1
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Quach TK, Taylor MF, Currie PD, Eynon N, Ruparelia AA. Skeletal Muscle Aging: Lessons From Teleosts. J Gerontol A Biol Sci Med Sci 2025; 80:glae052. [PMID: 38367020 PMCID: PMC12080710 DOI: 10.1093/gerona/glae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Indexed: 02/19/2024] Open
Abstract
Aging is the greatest risk factor for a multitude of age-related diseases including sarcopenia-the loss of skeletal muscle mass and strength-which occurs at remarkable rates each year. There is an unmet need not only to understand the mechanisms that drive sarcopenia but also to identify novel therapeutic strategies. Given the ease and affordability of husbandry, along with advances in genomics, genome editing technologies, and imaging capabilities, teleost models are increasingly used for aging and sarcopenia research. Here, we explain how teleost species such as zebrafish, African turquoise killifish, and medaka recapitulate many of the classical hallmarks of sarcopenia, and discuss the various dietary, pharmacological, and genetic approaches that have been used in teleosts to understand the mechanistic basis of sarcopenia.
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Affiliation(s)
- Tuyen K Quach
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Megan F Taylor
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- EMBL Australia, Victorian Node, Monash University, Clayton, Victoria, Australia
| | - Nir Eynon
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Avnika A Ruparelia
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia (Biological Sciences Section)
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2
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Dedukh D, Kulikova T, Dobrovolskaia M, Maslova A, Krasikova A. Lampbrush chromosomes of Danio rerio. Chromosome Res 2025; 33:2. [PMID: 39815120 DOI: 10.1007/s10577-024-09761-z] [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: 10/16/2024] [Revised: 12/15/2024] [Accepted: 12/31/2024] [Indexed: 01/18/2025]
Abstract
Danio rerio, commonly known as zebrafish, is an established model organism for the developmental and cell biology studies. Although significant progress has been made in the analysis of the D. rerio genome, cytogenetic studies face challenges due to the unclear identification of chromosomes. Here, we present a novel approach to the study of the D. rerio karyotype, focusing on the analysis of lampbrush chromosomes isolated from growing oocytes. Lampbrush chromosomes, existing during diplotene, serve as a powerful tool for high-resolution mapping and transcription analysis due to their profound decondensation and remarkable lateral loops decorated by RNA polymerases and ribonucleoprotein (RNP) matrix. In D. rerio, lampbrush chromosomes are about 20 times longer than corresponding metaphase chromosomes. We found that the lampbrush chromosome stage karyotype of D. rerio is generally undifferentiated, except for several bivalents bearing distinct marker structures, including loops with complex RNP matrix and locus-associated nuclear bodies. Locus-associated nuclear bodies were enriched for coilin and snRNAs; the loci where they formed presumably correspond to the histone gene clusters. Further, we observed the accumulation of splicing factors in giant terminal RNP aggregates on one bivalent. DAPI staining of Danio rerio lampbrush chromosomes revealed large and small chromomeres non-uniformly distributed along the axis. For example, D. rerio lampbrush chromosome 4, comprising the sex-determining region, is divided into two halves-with small chromomeres bearing long lateral loops and with large dense chromomeres bearing no or very tiny lateral loops. As centromeres were not distinguishable, we identified centromeric regions in all bivalents by FISH mapping of pericentromeric RFAL1, RFAL2, and RFAM tandem repeats. Through a combination of morphological analysis, immunostaining of marker structures, and centromere mapping, we developed cytological maps of D. rerio lampbrush chromosomes. Finally, by RNA FISH we revealed transcripts of pericentromeric and telomeric tandem repeats at the lampbrush chromosome stage.
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Affiliation(s)
- D Dedukh
- Saint-Petersburg State University, Saint-Petersburg, Russia
- Institute of Animal Physiology and Genetics, Libechov, Czech Republic
| | - T Kulikova
- Saint-Petersburg State University, Saint-Petersburg, Russia
| | | | - A Maslova
- Saint-Petersburg State University, Saint-Petersburg, Russia
| | - A Krasikova
- Saint-Petersburg State University, Saint-Petersburg, Russia.
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3
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Reimão-Pinto MM, Behrens A, Forcelloni S, Fröhlich K, Kaya S, Nedialkova DD. The dynamics and functional impact of tRNA repertoires during early embryogenesis in zebrafish. EMBO J 2024; 43:5747-5779. [PMID: 39402326 PMCID: PMC11574265 DOI: 10.1038/s44318-024-00265-4] [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: 03/07/2024] [Revised: 09/23/2024] [Accepted: 09/27/2024] [Indexed: 11/20/2024] Open
Abstract
Embryogenesis entails dramatic shifts in mRNA translation and turnover that reprogram gene expression during cellular proliferation and differentiation. Codon identity modulates mRNA stability during early vertebrate embryogenesis, but how the composition of tRNA pools is matched to translational demand is unknown. By quantitative profiling of tRNA repertoires in zebrafish embryos during the maternal-to-zygotic transition, we show that zygotic tRNA repertoires are established after the onset of gastrulation, succeeding the major wave of zygotic mRNA transcription. Maternal and zygotic tRNA pools are distinct, but their reprogramming does not result in a better match to the codon content of the zygotic transcriptome. Instead, we find that an increase in global translation at gastrulation sensitizes decoding rates to tRNA supply, thus destabilizing maternal mRNAs enriched in slowly translated codons. Translational activation and zygotic tRNA expression temporally coincide with an increase of TORC1 activity at gastrulation, which phosphorylates and inactivates the RNA polymerase III repressor Maf1a/b. Our data indicate that a switch in global translation, rather than tRNA reprogramming, determines the onset of codon-dependent maternal mRNA decay during zebrafish embryogenesis.
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Affiliation(s)
| | - Andrew Behrens
- Mechanisms of Protein Biogenesis Laboratory, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Sergio Forcelloni
- Mechanisms of Protein Biogenesis Laboratory, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | | | - Selay Kaya
- Mechanisms of Protein Biogenesis Laboratory, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Danny D Nedialkova
- Mechanisms of Protein Biogenesis Laboratory, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, 85748, Garching, Germany.
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4
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Warren WC, Rice ES, X M, Roback E, Keene A, Martin F, Ogeh D, Haggerty L, Carroll RA, McGaugh S, Rohner N. Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. G3 (BETHESDA, MD.) 2024; 14:jkae103. [PMID: 38771704 PMCID: PMC11304944 DOI: 10.1093/g3journal/jkae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/23/2024]
Abstract
The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.
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Affiliation(s)
- Wesley C Warren
- Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Edward S Rice
- Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Maggs X
- Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Emma Roback
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Alex Keene
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rachel A Carroll
- Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Suzanne McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, KU Medical Center, Kansas City, KS 66160, USA
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5
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Wang B, Saleh AA, Yang N, Asare E, Chen H, Wang Q, Chen C, Song C, Gao B. High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of Tetraodontiformes. Animals (Basel) 2024; 14:1425. [PMID: 38791643 PMCID: PMC11117352 DOI: 10.3390/ani14101425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
This study aimed to investigate the evolutionary profile (including diversity, activity, and abundance) of retrotransposons (RTNs) with long terminal repeats (LTRs) in ten species of Tetraodontiformes. These species, Arothron firmamentum, Lagocephalus sceleratus, Pao palembangensis, Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, Takifugu rubripes, Tetraodon nigroviridis, Mola mola, and Thamnaconus septentrionalis, are known for having the smallest genomes among vertebrates. Data mining revealed a high diversity and wide distribution of LTR retrotransposons (LTR-RTNs) in these compact vertebrate genomes, with varying abundances among species. A total of 819 full-length LTR-RTN sequences were identified across these genomes, categorized into nine families belonging to four different superfamilies: ERV (Orthoretrovirinae and Epsilon retrovirus), Copia, BEL-PAO, and Gypsy (Gmr, Mag, V-clade, CsRN1, and Barthez). The Gypsy superfamily exhibited the highest diversity. LTR family distribution varied among species, with Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, and Takifugu rubripes having the highest richness of LTR families and sequences. Additionally, evidence of recent invasions was observed in specific tetraodontiform genomes, suggesting potential transposition activity. This study provides insights into the evolution of LTR retrotransposons in Tetraodontiformes, enhancing our understanding of their impact on the structure and evolution of host genomes.
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Affiliation(s)
- Bingqing Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Ahmed A. Saleh
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
- Animal and Fish Production Department, Faculty of Agriculture (Al-Shatby), Alexandria University, Alexandria 11865, Egypt
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Emmanuel Asare
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Hong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Quan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Bo Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
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6
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Mandal AK. Recent insights into crosstalk between genetic parasites and their host genome. Brief Funct Genomics 2024; 23:15-23. [PMID: 36307128 PMCID: PMC10799329 DOI: 10.1093/bfgp/elac032] [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: 08/04/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2024] Open
Abstract
The bulk of higher order organismal genomes is comprised of transposable element (TE) copies, i.e. genetic parasites. The host-parasite relation is multi-faceted, varying across genomic region (genic versus intergenic), life-cycle stages, tissue-type and of course in health versus pathological state. The reach of functional genomics though, in investigating genotype-to-phenotype relations, has been limited when TEs are involved. The aim of this review is to highlight recent progress made in understanding how TE origin biochemical activity interacts with the central dogma stages of the host genome. Such interaction can also bring about modulation of the immune context and this could have important repercussions in disease state where immunity has a role to play. Thus, the review is to instigate ideas and action points around identifying evolutionary adaptations that the host genome and the genetic parasite have evolved and why they could be relevant.
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Affiliation(s)
- Amit K Mandal
- Corresponding author: A.K. Mandal, Nuffield Department of Surgical Sciences (NDS), University of Oxford, Old Road Campus Research building (ORCRB), Oxford OX3 7DQ, UK. Tel: +44 (0)1865 617123; Fax: +44 (0)1865 768876; E-mail:
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7
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De Paolo R, Munagala U, Cucco F, Sarti S, Pitto L, Martignano F, Conticello SG, Poliseno L. Modified Cas9-Guided Oxford Nanopore Technology Sequencing Uncovers Single and Multiple Transgene Insertion Sites in a Zebrafish Melanoma Model. CRISPR J 2023; 6:489-492. [PMID: 38108521 DOI: 10.1089/crispr.2023.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Affiliation(s)
- Raffaella De Paolo
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Uday Munagala
- Molecular Mechanisms of Oncogenesis Unit, Core Research Laboratory, ISPRO, Florence, Italy
| | - Francesco Cucco
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Samanta Sarti
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
| | | | - Filippo Martignano
- Molecular Mechanisms of Oncogenesis Unit, Core Research Laboratory, ISPRO, Florence, Italy
| | - Silvestro G Conticello
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Molecular Mechanisms of Oncogenesis Unit, Core Research Laboratory, ISPRO, Florence, Italy
| | - Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
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8
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Warren WC, Rice ES, Maggs X, Roback E, Keene A, Martin F, Ogeh D, Haggerty L, Carroll RA, McGaugh S, Rohner N. Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567450. [PMID: 38014157 PMCID: PMC10680795 DOI: 10.1101/2023.11.16.567450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and non-coding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared to other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared to a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.
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Affiliation(s)
- Wesley C. Warren
- Department of Animal Sciences, Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO
| | - Edward S. Rice
- Department of Animal Sciences, Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO
| | - X Maggs
- Department of Animal Sciences, Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO
| | - Emma Roback
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN
| | - Alex Keene
- Department of Biology, Texas AM University, College Station, TX
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rachel A. Carroll
- Department of Animal Sciences, Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO
| | - Suzanne McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, KU Medical Center, Kansas City, KS
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9
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Pinto BJ, Gamble T, Smith CH, Keating SE, Havird JC, Chiari Y. The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly. J Hered 2023; 114:513-520. [PMID: 36869788 PMCID: PMC10445513 DOI: 10.1093/jhered/esad016] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023] Open
Abstract
Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest-quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified 9 of the 19 chromosomal scaffolds were assembled as a near-single contig, whereas the other 10 chromosomes were each scaffolded together from multiple contigs. We qualitatively identified that the percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction of previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
- Department of Biological Sciences, Marquette University, Milwaukee WI, USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN, USA
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee WI, USA
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, USA
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10
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Jimenez Gonzalez A, Baranasic D, Müller F. Zebrafish regulatory genomic resources for disease modelling and regeneration. Dis Model Mech 2023; 16:dmm050280. [PMID: 37529920 PMCID: PMC10417509 DOI: 10.1242/dmm.050280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
In the past decades, the zebrafish has become a disease model with increasing popularity owing to its advantages that include fast development, easy genetic manipulation, simplicity for imaging, and sharing conserved disease-associated genes and pathways with those of human. In parallel, studies of disease mechanisms are increasingly focusing on non-coding mutations, which require genome annotation maps of regulatory elements, such as enhancers and promoters. In line with this, genomic resources for zebrafish research are expanding, producing a variety of genomic data that help in defining regulatory elements and their conservation between zebrafish and humans. Here, we discuss recent developments in generating functional annotation maps for regulatory elements of the zebrafish genome and how this can be applied to human diseases. We highlight community-driven developments, such as DANIO-CODE, in generating a centralised and standardised catalogue of zebrafish genomics data and functional annotations; consider the advantages and limitations of current annotation maps; and offer considerations for interpreting and integrating existing maps with comparative genomics tools. We also discuss the need for developing standardised genomics protocols and bioinformatic pipelines and provide suggestions for the development of analysis and visualisation tools that will integrate various multiomic bulk sequencing data together with fast-expanding data on single-cell methods, such as single-cell assay for transposase-accessible chromatin with sequencing. Such integration tools are essential to exploit the multiomic chromatin characterisation offered by bulk genomics together with the cell-type resolution offered by emerging single-cell methods. Together, these advances will build an expansive toolkit for interrogating the mechanisms of human disease in zebrafish.
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Affiliation(s)
- Ada Jimenez Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London SW7 2AZ, UK
- MRC London Institute of Medical Sciences, London W12 0NN, UK
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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11
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Willey C, Korstanje R. Sequencing and assembling bear genomes: the bare necessities. Front Zool 2022; 19:30. [PMID: 36451195 PMCID: PMC9710173 DOI: 10.1186/s12983-022-00475-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.
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ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain of Drosophila melanogaster. Int J Mol Sci 2022; 23:ijms232314892. [PMID: 36499217 PMCID: PMC9741293 DOI: 10.3390/ijms232314892] [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: 09/26/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
To date, different strategies of whole-genome sequencing (WGS) have been developed in order to understand the genome structure and functions. However, the analysis of genomic sequences obtained from natural populations is challenging and the biological interpretation of sequencing data remains the main issue. The MinION device developed by Oxford Nanopore Technologies (ONT) is able to generate long reads with minimal costs and time requirements. These valuable assets qualify it as a suitable method for performing WGS, especially in small laboratories. The long reads resulted using this sequencing approach can cover large structural variants and repetitive sequences commonly present in the genomes of eukaryotes. Using MinION, we performed two WGS assessments of a Romanian local strain of Drosophila melanogaster, referred to as Horezu_LaPeri (Horezu). In total, 1,317,857 reads with a size of 8.9 gigabytes (Gb) were generated. Canu and Flye de novo assembly tools were employed to obtain four distinct assemblies with both unfiltered and filtered reads, achieving maximum reference genome coverages of 94.8% (Canu) and 91.4% (Flye). In order to test the quality of these assemblies, we performed a two-step evaluation. Firstly, we considered the BUSCO scores and inquired for a supplemental set of genes using BLAST. Subsequently, we appraised the total content of natural transposons (NTs) relative to the reference genome (ISO1 strain) and mapped the mdg1 retroelement as a resolution assayer. Our results reveal that filtered data provide only slightly enhanced results when considering genes identification, but the use of unfiltered data had a consistent positive impact on the global evaluation of the NTs content. Our comparative studies also revealed differences between Flye and Canu assemblies regarding the annotation of unique versus repetitive genomic features. In our hands, Flye proved to be moderately better for gene identification, while Canu clearly outperformed Flye for NTs analysis. Data concerning the NTs content were compared to those obtained with ONT for the D. melanogaster ISO1 strain, revealing that our strategy conducted to better results. Additionally, the parameters of our ONT reads and assemblies are similar to those reported for ONT experiments performed on various model organisms, revealing that our assembly data are appropriate for a proficient annotation of the Horezu genome.
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Lee Y, Ha U, Moon S. Ongoing endeavors to detect mobilization of transposable elements. BMB Rep 2022. [PMID: 35725016 PMCID: PMC9340088 DOI: 10.5483/bmbrep.2022.55.7.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of ‘Dissociation (Dc) locus’ by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.
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Affiliation(s)
- Yujeong Lee
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Una Ha
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Sungjin Moon
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
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Lee Y, Ha U, Moon S. Ongoing endeavors to detect mobilization of transposable elements. BMB Rep 2022; 55:305-315. [PMID: 35725016 PMCID: PMC9340088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/26/2022] [Accepted: 06/14/2022] [Indexed: 02/21/2025] Open
Abstract
Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of 'Dissociation (Dc) locus' by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host. [BMB Reports 2022; 55(7): 305-315].
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Affiliation(s)
- Yujeong Lee
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Una Ha
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Sungjin Moon
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
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