellite DNA and most part of the major ribosomal DNA present on the germinal line. 5-Methylcytosine immunolocation revealed that the GC-rich heterochromatin is highly methylated in the germ line but significantly less in somatic chromosomes. These findings not only support previous observations about genome rearrangements but also give new information about epigenetic changes in P. marinus. The key position of lampreys in the vertebrate phylogenetic tree makes them an interesting taxon to provide relevant information about genome evolution in vertebrates.
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23
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Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nat Genet 2014; 46:1293-302. [PMID: 25326701 PMCID: PMC4244265 DOI: 10.1038/ng.3120] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 09/25/2014] [Indexed: 12/14/2022]
Abstract
Recurrent deletions of chromosome 15q13.3 associate with intellectual disability, schizophrenia, autism and epilepsy. To gain insight into its instability, we sequenced the region in patients, normal individuals and nonhuman primates. We discovered five structural configurations of the human chromosome 15q13.3 region ranging in size from 2 to 3 Mbp. These configurations arose recently (~0.5–0.9 million years ago) as a result of human-specific expansions of segmental duplications and two independent inversion events. All inversion breakpoints map near GOLGA8 core duplicons—a ~14 kbp primate-specific chromosome 15 repeat that became organized into larger palindromic structures. GOLGA8-flanked palindromes also demarcate the breakpoints of recurrent 15q13.3 microdeletions, the expansion of chromosome 15 segmental duplications in the human lineage, and independent structural changes in apes. The significant clustering (p=0.002) of breakpoints provides mechanistic evidence for the role of this core duplicon and its palindromic architecture in promoting evolutionary and disease-related instability of chromosome 15.
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24
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Wang J, Davis RE. Programmed DNA elimination in multicellular organisms. Curr Opin Genet Dev 2014; 27:26-34. [PMID: 24886889 DOI: 10.1016/j.gde.2014.03.012] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/17/2014] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
Abstract
Genetic information typically remains constant in all cells throughout the life cycle of most organisms. However, there are exceptions where DNA elimination is an integral, developmental program for some organisms, associated with generating distinct germline versus somatic genomes. Programmed DNA elimination occurs in unicellular ciliates and diverse metazoa ranging from nematodes to vertebrates. DNA elimination can occur through chromosome breakage and selective loss of chromosome regions or the elimination of individual chromosomes. Recent studies provide compelling evidence that DNA elimination is a novel form of gene silencing, dosage compensation, and sex determination. Further identification of the eliminated sequences, genome changes, and in depth characterization of this phenomenon in diverse metazoans is needed to shed new light on the functions and mechanisms of this regulated process.
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Affiliation(s)
- Jianbin Wang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, United States.
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, United States.
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25
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Green SA, Bronner ME. The lamprey: a jawless vertebrate model system for examining origin of the neural crest and other vertebrate traits. Differentiation 2014; 87:44-51. [PMID: 24560767 PMCID: PMC3995830 DOI: 10.1016/j.diff.2014.02.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 01/26/2014] [Accepted: 02/04/2014] [Indexed: 11/15/2022]
Abstract
Lampreys are a group of jawless fishes that serve as an important point of comparison for studies of vertebrate evolution. Lampreys and hagfishes are agnathan fishes, the cyclostomes, which sit at a crucial phylogenetic position as the only living sister group of the jawed vertebrates. Comparisons between cyclostomes and jawed vertebrates can help identify shared derived (i.e. synapomorphic) traits that might have been inherited from ancestral early vertebrates, if unlikely to have arisen convergently by chance. One example of a uniquely vertebrate trait is the neural crest, an embryonic tissue that produces many cell types crucial to vertebrate features, such as the craniofacial skeleton, pigmentation of the skin, and much of the peripheral nervous system (Gans and Northcutt, 1983). Invertebrate chordates arguably lack unambiguous neural crest homologs, yet have cells with some similarities, making comparisons with lampreys and jawed vertebrates essential for inferring characteristics of development in early vertebrates, and how they may have evolved from nonvertebrate chordates. Here we review recent research on cyclostome neural crest development, including research on lamprey gene regulatory networks and differentiated neural crest fates.
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Affiliation(s)
- Stephen A Green
- California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
| | - Marianne E Bronner
- California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA.
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26
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Decatur WA, Hall JA, Smith JJ, Li W, Sower SA. Insight from the lamprey genome: glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropin-releasing hormone (GnRH). Gen Comp Endocrinol 2013; 192:237-45. [PMID: 23770021 PMCID: PMC8715641 DOI: 10.1016/j.ygcen.2013.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/16/2013] [Accepted: 05/29/2013] [Indexed: 01/05/2023]
Abstract
Study of the ancient lineage of jawless vertebrates is key to understanding the origins of vertebrate biology. The establishment of the neuroendocrine system with the hypothalamic-pituitary axis at its crux is of particular interest. Key neuroendocrine hormones in this system include the pivotal gonadotropin-releasing hormones (GnRHs) responsible for controlling reproduction via the pituitary. Previous data incorporating several lines of evidence showed all known vertebrate GnRHs were grouped into four paralogous lineages: GnRH1, 2, 3 and 4; with proposed evolutionary paths. Using the currently available lamprey genome assembly, we searched genes of the neuroendocrine system and summarize here the details representing the state of the current lamprey genome assembly. Additionally, we have analyzed in greater detail the evolutionary history of the GnRHs based on the information of the genomic neighborhood of the paralogs in lamprey as compared to other gnathostomes. Significantly, the current evidence suggests that two genome duplication events (both 1R and 2R) that generated the different fish and tetrapod paralogs took place before the divergence of the ancestral agnathans and gnathostome lineages. Syntenic analysis supports this evidence in that the previously-classified type IV GnRHs in lamprey (lGnRH-I and -III) share a common ancestry with GnRH2 and 3, and thus are no longer considered type IV GnRHs. Given the single amino acid difference between lGnRH-II and GnRH2 we propose that a GnRH2-like gene existed before the lamprey/gnathostome split giving rise to lGnRH-II and GnRH2. Furthermore, paralogous type 3 genes (lGnRH-I/III and GnRH3) evolved divergent structure/function in lamprey and gnathostome lineages.
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Affiliation(s)
- Wayne A. Decatur
- Center for Molecular and Comparative Endocrinology and Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Jeffrey A. Hall
- Center for Molecular and Comparative Endocrinology and Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | | | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Stacia A. Sower
- Center for Molecular and Comparative Endocrinology and Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
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27
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Caputo Barucchi V, Giovannotti M, Nisi Cerioni P, Splendiani A. Genome duplication in early vertebrates: insights from agnathan cytogenetics. Cytogenet Genome Res 2013; 141:80-9. [PMID: 23949002 DOI: 10.1159/000354098] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Agnathans represent a remnant of a primitive offshoot of the vertebrates, and the long evolutionary separation between their 2 living groups, namely hagfishes and lampreys, could explain profound biological differences, also in karyotypes and genome sizes. Here, cytogenetic studies available on these vertebrates were summarized and data discussed with reference to the recently demonstrated monophyly of this group and to the 2 events of whole genome duplication (1R and 2R) characterizing the evolution of vertebrates. The comparison of cytogenetic data and phylogenetic relationships among agnathans and gnathostomes seems to support the hypothesis that 1R and 2R occurred before the evolutionary divergence between jawless and jawed vertebrates.
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McKinnon C, Drouin G. Chromatin diminution in the copepod Mesocyclops edax: elimination of both highly repetitive and nonhighly repetitive DNA. Genome 2013; 56:1-8. [PMID: 23379333 DOI: 10.1139/gen-2012-0097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chromatin diminution, a developmentally regulated process of DNA elimination, is found in numerous eukaryotic species. In the copepod Mesocyclops edax, some 90% of its genomic DNA is eliminated during the differentiation of embryonic cells into somatic cells. Previous studies have shown that the eliminated DNA contains highly repetitive sequences. Here, we sequenced DNA fragments from pre- and postdiminution cells to determine whether nonhighly repetitive sequences are also eliminated during the process of chromatin diminution. Comparative analyses of these sequences, as well as the sequences eliminated from the genome of the copepod Cyclops kolensis, show that they all share similar abundances of tandem repeats, dispersed repeats, transposable elements, and various coding and noncoding sequences. This suggests that, in the chromatin diminution observed in M. edax, both highly repetitive and nonhighly repetitive sequences are eliminated and that there is no bias in the type of nonhighly repetitive DNA being eliminated.
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Affiliation(s)
- Christian McKinnon
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, ON K1N 6N5, Canada
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29
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Smith JJ, Baker C, Eichler EE, Amemiya CT. Genetic consequences of programmed genome rearrangement. Curr Biol 2012; 22:1524-9. [PMID: 22818913 PMCID: PMC3427415 DOI: 10.1016/j.cub.2012.06.028] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/03/2012] [Accepted: 06/07/2012] [Indexed: 11/17/2022]
Abstract
The lamprey (Petromyzon marinus) undergoes developmentally programmed genome rearrangements that mediate deletion of∼20% of germline DNA from somatic cells during early embryogenesis. This genomic differentiation of germline and soma is intriguing, because the germline plays a unique biological role wherein it must possess the ability to undergo meiotic recombination and the capacity to differentiate into every cell type. These evolutionarily indispensable functions set the germline at odds with somatic tissues, because factors that promote recombination and pluripotency can potentially disrupt genome integrity or specification of cell fate when misexpressed in somatic cell lineages (e.g., in oncogenesis). Here, we describe the development of new genomic and transcriptomic resources for lamprey and use these to identify hundreds of genes that are targeted for programmed deletion from somatic cell lineages. Transcriptome sequencing and targeted validation studies further confirm that somatically deleted genes function both in adult (meiotic) germline and in the development of primordial germ cells during embryogenesis. Inferred functional information from deleted regions indicates that developmentally programmed rearrangement serves as a (perhaps ancient) biological strategy to ensure segregation of pluripotency functions to the germline, effectively eliminating the potential for somatic misexpression.
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Affiliation(s)
- Jeramiah J Smith
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA.
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King BL, Gillis JA, Carlisle HR, Dahn RD. A natural deletion of the HoxC cluster in elasmobranch fishes. Science 2012; 334:1517. [PMID: 22174244 DOI: 10.1126/science.1210912] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hox proteins are a metazoan-specific family of transcription factors that are required for developmental patterning. The genomic arrangement of Hox genes into four paralogous clusters is a primitive feature of jawed vertebrates. By using high-throughput sequencing, we demonstrate the absence of all HoxC transcripts from embryos of the shark Scyliorhinus canicula and the skate Leucoraja erinacea and the absence of all HoxC genes and two HoxC-associated microRNAs from the genome of L. erinacea. These data suggest a loss of the entire HoxC cluster in elasmobranch fishes and represent evidence for the natural deletion of an entire Hox cluster in vertebrates.
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Affiliation(s)
- Benjamin L King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA.
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31
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Bigot Y, Jegot G, Casteret S, Aupinel P, Tasei JN. DNA modifications and genome rearrangements during the development and sex differentiation of the bumble bee Bombus terrestris. INSECT MOLECULAR BIOLOGY 2011; 20:165-175. [PMID: 20977508 DOI: 10.1111/j.1365-2583.2010.01052.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Bombus terrestris is a bumble bee that, like most hymenopteran species, exhibits ploidy-specific sex determination controlled by a single sex gene. Depending on their ploidy and the queen pheromone repression, the imagoes differentiate into three castes: males, workers and queens. Here, we focus on the differences of genome organization that occur during development and sex differentiation. We found that cytosine methylation is a significant epigenetic factor with profiles that can be correlated with both processes. We also showed that two kinds of genomic rearrangement occur. The first consists of important DNA amplifications that have sequence profiles that differ in the different developmental instars and sexes. In the second kind, DNA losses also occur, at least involving the mosaic transposable element B. terrestris mosaic repeat 1 (BTMR1).
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Affiliation(s)
- Y Bigot
- UMR CNRS 6239, UFR des Sciences et Techniques, Tours, France.
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32
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Caputo V, Giovannotti M, Cerioni PN, Splendiani A, Tagliavini J, Olmo E. Chromosomal study of a lamprey (Lampetra zanandreai Vladykov, 1955) (Petromyzonida: Petromyzontiformes): conventional and FISH analysis. Chromosome Res 2011; 19:481-91. [DOI: 10.1007/s10577-011-9197-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/21/2011] [Accepted: 02/24/2011] [Indexed: 12/22/2022]
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