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do Nascimento Moreira C, Crampton WGR, de Andrade Affonso PH, Martins C, Cardoso AL. Genomic landscape of repetitive DNAs in Neotropical electric fishes. Mol Genet Genomics 2025; 300:40. [PMID: 40186627 DOI: 10.1007/s00438-025-02248-4] [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: 10/28/2024] [Accepted: 03/21/2025] [Indexed: 04/07/2025]
Abstract
The Neotropical electric fishes of the order Gymnotiformes, known for their unique electrogenic and electrosensory systems, provide exceptional models for investigating ecological and evolutionary questions. While their phylogenetic and cytogenetic diversity is well documented, information about the diversity and evolution of repetitive DNA in gymnotiform genomes remains limited. To understand how repetitive DNA has shaped genome evolution in this group, we conducted bioinformatic analyses on raw sequencing data and genome assemblies from multiple species representing three major families. Our analysis revealed that closely related species share similar patterns of repetitive DNA composition, with Gymnotidae and Apteronotidae exhibiting the highest (16.5%) and lowest (9.4%) proportions of repetitive DNA, respectively. We identified 40 satellite DNA families, with five exclusive to Gymnotidae, twenty-two to Hypopomidae, and six shared between Apteronotidae species. Only one satellite DNA (NEFSat3-18) was conserved across all analyzed species, suggesting rapid evolutionary turnover of these sequences. The evolutionary dynamics of transposable elements varied among families, with Gymnotidae showing recent expansion of LINE elements and DNA transposons, while Apteronotidae displayed more ancient patterns of transposon activity. Analysis of transposable element landscapes revealed that all species experienced at least one burst of transposition during their evolution. Our findings demonstrate that repetitive DNA diversification parallels the evolutionary history of gymnotiform species. We also present a comprehensive dataset of repetitive DNA sequences that can be used as cytogenomic markers in comparative and evolutionary studies.
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Affiliation(s)
- Camila do Nascimento Moreira
- Instituto de Biociências, Câmpus de Botucatu, Universidade Estadual Paulista (UNESP), R. Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, 18618 - 689, Brazil
- Centro de Estudos Em Células Tronco, Terapia Celular E Genética Toxicológica, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, 79080 - 190, Brazil
| | | | - Pedro Henrique de Andrade Affonso
- Instituto de Biociências, Câmpus de Botucatu, Universidade Estadual Paulista (UNESP), R. Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, 18618 - 689, Brazil
| | - Cesar Martins
- Instituto de Biociências, Câmpus de Botucatu, Universidade Estadual Paulista (UNESP), R. Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, 18618 - 689, Brazil
| | - Adauto Lima Cardoso
- Instituto de Biociências, Câmpus de Botucatu, Universidade Estadual Paulista (UNESP), R. Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, 18618 - 689, Brazil.
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de Oliveira FS, Brann T, Wolf IR, Nogaroto V, Martins C, Protasio AV, Vicari MR. The landscape of transposable element distribution in the genome of Neotropical fish Apareiodon sp. (Characiformes: Parodontidae). Chromosome Res 2025; 33:6. [PMID: 40186682 DOI: 10.1007/s10577-025-09765-3] [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: 12/19/2024] [Revised: 03/07/2025] [Accepted: 03/17/2025] [Indexed: 04/07/2025]
Abstract
Transposable elements (TEs) are widely present in eukaryotic genomes, where they can contribute to genome size and functional modifications. As new genomes are sequenced and annotated, more studies can be conducted regarding TE content, distribution, and genome evolution. TEs are extensively diversified in fish genomes resulting in an important role in genome and chromosome evolution. However, curated TE libraries are still scarce in non-model organisms, making it difficult to evaluate TE's impact on genomic modifications thoroughly. Here, we aimed to obtain a curated TE library from the neotropical fish Apareiodon sp. genome. The prospection and curation of the TE library resulted in 244 families from 18 superfamilies of DNA transposons and retrotransposons, which comprise about 10% of the genome, with most insertions fitting in one or a few families. A greater diversity of retrotransposon families is present, especially for Ty3 superfamily. Despite the greater number of retrotransposon families, DNA transposons are the most abundant in the genome, with 37% of all TE insertions belonging to the Tc1-Mariner superfamily. Complete TE copies were observed for almost all superfamilies, with most of the sequences on the Tc1-Mariner group. DNA transposons and SINEs presented older insertions in the genome, followed by LINEs and LTR retrotransposons. TE genome density is highest in the cs25 scaffold, and enriched for Helitron elements. With these data, allied to previous studies on chromosome evolution, we suggest that cs25 bears the W chromosome specific region of the Apareiodon sp. genome, with the presence of significant amount of Helitron insertions.
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Affiliation(s)
- Fernanda Souza de Oliveira
- Programa de Pós-Graduação Em Genética, Universidade Federal Do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Toby Brann
- Department of Pathology, University of Cambridge, Cambridge, Cambridgeshire, CB2 1QP, UK
| | - Ivan Rodrigo Wolf
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular E Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Anna Victoria Protasio
- Department of Pathology, University of Cambridge, Cambridge, Cambridgeshire, CB2 1QP, UK
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação Em Genética, Universidade Federal Do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil.
- Departamento de Biologia Estrutural, Molecular E Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil.
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Ancona L, Nitta Fernandes FA, Biello R, Chiocchio A, Castrignanò T, Barucca M, Canestrelli D, Trucchi E. Evolutionary Dynamics of Transposable Element Activity and Regulation in the Apennine Yellow-Bellied Toad (Bombina pachypus). Genome Biol Evol 2025; 17:evaf062. [PMID: 40211594 PMCID: PMC12008745 DOI: 10.1093/gbe/evaf062] [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] [Accepted: 03/27/2025] [Indexed: 04/20/2025] Open
Abstract
Transposable elements (TEs) expansion and accumulation represent one of the main drivers of genomic gigantism. Different host genome silencing mechanisms have evolved to counteract TE amplification, leading to a genomic arms race between them. Nevertheless, the evolutionary relationship between TEs and host genome silencing pathways remains poorly understood. Here, we investigate the activity of TEs and TE-silencing mechanisms in somatic and germline tissues of Bombina pachypus, a 10 Gb anuran genome. Our findings reveal a higher activity of TEs in the gonads compared to the brain, with retrotransposons as the most active class in both gonads (∼15% increased expression compared to the brain) and DNA transposons showing a 2-fold higher activity in ovaries. However, analysis of differentially expressed TEs between male and female gonads revealed a greater number of overexpressed TEs in testes (231 vs. 169), with maximum fold changes up to 22 in testes versus 8 in ovaries. This suggests a more permissive environment for TE expression in male gonads. Accordingly, increased activity of TE-silencing pathways was observed in ovaries compared to testes, with the KRAB-ZFP complex showing not only the highest overall expression levels but also a distinct ovary-specific expression pattern. Summarizing, while the higher TE activity in the male gonad may result from the lower efficiency of the KRAB-ZFP complex, the elevated activity of KRAB-ZFPs in ovaries, along with growing evidence of the functional role of TEs in the germline, suggests the existence of a broad range of host-TE dynamics going beyond the arms race model.
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Affiliation(s)
- Lorena Ancona
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Roberto Biello
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Chiocchio
- Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy
| | - Marco Barucca
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Petroll R, Papareddy RK, Krela R, Laigle A, Rivière Q, Bišova K, Mozgová I, Borg M. The Expansion and Diversification of Epigenetic Regulatory Networks Underpins Major Transitions in the Evolution of Land Plants. Mol Biol Evol 2025; 42:msaf064. [PMID: 40127687 PMCID: PMC11982613 DOI: 10.1093/molbev/msaf064] [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: 09/23/2024] [Revised: 02/26/2025] [Accepted: 03/05/2025] [Indexed: 03/26/2025] Open
Abstract
Epigenetic silencing is essential for regulating gene expression and cellular diversity in eukaryotes. While DNA and H3K9 methylation silence transposable elements (TEs), H3K27me3 marks deposited by the Polycomb repressive complex 2 (PRC2) silence varying proportions of TEs and genes across different lineages. Despite the major development role epigenetic silencing plays in multicellular eukaryotes, little is known about how epigenetic regulatory networks were shaped over evolutionary time. Here, we analyze epigenomes from diverse species across the green lineage to infer the chronological epigenetic recruitment of genes during land plant evolution. We first reveal the nature of plant heterochromatin in the unicellular chlorophyte microalga Chlorella sorokiniana and identify several genes marked with H3K27me3, highlighting the deep origin of PRC2-regulated genes in the green lineage. By incorporating genomic phylostratigraphy, we show how genes of differing evolutionary age occupy distinct epigenetic states in plants. While young genes tend to be silenced by H3K9 methylation, genes that emerged in land plants are preferentially marked with H3K27me3, some of which form part of a common network of PRC2-repressed genes across distantly related species. Finally, we analyze the potential recruitment of PRC2 to plant H3K27me3 domains and identify conserved DNA-binding sites of ancient transcription factor families known to interact with PRC2. Our findings shed light on the conservation and potential origin of epigenetic regulatory networks in the green lineage, while also providing insight into the evolutionary dynamics and molecular triggers that underlie the adaptation and elaboration of epigenetic regulation, laying the groundwork for its future consideration in other eukaryotic lineages.
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Affiliation(s)
- Romy Petroll
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Ranjith K Papareddy
- Gregor Mendel Institute for Molecular Plant Biology, Vienna Biocenter, Vienna, Austria
| | - Rafal Krela
- Biology Centre CAS—Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Alice Laigle
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Quentin Rivière
- Biology Centre CAS—Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Kateřina Bišova
- Institute of Microbiology CAS, Centre Algatech, Třeboň, Czech Republic
| | - Iva Mozgová
- Biology Centre CAS—Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen, Germany
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Varga Z, Kagan F, Maegawa S, Nagy Á, Okendo J, Burgess SM, Weinberg ES, Varga M. Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod ( ich) mutation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.28.640854. [PMID: 40093107 PMCID: PMC11908130 DOI: 10.1101/2025.02.28.640854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
The maternal-effect mutation ichabod (ich) results in ventralized zebrafish embryos due to impaired induction of the dorsal canonical Wnt-signaling pathway. While previous studies linked the phenotype to reduced ctnnb2 transcript levels, the causative mutation remained unidentified. Using long-read sequencing, we discovered that the ich phenotype stems from the insertion of a non-autonomous CMC-Enhancer/Suppressor-mutator (CMC-EnSpm) transposon in the 3'UTR of the gene. Through reporter assays, we demonstrate that while wild type ctnnb2 mRNAs exhibit remarkably high stability throughout the early stages of development, the insertion of the transposon dramatically reduces transcript stability. Genome-wide mapping of the CMC-EnSpm transposons across multiple zebrafish strains also indicated ongoing transposition activity in the zebrafish genome. Our findings not only resolve the molecular basis of the ich mutation but also highlight the continuing mutagenic potential of endogenous transposons and reveal unexpected aspects of maternal transcript regulation during early zebrafish development.
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Affiliation(s)
- Zsombor Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ferenc Kagan
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Shingo Maegawa
- Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Japan
| | - Ágnes Nagy
- Hungarian Defence Forces Medical Centre, Budapest, Hungary
| | - Javan Okendo
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Eric S Weinberg
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
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Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK, Smith AM, Joyce DA, Butter F, Haase AD, Durbin R, Santos ME, Miska EA. Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. Genome Biol 2025; 26:14. [PMID: 39844208 PMCID: PMC11753138 DOI: 10.1186/s13059-025-03475-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 01/06/2025] [Indexed: 01/24/2025] Open
Abstract
BACKGROUND East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap and to understand the interactions between TEs and their cichlid hosts. RESULTS Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed strong conservation of TE silencing factors in cichlids, and an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that targets TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. CONCLUSIONS Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.
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Affiliation(s)
- Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
| | - Moritz Blumer
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Pío Sierra
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jonathan L Price
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Aleksandr Friman
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- Biophysics Graduate Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742, USA
| | - Alexandra Dallaire
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Comparative Fungal Biology, Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, TW9 3DS, UK
| | - Grégoire Vernaz
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Present Address: Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
| | - Audrey L K Putman
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Alan M Smith
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Domino A Joyce
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Falk Butter
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Ackermannweg 4, Mainz, 55128, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Südufer, Greifswald, 17493, Germany
| | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Eric A Miska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
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Mallik R, Wcisel DJ, Near TJ, Yoder JA, Dornburg A. Investigating the Impact of Whole-Genome Duplication on Transposable Element Evolution in Teleost Fishes. Genome Biol Evol 2025; 17:evae272. [PMID: 39715451 PMCID: PMC11785729 DOI: 10.1093/gbe/evae272] [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: 04/18/2024] [Revised: 12/08/2024] [Accepted: 12/13/2024] [Indexed: 12/25/2024] Open
Abstract
Transposable elements (TEs) can make up more than 50% of any given vertebrate's genome, with substantial variability in TE composition among lineages. TE variation is often linked to changes in gene regulation, genome size, and speciation. However, the role that genome duplication events have played in generating abrupt shifts in the composition of the mobilome over macroevolutionary timescales remains unclear. We investigated the degree to which the teleost genome duplication (TGD) shaped the diversification trajectory of the teleost mobilome. We integrate a new high coverage genome of Polypterus bichir with data from over 100 publicly available actinopterygian genomes to assess the macroevolutionary implications of genome duplication events on TE evolution in teleosts. Our results provide no evidence for a substantial shift in mobilome composition following the TGD event. Instead, the diversity of the teleost mobilome appears to have been shaped by a history of lineage-specific shifts in composition that are not correlated with commonly evoked drivers of diversification such as body size, water column usage, or latitude. Collectively, these results provide additional evidence for an emerging perspective that TGD did not catalyze bursts of diversification and innovation in the actinopterygian mobilome.
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Affiliation(s)
- Rittika Mallik
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum, Yale University, New Haven, CT, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, Genetics and Genomics Academy, and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
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Zhao J, Xie L, Zhao X, Li L, Cui J, Chen J. Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae). G3 (BETHESDA, MD.) 2024; 14:jkae223. [PMID: 39290157 PMCID: PMC11540328 DOI: 10.1093/g3journal/jkae223] [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: 05/28/2024] [Revised: 08/27/2024] [Accepted: 09/11/2024] [Indexed: 09/19/2024]
Abstract
The sugarcane aphid, Melanaphis sacchari, is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. In this study, we used nanopore long reads and a high-throughput chromosome conformation capture chromatin interaction maps to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the 3 autosomes and the X chromosome. Repetitive sequences accounted for 16.29% of the chromosomes, and a total of 12,530 protein-coding genes were annotated, achieving 95.8% Benchmarking Universal Single-Copy Ortholog gene completeness. This offered a substantial improvement compared with previous low-quality genomic resources. A phylogenomic analysis by comparing M. sacchari with 24 published aphid genomes representing 3 aphid tribes revealed that M. sacchari belonged to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The high-quality genomic resources reported in this study are useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.
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Affiliation(s)
- Jinshuai Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqiang Xie
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinrui Zhao
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, Hebei 07100, China
| | - Luhua Li
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Jianghui Cui
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, Hebei 07100, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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9
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Zhao L, Gong F, Lou K, Wang L, Wang J, Sun H, Wang D, Shi Y, Wang Z. Retrotransposon involves in photoperiodic spermatogenesis in Brandt's voles (Lasiopodomys brandtii) by co-transcription with flagellar genes. Int J Biol Macromol 2024; 281:136224. [PMID: 39362423 DOI: 10.1016/j.ijbiomac.2024.136224] [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: 06/04/2024] [Revised: 09/10/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024]
Abstract
Photoperiod is a pivotal factor in affecting spermatogenesis in seasonal-breeding animals. Transposable elements have regulatory functions during spermatogenesis. However, whether it also functions in photoperiodic spermatogenesis in seasonal breeding animals is unknown. To explore this, we first annotated 5,501,822 transposons in the whole genome of Brandt's voles (Lasiopodomys brandtii), and revealed that LINEs were the most abundant, comprising 16.61 % of the genome. Following closely, SINEs accounted for 10.13 %, LTRs for 7.54 %, and DNA transposons for 0.70 %. Subsequently, we exposed male Brandt's voles to long-photoperiod (LP, 16 h/day) and short-photoperiod (SP, 8 h/day) from their embryonic stages, and obtained testes transcriptome at 4 and 10 weeks after birth. Differential expression and Pearson analysis indicated strongly positive correlations between the expression of differentially expressed retrotransposons and the adjacent genes. KO, KEGG and GSEA results showed that sperm flagellar genes were most enriched nearby the retrotransposons such as Dnah1, Dnah2, Dnah17, Dnali1. RT-PCR results showed that SINE/Alu_1213291 co-transcripted with Dnali1 gene. Our findings first reveal the regulatory function of transposons in photoperiodic spermatogenesis, providing insights into the role of photoperiod in seasonal reproduction in wild animals.
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Affiliation(s)
- Lijuan Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Fanglei Gong
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Kang Lou
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Lewen Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Western Agricultural Research Center, Chinese Academy of Agriculture Science, Changji 831100, China
| | - Jingou Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Hong Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Centre for Sport Nutrition and Health, School of Physical Education (Main Campus), Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Dawei Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Western Agricultural Research Center, Chinese Academy of Agriculture Science, Changji 831100, China.
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China.
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China.
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10
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Decena-Segarra LP, Rovito SM. Transposable Element Diversity and Activity Patterns in Neotropical Salamanders. Mol Biol Evol 2024; 41:msae225. [PMID: 39470441 PMCID: PMC11562844 DOI: 10.1093/molbev/msae225] [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: 05/31/2024] [Revised: 09/10/2024] [Accepted: 10/23/2024] [Indexed: 10/30/2024] Open
Abstract
Transposable elements (TEs) compose a substantial proportion of the largest eukaryotic genomes. TE diversity has been hypothesized to be negatively correlated with genome size, yet empirical demonstrations of such a relationship in a phylogenetic context are largely lacking. Furthermore, the most abundant type of TEs in genomes varies across groups, and it is not clear if there are patterns of TE activity consistent with genome size among different taxa with large genome sizes. We use low-coverage sequencing of 16 species of Neotropical salamanders, which vary ∼7-fold in genome size, to estimate TE relative abundance and diversity for each species. We also compare the divergence of copies of each TE superfamily to estimate patterns of TE activity in each species. We find a negative relationship between TE diversity and genome size, which is consistent with the hypothesis that either competition among TEs or reduced selection against ectopic recombination may result in lower diversity in the largest genomes. We also find divergent activity patterns in the largest versus the smallest genomes, suggesting that the history of TE activity may explain differences in genome size. Our results suggest that both TE diversity and relative abundance may be predictable, at least within taxonomic groups.
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Affiliation(s)
- Louis Paul Decena-Segarra
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
| | - Sean M Rovito
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, Mexico
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11
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Sun X, Chen X, Wu B, Zhou L, Chen Y, Zheng S, Wang S, Liu Z. Clam Genome and Transcriptomes Provide Insights into Molecular Basis of Morphological Novelties and Adaptations in Mollusks. BIOLOGY 2024; 13:870. [PMID: 39596825 PMCID: PMC11592408 DOI: 10.3390/biology13110870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 10/17/2024] [Accepted: 10/23/2024] [Indexed: 11/29/2024]
Abstract
Bivalve mollusks, comprising animals enclosed in two shell valves, are well-adapted to benthic life in many intertidal zones. Clams have evolved the buried lifestyle, which depends on their unique soft tissue structure and their wedge-shaped muscular foot and long extendible siphons. However, molecular mechanisms of adaptative phenotype evolution remain largely unknown. In the present study, we obtain the high-quality chromosome-level genome of Manila clam R. philippinarum, an economically important marine bivalve in many coastal areas. The genome is constructed by the Hi-C assisted assembly, which yields 19 chromosomes with a total of 1.17 Gb and BUSCO integrity of 92.23%. The de novo assembled genome has a contig N50 length of 307.7 kb and scaffold N50 of 59.5 Mb. Gene family expansion analysis reveals that a total of 24 single-copy gene families have undergone the significant expansion or contraction, including E3 ubiquitin ligase and dynein heavy chain. The significant expansion of transposable elements has been also identified, including long terminal repeats (LTR) and non-LTR retrotransposons. The comparative transcriptomics among different clam tissues reveals that extracellular matrix (ECM) receptors and neuroactive ligand receptors may play the important roles in tissue structural support and neurotransmission during their infaunal life. These findings of gene family expansion and tissue-specific expression may reflect the unique soft tissue structure of clams, suggesting the evolution of lineage-specific morphological novelties. The high-quality genome and transcriptome data of R. philippinarum will not only facilitate the genetic studies on clams but will also provide valuable information on morphological novelties in mollusks.
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Affiliation(s)
- Xiujun Sun
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
| | - Xi Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
| | - Biao Wu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
| | - Liqing Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
| | - Yancui Chen
- Zhangzhou Aquatic Technology Promotion Station, Zhangzhou 363000, China;
| | - Sichen Zheng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Songlin Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhihong Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
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12
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de Oliveira FS, Azambuja M, Schemberger MO, Nascimento VD, Oliveira JIN, Wolf IR, Nogaroto V, Martins C, Vicari MR. Characterization of hAT DNA transposon superfamily in the genome of Neotropical fish Apareiodon sp. Mol Genet Genomics 2024; 299:96. [PMID: 39382723 DOI: 10.1007/s00438-024-02190-x] [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: 12/06/2023] [Accepted: 09/28/2024] [Indexed: 10/10/2024]
Abstract
DNA transposons are diverse in fish genomes and have been described to generate genomic evolutionary novelties. hAT transposable element data are scarce in Teleostei genomes, making it challenging to conduct comparative genomic studies to understand their neutrality or function. This study aimed to perform a genomic and molecular characterization of hAT copies to assess the diversity of these elements and associate changes in these sequences to genomic and karyotypic novelties in Apareiodon sp. The data revealed that hAT TEs are highly abundant in the Apareiodon sp. genome, with few possibly autonomous copies. Highly conserved sequences with likely functional transposases were observed in nine hAT elements. A great diversity of hAT subgroups was observed, especially from Ac, Charlie, Blackjack, Tip100, hAT6, and hAT5, and a similar wave of hAT genomic invasion was identified in the genome for these six groups of hAT sequences. The data also revealed a distinct number of microsatellites within degenerated hAT copies. hAT sites were demonstrated to be dispersed in the Apareiodon sp. chromosomes and not involved in W chromosome-specific region differentiation. In conclusion, the genomic analysis revealed a great diversity of hAT elements, possible autonomous copies, and differentiation of degenerated transposable elements into tandem sequences.
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Affiliation(s)
- Fernanda Souza de Oliveira
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Michelle Orane Schemberger
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Viviane Demetrio Nascimento
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil
| | - Jordana Inácio Nascimento Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Ivan Rodrigo Wolf
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, S/N, Botucatu, São Paulo, 18618-689, Brazil
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. Dos Santos, 100, Curitiba, Paraná, 81531-990, Brazil.
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil.
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13
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Duval KL, Artis AR, Goll MG. The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis. Genetics 2024; 228:iyae138. [PMID: 39166515 PMCID: PMC11457944 DOI: 10.1093/genetics/iyae138] [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: 07/01/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
The structural organization of eukaryotic genomes is contingent upon the fractionation of DNA into transcriptionally permissive euchromatin and repressive heterochromatin. However, we have a limited understanding of how these distinct states are first established during animal embryogenesis. Histone 3 lysine 9 trimethylation (H3K9me3) is critical to heterochromatin formation, and bulk establishment of this mark is thought to help drive large-scale remodeling of an initially naive chromatin state during animal embryogenesis. However, a detailed understanding of this process is lacking. Here, we leverage CUT&RUN to define the emerging H3K9me3 landscape of the zebrafish embryo with high sensitivity and temporal resolution. Despite the prevalence of DNA transposons in the zebrafish genome, we found that LTR transposons are preferentially targeted for embryonic H3K9me3 deposition, with different families exhibiting distinct establishment timelines. High signal-to-noise ratios afforded by CUT&RUN revealed new, emerging sites of low-amplitude H3K9me3 that initiated before the major wave of zygotic genome activation (ZGA). Early sites of establishment predominated at specific subsets of transposons and were particularly enriched for transposon sequences with maternal piRNAs and pericentromeric localization. Notably, the number of H3K9me3 enriched sites increased linearly across blastula development, while quantitative comparison revealed a >10-fold genome-wide increase in H3K9me3 signal at established sites over just 30 min at the onset of major ZGA. Continued maturation of the H3K9me3 landscape was observed beyond the initial wave of bulk establishment.
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Affiliation(s)
- Katherine L Duval
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Ashley R Artis
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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14
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Schartl M, Woltering JM, Irisarri I, Du K, Kneitz S, Pippel M, Brown T, Franchini P, Li J, Li M, Adolfi M, Winkler S, de Freitas Sousa J, Chen Z, Jacinto S, Kvon EZ, Correa de Oliveira LR, Monteiro E, Baia Amaral D, Burmester T, Chalopin D, Suh A, Myers E, Simakov O, Schneider I, Meyer A. The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature 2024; 634:96-103. [PMID: 39143221 PMCID: PMC11514621 DOI: 10.1038/s41586-024-07830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 07/15/2024] [Indexed: 08/16/2024]
Abstract
The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.
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Affiliation(s)
- Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
| | | | - Iker Irisarri
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Pippel
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Thomas Brown
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Leibniz Institute for Zoo & Wildlife Research, Berlin, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Jing Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ming Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Mateus Adolfi
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sylke Winkler
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Zhuoxin Chen
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | | | - Erika Monteiro
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | | | - Domitille Chalopin
- Institute of Cellular Biochemistry and Genetics, CNRS, University of Bordeaux, Bordeaux, France
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eugene Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center of Systems Biology Dresden, Dresden, Germany
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Igor Schneider
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
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15
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Crepaldi C, Cabral-de-Mello DC, Parise-Maltempi PP. Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems. Genome 2024; 67:339-350. [PMID: 38739948 DOI: 10.1139/gen-2023-0134] [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] [Indexed: 05/16/2024]
Abstract
Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.
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Affiliation(s)
- Carolina Crepaldi
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
| | - Patricia Pasquali Parise-Maltempi
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
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16
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Zhou C, Zheng X, Wang L, Yue B, DU C, Liu X. The first chromosome-level genome assembly and transcriptome sequencing provide insights into cantharidin production of the blister beetles. Integr Zool 2024; 19:929-940. [PMID: 37881135 DOI: 10.1111/1749-4877.12783] [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] [Indexed: 10/27/2023]
Abstract
Blister beetles (Coleoptera: Meloidae) produce a natural defensive toxin cantharidin (CTD), which has been used for various cancer treatments and other diseases. Currently, the lack of chromosome-level reference genomes in Meloidae limits further understanding of the mechanism of CTD biosynthesis and environmental adaptation. In this study, the chromosome-level genome assembly of Mylabris phalerata was generated based on PacBio and Hi-C sequencing. This reference genome was about 136.68 Mb in size with contig N50 of 9.17 Mb and composed of 12 chromosomes. In comparison to six other Coleoptera insects, M. phalerata exhibited multiple expanded gene families enriched in juvenile hormone (JH) biosynthetic process pathway, farnesol dehydrogenase activity, and cytochrome P450, which may be related to CTD biosynthesis. Consistently, the transcriptomic analysis suggested the "terpenoid backbone biosynthesis" pathway and "the juvenile hormone" as putative core pathways of CTD biosynthesis and presented eight up-regulated differential expression genes in male adults as candidate genes. It is possible that the restricted feeding niche and lifestyle of M. phalerata were the cause of the gene family's contraction of odorant binding proteins. The ABC transporters (ABCs) related to exporting bound toxins out of the cell and the resistance to the self-secreted toxins (e.g. CTD) were also contracted, possibly due to other self-protection strategies in M. phalerata. A foundation of understanding CTD biosynthesis and environmental adaptation of blister beetles will be established by our reference genome and discoveries.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - Xiaofeng Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - Lei Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, P. R. China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - Chao DU
- Baotou Teachers College, Baotou, P. R. China
| | - Xu Liu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, P. R. China
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17
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Gable SM, Bushroe NA, Mendez JM, Wilson A, Pinto BJ, Gamble T, Tollis M. Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles. Genome Biol Evol 2024; 16:evae157. [PMID: 39031594 PMCID: PMC11303007 DOI: 10.1093/gbe/evae157] [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: 02/14/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/22/2024] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Brendan J Pinto
- 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
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
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18
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Skalon EK, Panyushev NV, Podgornaya OI, Smolyaninova AR, Solovyeva AI. Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle. Noncoding RNA 2024; 10:39. [PMID: 39051373 PMCID: PMC11270206 DOI: 10.3390/ncrna10040039] [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: 04/29/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Transposable elements (TEs) are major components of eukaryotic genomes. The extensive body of evidence suggests that although they were once considered "genomic parasites", transposons and their transcripts perform specific functions, such as regulation of early embryo development. Understanding the role of TEs in such parasites as trematodes is becoming critically important. Fasciola hepatica, a parasite affecting humans and livestock, undergoes a complex life cycle in diverse environments and hosts, and knowledge about its life cycle regulation is scarce so far. METHODS We summarized the data regarding the repetitive elements in F. hepatica and conducted bulk RNA-seq analysis across its life cycle stages. TE expression profiles were analyzed, focusing on differential expression and potential homology with previously described long non-coding RNAs (lncRNAs). RESULTS Differential expression analysis revealed stage-specific TE transcription patterns, notably peaking during egg and metacercariae stages. Some TEs showed homology with known lncRNAs and contained putative transcription factor binding sites. Interestingly, TE transcription levels were highest in eggs and metacercariae compared to adults, suggesting regulatory roles in trematode life cycle transitions. CONCLUSIONS These findings suggest that TEs may play roles in regulating trematode life cycle transitions. Moreover, TE homology with lncRNAs underscores their significance in gene regulation.
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Affiliation(s)
- Elizaveta K. Skalon
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
| | | | - Olga I. Podgornaya
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
| | - Anastasia R. Smolyaninova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
| | - Anna I. Solovyeva
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
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19
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Dittrich C, Hoelzl F, Smith S, Fouilloux CA, Parker DJ, O’Connell LA, Knowles LS, Hughes M, Fewings A, Morgan R, Rojas B, Comeault AA. Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution. Genome Biol Evol 2024; 16:evae109. [PMID: 38753031 PMCID: PMC11152451 DOI: 10.1093/gbe/evae109] [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] [Accepted: 05/12/2024] [Indexed: 06/07/2024] Open
Abstract
Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimize primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.
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Affiliation(s)
- Carolin Dittrich
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Franz Hoelzl
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Steve Smith
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Chloe A Fouilloux
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Darren J Parker
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
| | | | - Lucy S Knowles
- NERC Environmental Omics Facility, University of Sheffield, Sheffield, UK
| | - Margaret Hughes
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Ade Fewings
- Supercomputing Wales, Digital Services, Bangor University, Bangor, UK
| | - Rhys Morgan
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
| | - Bibiana Rojas
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Aaron A Comeault
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
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20
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Shao F, Zeng M, Xu X, Zhang H, Peng Z. FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research. Database (Oxford) 2024; 2024:baae044. [PMID: 38829853 PMCID: PMC11146639 DOI: 10.1093/database/baae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/04/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
Abstract
We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.
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Affiliation(s)
- Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
| | - Minzhi Zeng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
| | - Xiaofei Xu
- School of Computing Technologies, RMIT University, 124 La Trobe Street, Victoria 3000, Australia
| | - Huahao Zhang
- College of Pharmacy and Life Science, Jiujiang University, 551 Qianjin East Road, Jiujiang 332005, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
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21
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Münch L, Helmprobst F, Volff JN, Chalopin D, Schartl M, Kneitz S. Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of Xiphophorus. Genes (Basel) 2024; 15:620. [PMID: 38790249 PMCID: PMC11121471 DOI: 10.3390/genes15050620] [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: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Transposable elements (TEs) are characterized by their ability to change their genomic position. Through insertion or recombination leading to deletions and other chromosomal aberrations, they can cause genetic instability. The extent to which they thereby exert regulatory influence on cellular functions is unclear. To better characterize TEs in processes such as carcinogenesis, we used the well-established Xiphophorus melanoma model. By transcriptome sequencing, we show that an increasing total number in transposons correlates with progression of malignancy in melanoma samples from Xiphophorus interspecific hybrids. Further, by comparing the presence of TEs in the parental genomes of Xiphophorus maculatus and Xiphophorus hellerii, we could show that even in closely related species, genomic location and spectrum of TEs are considerably different.
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Affiliation(s)
- Luca Münch
- Neurology Asklepios Klinik Barmbek, Rübenkamp 220, 22307 Hamburg, Germany;
| | - Frederik Helmprobst
- Institute of Neuropathology, Philipps-University Marburg, 35037 Marburg, Germany;
| | | | | | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 786666, USA
- Developmental Biochemistry, University of Würzburg, 97974 Würzburg, Germany
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
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22
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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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23
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Duval KL, Artis AR, Goll MG. The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.582530. [PMID: 38496550 PMCID: PMC10942377 DOI: 10.1101/2024.03.05.582530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The structural organization of eukaryotic genomes is contingent upon the fractionation of DNA into transcriptionally permissive euchromatin and repressive heterochromatin. However, we have a limited understanding of how these distinct states are first established during animal embryogenesis. Histone 3 lysine 9 trimethylation (H3K9me3) is critical to heterochromatin formation and bulk establishment of this mark is thought to help drive large-scale remodeling of an initially naive chromatin state during animal embryogenesis. However, a detailed understanding of this process is lacking. Here, we leverage CUT&RUN to define the emerging H3K9me3 landscape of the zebrafish embryo with high sensitivity and temporal resolution. Despite the prevalence of DNA transposons in the zebrafish genome, we found that LTR transposons are preferentially targeted for embryonic H3K9me3 deposition, with different families exhibiting distinct establishment timelines. High signal-to-noise ratios afforded by CUT&RUN revealed new, emerging sites of low-amplitude H3K9me3 that initiated before the major wave of zygotic genome activation (ZGA). Early sites of establishment predominated at specific subsets of transposons and were particularly enriched for transposon sequences with maternal piRNAs and pericentromeric localization. Notably, the number of H3K9me3 enriched sites increased linearly across blastula development, while quantitative comparison revealed a >10-fold genome-wide increase in H3K9me3 signal at established sites over just 30 minutes at the onset of ZGA. Continued maturation of the H3K9me3 landscape was observed beyond the initial wave of bulk establishment.
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Affiliation(s)
| | - Ashley R. Artis
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Mary G. Goll
- Department of Genetics, University of Georgia, Athens, GA, USA
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24
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Lin L, Sun T, Guo J, Lin L, Chen M, Wang Z, Bao J, Norvienyeku J, Zhang D, Han Y, Lu G, Rensing C, Zheng H, Zhong Z, Wang Z. Transposable elements impact the population divergence of rice blast fungus Magnaporthe oryzae. mBio 2024; 15:e0008624. [PMID: 38534157 PMCID: PMC11077969 DOI: 10.1128/mbio.00086-24] [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: 01/13/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Dynamic transposition of transposable elements (TEs) in fungal pathogens has significant impact on genome stability, gene expression, and virulence to the host. In Magnaporthe oryzae, genome plasticity resulting from TE insertion is a major driving force leading to the rapid evolution and diversification of this fungus. Despite their importance in M. oryzae population evolution and divergence, our understanding of TEs in this context remains limited. Here, we conducted a genome-wide analysis of TE transposition dynamics in the 11 most abundant TE families in M. oryzae populations. Our results show that these TEs have specifically expanded in recently isolated M. oryzae rice populations, with the presence/absence polymorphism of TE insertions highly concordant with population divergence on Geng/Japonica and Xian/Indica rice cultivars. Notably, the genes targeted by clade-specific TEs showed clade-specific expression patterns and are involved in the pathogenic process, suggesting a transcriptional regulation of TEs on targeted genes. Our study provides a comprehensive analysis of TEs in M. oryzae populations and demonstrates a crucial role of recent TE bursts in adaptive evolution and diversification of the M. oryzae rice-infecting lineage. IMPORTANCE Magnaporthe oryzae is the causal agent of the destructive blast disease, which caused massive loss of yield annually worldwide. The fungus diverged into distinct clades during adaptation toward the two rice subspecies, Xian/Indica and Geng/Japonica. Although the role of TEs in the adaptive evolution was well established, mechanisms underlying how TEs promote the population divergence of M. oryzae remain largely unknown. In this study, we reported that TEs shape the population divergence of M. oryzae by differentially regulating gene expression between Xian/Indica-infecting and Geng/Japonica-infecting populations. Our results revealed a TE insertion-mediated gene expression adaption that led to the divergence of M. oryzae population infecting different rice subspecies.
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Affiliation(s)
- Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meilian Chen
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Zhe Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiandong Bao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Justice Norvienyeku
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Dongmei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yijuan Han
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huakun Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
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25
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Hassan NT, Galbraith JD, Adelson DL. Multiple horizontal transfer events of a DNA transposon into turtles, fishes, and a frog. Mob DNA 2024; 15:7. [PMID: 38605364 PMCID: PMC11008031 DOI: 10.1186/s13100-024-00318-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Horizontal transfer of transposable elements (HTT) has been reported across many species and the impact of such events on genome structure and function has been well described. However, few studies have focused on reptilian genomes, especially HTT events in Testudines (turtles). Here, as a consequence of investigating the repetitive content of Malaclemys terrapin terrapin (Diamondback turtle) we found a high similarity DNA transposon, annotated in RepBase as hAT-6_XT, shared between other turtle species, ray-finned fishes, and a frog. hAT-6_XT was notably absent in reptilian taxa closely related to turtles, such as crocodiles and birds. Successful invasion of DNA transposons into new genomes requires the conservation of specific residues in the encoded transposase, and through structural analysis, these residues were identified indicating some retention of functional transposition activity. We document six recent independent HTT events of a DNA transposon in turtles, which are known to have a low genomic evolutionary rate and ancient repeats.
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Affiliation(s)
- Nozhat T Hassan
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - James D Galbraith
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, Australia.
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26
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Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK, Smith AM, Joyce DA, Butter F, Haase AD, Durbin R, Santos ME, Miska EA. Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587621. [PMID: 38617250 PMCID: PMC11014572 DOI: 10.1101/2024.04.01.587621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.
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Affiliation(s)
- Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Moritz Blumer
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- These authors contributed equally
| | - Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- These authors contributed equally
| | - Pío Sierra
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jonathan L. Price
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Aleksandr Friman
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Biophysics Graduate Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Alexandra Dallaire
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
| | - Grégoire Vernaz
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Present address: Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
| | - Audrey L. K. Putman
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Alan M. Smith
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Domino A. Joyce
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Falk Butter
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Ackermannweg 4, Mainz, 55128, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Südufer, Greifswald, 17493, Germany
| | - Astrid D. Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - M. Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Eric A. Miska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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27
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Villarreal F, Burguener GF, Sosa EJ, Stocchi N, Somoza GM, Turjanski AG, Blanco A, Viñas J, Mechaly AS. Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure. BMC Genomics 2024; 25:297. [PMID: 38509481 PMCID: PMC10956332 DOI: 10.1186/s12864-024-10081-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: 07/31/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the development of this activity. In this study, we first employed Illumina sequencing technology to sequence the entire genome of Black flounder. Utilizing two independent libraries-one from a female and another from a male-with 150 bp paired-end reads, a mean insert length of 350 bp, and over 35 X-fold coverage, we achieved assemblies resulting in a genome size of ~ 538 Mbp. Analysis of the assemblies revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. Black flounder, along with pufferfishes, seahorses, pipefishes, and anabantid fish, displays a smaller genome compared to most other teleost groups. In vertebrates, the number of transposable elements (TEs) is often correlated with genome size. However, it remains unclear whether the sizes of introns and exons also play a role in determining genome size. Hence, to elucidate the potential factors contributing to this reduced genome size, we conducted a comparative genomic analysis between Black flounder and other teleost orders to determine if the small genomic size could be explained by repetitive elements or gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder. Despite these insights, the full implications and potential benefits of genome reduction in Black flounder for reproduction and aquaculture remain incompletely understood, necessitating further research.
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Affiliation(s)
- Fernando Villarreal
- Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Germán F Burguener
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Nicolas Stocchi
- Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Gustavo M Somoza
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (UNSAM), Buenos Aires, Argentina
| | - Adrián G Turjanski
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrés Blanco
- Facultade de Veterinaria, Universidade de Santiago de Compostela, Santiago de Compostela, Lugo, Spain
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus Terra, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jordi Viñas
- Laboratori d'Ictiologia Genètica, Departament de Biologia, Universitat de Girona, Maria Aurèlia Campmany, 40, Girona, Spain
| | - Alejandro S Mechaly
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Mar del Plata, Argentina.
- Fundación Para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina.
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28
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Xu L, Ren Y, Wu J, Cui T, Dong R, Huang C, Feng Z, Zhang T, Yang P, Yuan J, Xu X, Liu J, Wang J, Chen W, Mi D, Irwin DM, Yan Y, Xu L, Yu X, Li G. Evolution and expression patterns of the neo-sex chromosomes of the crested ibis. Nat Commun 2024; 15:1670. [PMID: 38395916 PMCID: PMC10891136 DOI: 10.1038/s41467-024-46052-x] [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: 06/21/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology and behavior of bird species. Core waterbirds, a major clade of birds, share the common characteristics of being sexually monomorphic and having lower levels of inter-sexual conflict, yet their sex chromosome evolution remains poorly understood. Here, by we analyse of a chromosome-level assembly of a female crested ibis (Nipponia nippon), a typical core waterbird. We identify neo-sex chromosomes resulting from fusion of microchromosomes with ancient sex chromosomes. These fusion events likely occurred following the divergence of Threskiornithidae and Ardeidae. The neo-W chromosome of the crested ibis exhibits the characteristics of slow degradation, which is reflected in its retention of abundant gametologous genes. Neo-W chromosome genes display an apparent ovary-biased gene expression, which is largely driven by genes that are retained on the crested ibis W chromosome but lost in other bird species. These results provide new insights into the evolutionary history and expression patterns for the sex chromosomes of bird species.
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Affiliation(s)
- Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiahong Wu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Tingting Cui
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Rong Dong
- Research Center for Qinling Giant Panda, Shaanxi Academy of Forestry, Xi'an, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Zhe Feng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Tianmin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiao Liu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., LTD, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yaping Yan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China.
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China.
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29
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Liang Y, Xian L, Pan J, Zhu K, Guo H, Liu B, Zhang N, Ou-Yang Y, Zhang Q, Zhang D. De Novo Genome Assembly of the Whitespot Parrotfish ( Scarus forsteni): A Valuable Scaridae Genomic Resource. Genes (Basel) 2024; 15:249. [PMID: 38397238 PMCID: PMC10888354 DOI: 10.3390/genes15020249] [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: 12/26/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Scarus forsteni, a whitespot parrotfish from the Scaridae family, is a herbivorous fish inhabiting coral reef ecosystems. The deterioration of coral reefs has highly affected the habitats of the parrotfish. The decline in genetic diversity of parrotfish emphasizes the critical importance of conserving their genetic variability to ensure the resilience and sustainability of marine ecosystems for future generations. In this study, a genome of S. forsteni was assembled de novo through using Illumina and Nanopore sequencing. The 1.71-Gb genome of S. forsteni, was assembled into 544 contigs (assembly level: contig). It exhibited an N50 length of 17.97 Mb and a GC content percentage of 39.32%. Our BUSCO analysis revealed that the complete protein of the S. forsteni genome had 98.10% integrity. Combined with structure annotation data, 34,140 (74.81%) genes were functionally annotated out of 45,638 predicted protein-coding genes. Upon comparing the genome size and TE content of teleost fishes, a roughly linear relationship was observed between these two parameters. However, TE content is not a decisive factor in determining the genome size of S. forsteni. Population history analysis results indicate that S. forsteni experienced two major population expansions, both of which occurred before the last interglacial period. In addition, through a comparative genomic analysis of the evolutionary relationship of other species, it was found that S. forsteni had the closest relationship with Cheilinus undulatus, another member of the Labridae family. Our expansion and contraction analysis of the gene family showed that the expansion genes were mainly associated with immune diseases, organismal systems, and cellular processes. At the same time, cell transcription and translation, sex hormone regulation, and other related pathways were also more prominent in the positive selection genes. The genomic sequence of S. forsteni offers valuable resources for future investigations on the conservation, evolution, and behavior of fish species.
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Affiliation(s)
- Yu Liang
- Guangxi Marine Microbial Resources Industrialization Engineering Technology Research Center, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 University Road, Nanning 530008, China
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Lin Xian
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Jinmin Pan
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Kecheng Zhu
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Huayang Guo
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Baosuo Liu
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Nan Zhang
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Yan Ou-Yang
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Qin Zhang
- Guangxi Marine Microbial Resources Industrialization Engineering Technology Research Center, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 University Road, Nanning 530008, China
| | - Dianchang Zhang
- Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
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30
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Gable SM, Bushroe N, Mendez J, Wilson A, Pinto B, Gamble T, Tollis M. Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579686. [PMID: 38405926 PMCID: PMC10888918 DOI: 10.1101/2024.02.09.579686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.
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Affiliation(s)
- Simone M. Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Jasmine Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Brendan Pinto
- 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
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
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31
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Souza-Borges CH, Utsunomia R, Varani AM, Uliano-Silva M, Lira LVG, Butzge AJ, Gomez Agudelo JF, Manso S, Freitas MV, Ariede RB, Mastrochirico-Filho VA, Penaloza C, Barria A, Porto-Foresti F, Foresti F, Hattori R, Guiguen Y, Houston RD, Hashimoto DT. De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus. Gigascience 2024; 13:giae085. [PMID: 39589439 PMCID: PMC11590113 DOI: 10.1093/gigascience/giae085] [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: 01/15/2024] [Revised: 07/31/2024] [Accepted: 10/14/2024] [Indexed: 11/27/2024] Open
Abstract
BACKGROUND Megaleporinus macrocephalus (piauçu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex determination system and thus constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for M. macrocephalus. We generated family segregation information to construct a genetic map, pool sequencing of males and females to characterize its sex system, and RNA sequencing to highlight candidate genes of M. macrocephalus sex determination. RESULTS The reference genome of M. macrocephalus is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. In the sex chromosome, based on patterns of recombination suppression, coverage, FST, and sex-specific SNPs, we distinguished a putative W-specific region that is highly differentiated, a region where Z and W still share some similarities and is undergoing degeneration, and the PAR. The sex chromosome gene repertoire includes genes from the TGF-β family (amhr2, bmp7) and the Wnt/β-catenin pathway (wnt4, wnt7a), some of which are differentially expressed. CONCLUSIONS The chromosome-level genome of piauçu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably, amhr2 and bmp7 are potential candidate genes for sex determination in M. macrocephalus.
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Affiliation(s)
| | - Ricardo Utsunomia
- School of Sciences, São Paulo State University (Unesp), Bauru, SP, 17033-360, Brazil
| | - Alessandro M Varani
- School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil
| | | | - Lieschen Valeria G Lira
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil
| | - Arno J Butzge
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil
| | - John F Gomez Agudelo
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil
| | - Shisley Manso
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil
| | - Milena V Freitas
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil
| | - Raquel B Ariede
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil
| | | | - Carolina Penaloza
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Agustín Barria
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Fábio Porto-Foresti
- School of Sciences, São Paulo State University (Unesp), Bauru, SP, 17033-360, Brazil
| | - Fausto Foresti
- Institute of Biosciences, São Paulo State University (Unesp), Botucatu, SP, 18618-689, Brazil
| | - Ricardo Hattori
- São Paulo Agency of Agribusiness and Technology (APTA), São Paulo, SP, 01037-010, Brazil
| | | | - Ross D Houston
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Diogo Teruo Hashimoto
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil
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32
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Zhao Y, Su C, He B, Nie R, Wang Y, Ma J, Song J, Yang Q, Hao J. Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome. Nat Commun 2023; 14:8190. [PMID: 38081828 PMCID: PMC10713551 DOI: 10.1038/s41467-023-44023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Parnassius glacialis is a typical "Out of the QTP" alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for "Out of the QTP" of P. glacialis.
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Affiliation(s)
- Youjie Zhao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Ruie Nie
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Junye Ma
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jingyu Song
- College of Animal Science, Shandong Agricultural University, Taian, 271000, China
| | - Qun Yang
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China.
- Nanjing College, University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
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33
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Chailertrit V, Panthum T, Kongkaew L, Chalermwong P, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Peyachoknagul S, Han K, Srikulnath K. Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus). Genomics Inform 2023; 21:e47. [PMID: 38224714 PMCID: PMC10788355 DOI: 10.5808/gi.23075] [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: 09/18/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/17/2024] Open
Abstract
Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.
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Affiliation(s)
- Visarut Chailertrit
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division, Department of Fisheries, Pathum Thani 12120, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Lalida Kongkaew
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Botany, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Surin Peyachoknagul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Korea
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources (CASTNAR), National Research University-Kasetsart University (NRU-KU), Kasetsart University, Bangkok 10900, Thailand
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Xu Y, Tang Y, Feng W, Yang Y, Cui Z. Comparative Analysis of Transposable Elements Reveals the Diversity of Transposable Elements in Decapoda and Their Effects on Genomic Evolution. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1136-1146. [PMID: 37923816 DOI: 10.1007/s10126-023-10265-w] [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: 08/20/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023]
Abstract
Transposable elements (TEs) are mobile genetic elements that exist in the host genome and exert considerable influence on the evolution of the host genome. Since crustaceans, including decapoda, are considered ideal models for studying the relationship between adaptive evolution and TEs, TEs were identified and classified in the genomes of eight decapoda species and one diplostraca species (as the outgroup) using two strategies, namely homology-based annotation and de novo annotation. The statistics and classification of TEs showed that their proportion in the genome and their taxonomic composition in decapoda were different. Moreover, correlation analysis and transcriptome data demonstrated that there were more PIF-Harbinger TEs in the genomes of Eriocheir sinensis and Scylla paramamosain, and the expression patterns of PIF-Harbingers were significantly altered under air exposure stress conditions. These results signaled that PIF-Harbingers expanded in the genome of E. sinensis and S. paramamosain and might be related to their air exposure tolerance levels. Meanwhile, sequence alignment revealed that some Jockey-like sequences (JLSs) with high similarity to specific regions of the White spot syndrome virus (WSSV) genome existed in all eight decapod species. At the same time, phylogenetic comparison exposed that the phylogenetic tree constructed by JLSs was not in agreement with that of the species tree, and the distribution of each branch was significantly different. The abovementioned results signaled that these WSSV-specific JLSs might transfer horizontally and contribute to the emergence of WSSV. This study accumulated data for expanding research on TEs in decapod species and also provided new insights and future direction for the breeding of stress-resistant and disease-resistant crab breeds.
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Affiliation(s)
- Yuanfeng Xu
- School of Marine Sciences, Ningbo University, Ningbo, 315020, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenrong Feng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yanan Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315020, China.
| | - Zhaoxia Cui
- School of Marine Sciences, Ningbo University, Ningbo, 315020, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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35
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Dallaire X, Bouchard R, Hénault P, Ulmo-Diaz G, Normandeau E, Mérot C, Bernatchez L, Moore JS. Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication. Genome Biol Evol 2023; 15:evad229. [PMID: 38085037 PMCID: PMC10752349 DOI: 10.1093/gbe/evad229] [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] [Accepted: 11/30/2023] [Indexed: 12/28/2023] Open
Abstract
Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.
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Affiliation(s)
- Xavier Dallaire
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Centre d'Études Nordiques, Université Laval, Québec, Canada
| | - Raphael Bouchard
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
| | - Philippe Hénault
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
| | - Gabriela Ulmo-Diaz
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
| | - Eric Normandeau
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
- Plateforme de bio-informatique de l’IBIS, Université Laval, Québec, Canada
| | - Claire Mérot
- CNRS, UMR 6553 ECOBIO, Université de Rennes, Rennes, France
| | - Louis Bernatchez
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
| | - Jean-Sébastien Moore
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- Centre d'Études Nordiques, Université Laval, Québec, Canada
- Ressources Aquatique Québec, Université de Rimouski, Rimouski, Canada
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Lyu K, Xiao J, Lyu S, Liu R. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. Int J Mol Sci 2023; 24:16935. [PMID: 38069258 PMCID: PMC10706760 DOI: 10.3390/ijms242316935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.
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Affiliation(s)
- Keliang Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jiajing Xiao
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shiheng Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
| | - Renyi Liu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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Bush ZD, Naftaly AFS, Dinwiddie D, Albers C, Hillers KJ, Libuda DE. Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages of C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523974. [PMID: 37961628 PMCID: PMC10634987 DOI: 10.1101/2023.01.13.523974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Genomic structural variations (SVs) and transposable elements (TEs) can be significant contributors to genome evolution, altered gene expression, and risk of genetic diseases. Recent advancements in long-read sequencing have greatly improved the quality of de novo genome assemblies and enhanced the detection of sequence variants at the scale of hundreds or thousands of bases. Comparisons between two diverged wild isolates of Caenorhabditis elegans, the Bristol and Hawaiian strains, have been widely utilized in the analysis of small genetic variations. Genetic drift, including SVs and rearrangements of repeated sequences such as TEs, can occur over time from long-term maintenance of wild type isolates within the laboratory. To comprehensively detect both large and small structural variations as well as TEs due to genetic drift, we generated de novo genome assemblies and annotations for each strain from our lab collection using both long- and short-read sequencing and compared our assemblies and annotations with that of other lab wild type strains. Within our lab assemblies, we annotate over 3.1Mb of sequence divergence between the Bristol and Hawaiian isolates: 337,584 SNPs, 94,503 small insertion-deletions (<50bp), and 4,334 structural variations (>50bp). Further, we define the location and movement of specific DNA TEs between N2 Bristol and CB4856 Hawaiian wild type isolates. Specifically, we find the N2 Bristol genome has 20.6% more TEs from the Tc1/mariner family than the CB4856 Hawaiian genome. Moreover, we identified Zator elements as the most abundant and mobile TE family in the genome. Using specific TE sequences with unique SNPs, we also identify 38 TEs that moved intrachromosomally and 9 TEs that moved interchromosomally between the N2 Bristol and CB4856 Hawaiian genomes. By comparing the de novo genome assembly of our lab collection Bristol isolate to the VC2010 Bristol assembly, we also reveal that lab lineages display over 2 Mb of total variation: 1,162 SNPs, 1,528 indels, and 897 SVs with 95% of the variation due to SVs. Overall, our work demonstrates the unique contribution of SVs and TEs to variation and genetic drift between wild type laboratory strains assumed to be isogenic despite growing evidence of genetic drift and phenotypic variation.
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Affiliation(s)
- Zachary D. Bush
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Alice F. S. Naftaly
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Devin Dinwiddie
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Cora Albers
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Kenneth J. Hillers
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| | - Diana E. Libuda
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
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Dionisio JF, Pezenti LF, de Souza RF, Sosa-Gómez DR, da Rosa R. Annotation of transposable elements in the transcriptome of the Neotropical brown stink bug Euschistus heros and its chromosomal distribution. Mol Genet Genomics 2023; 298:1377-1388. [PMID: 37646857 DOI: 10.1007/s00438-023-02063-9] [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: 01/30/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
Transposable elements (TEs) are DNA sequences capable of moving within the genome. Their distribution is very dynamic among organisms, and despite advances, there are still gaps in the understanding of the diversity and evolution of TEs in many insect species. In the case of Euschistus heros, considered the main stink bug in the soybean crop in Brazil, little is known about the participation of these elements. Therefore, the objective of the current work was to identify the different groups of transposable elements present in the E. heros transcriptome, evidencing their chromosomal distribution. Through RNA-Seq and de novo assembly, 60,009 transcripts were obtained, which were annotated locally via Blastn against specific databases. Of the 367 transcripts identified as TEs, 202 belong to Class II, with emphasis on the TIR order. Among Class I elements or retrotransposons, most were characterized as LINE. Phylogenetic analyses were performed with the protein domains, evidencing differences between Tc1-mariner sequences, which may be related to possible horizontal transfer events. The transposable elements that stood out in the transcriptome were selected for fluorescent in situ hybridization. DNA transposon probes hAT, Helitron, and Tc1-mariner showed mostly scattered signals, with the presence of some blocks. Retrotransposon probes Copia, Gypsy, Jockey, and RTE showed a more pulverized hybridization pattern, with the presence of small interstitial and/or terminal blocks. Studies like this one, integrating functional genomics and molecular cytogenetic tools, are essential to expanding knowledge about transcriptionally active mobile elements, and their behavior in the chromosomes.
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Affiliation(s)
- Jaqueline Fernanda Dionisio
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Larissa Forim Pezenti
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Daniel Ricardo Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária/Centro Nacional de Pesquisa de Soja (Embrapa Soja), Caixa Postal: 4006, Londrina, PR, CEP: 86085-981, Brazil
| | - Renata da Rosa
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil.
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39
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Reinar WB, Tørresen OK, Nederbragt AJ, Matschiner M, Jentoft S, Jakobsen KS. Teleost genomic repeat landscapes in light of diversification rates and ecology. Mob DNA 2023; 14:14. [PMID: 37789366 PMCID: PMC10546739 DOI: 10.1186/s13100-023-00302-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.
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Affiliation(s)
| | - Ole K Tørresen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Alexander J Nederbragt
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Michael Matschiner
- Department of Biosciences, University of Oslo, Oslo, Norway
- University of Oslo, Natural History Museum, Oslo, Norway
| | - Sissel Jentoft
- Department of Biosciences, University of Oslo, Oslo, Norway
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Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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41
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DiRusso JA, Clark AT. Transposable elements in early human embryo development and embryo models. Curr Opin Genet Dev 2023; 81:102086. [PMID: 37441874 PMCID: PMC10917458 DOI: 10.1016/j.gde.2023.102086] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Transposable elements (TEs), long discounted as 'selfish genomic elements,' are increasingly appreciated as the drivers of genomic evolution, genome organization, and gene regulation. TEs are particularly important in early embryo development, where advances in stem cell technologies, in tandem with improved computational and next-generation sequencing approaches, have provided an unprecedented opportunity to study the contribution of TEs to early mammalian development. Here, we summarize advances in our understanding of TEs in early human development and expand on how new stem cell-based embryo models can be leveraged to augment this understanding.
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Affiliation(s)
- Jonathan A DiRusso
- Department of Molecular, Cell and Developmental Biology, University of California, 90095 Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, 90095 Los Angeles, CA, USA.; Molecular Biology Institute, University of California, 90095 Los Angeles, CA, USA; Center for Reproductive Science, Health and Education, University of California, 90095 Los Angeles, CA, USA
| | - Amander T Clark
- Department of Molecular, Cell and Developmental Biology, University of California, 90095 Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, 90095 Los Angeles, CA, USA.; Molecular Biology Institute, University of California, 90095 Los Angeles, CA, USA; Center for Reproductive Science, Health and Education, University of California, 90095 Los Angeles, CA, USA.
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42
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Fornaini NR, Bergelová B, Gvoždík V, Černohorská H, Krylov V, Kubíčková S, Fokam EB, Badjedjea G, Evans BJ, Knytl M. Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs ( Xenopus, Pipidae). EUR J WILDLIFE RES 2023; 69:81. [PMID: 37483536 PMCID: PMC10361878 DOI: 10.1007/s10344-023-01709-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/13/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Repetitive elements have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here, we used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events - one that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.
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Affiliation(s)
- Nicola R. Fornaini
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Barbora Bergelová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Halina Černohorská
- Department of Genetics and Reproduction, CEITEC - Veterinary Research Institute, Hudcova 296/70, Brno, 62100 Czech Republic
| | - Vladimír Krylov
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Svatava Kubíčková
- Department of Genetics and Reproduction, CEITEC - Veterinary Research Institute, Hudcova 296/70, Brno, 62100 Czech Republic
| | - Eric B. Fokam
- Department of Animal Biology and Conservation, University of Buea, PO Box 63, Buea, 00237 Cameroon
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Ben J. Evans
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4K1 Canada
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4K1 Canada
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43
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Carotti E, Carducci F, Barucca M, Canapa A, Biscotti MA. Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin. Int J Mol Sci 2023; 24:11591. [PMID: 37511347 PMCID: PMC10380595 DOI: 10.3390/ijms241411591] [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: 07/04/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for genome instability, and thus silencing mechanisms were evolved to allow the coexistence between TEs and eukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatory elements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs are not sequences merely to silence; rather, they can be domesticated for the regulation of host-coding gene expression, permitting species adaptation and resilience as well as ensuring human health. This review presents the main silencing mechanisms acting in vertebrates and the importance of exploiting these mechanisms for TE control to rewire gene expression networks, challenging the general view of TEs as threatening elements.
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Affiliation(s)
| | - Federica Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (E.C.); (M.B.); (A.C.); (M.A.B.)
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44
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Gable SM, Mendez JM, Bushroe NA, Wilson A, Byars MI, Tollis M. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order. Genes (Basel) 2023; 14:1387. [PMID: 37510292 PMCID: PMC10379679 DOI: 10.3390/genes14071387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
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45
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Martelossi J, Nicolini F, Subacchi S, Pasquale D, Ghiselli F, Luchetti A. Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution. BMC Biol 2023; 21:145. [PMID: 37365567 DOI: 10.1186/s12915-023-01632-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics. RESULTS We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived ~ 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads. CONCLUSIONS We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes.
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Affiliation(s)
- Jacopo Martelossi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Filippo Nicolini
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
- Fano Marine Center, Department of Biological, Geological and Environmental Sciences, University of Bologna, Viale Adriatico 1/N, 61032, Fano, Italy
| | - Simone Subacchi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniela Pasquale
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
| | - Andrea Luchetti
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
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Paulat NS, Storer JM, Moreno-Santillán DD, Osmanski AB, Sullivan KAM, Grimshaw JR, Korstian J, Halsey M, Garcia CJ, Crookshanks C, Roberts J, Smit AFA, Hubley R, Rosen J, Teeling EC, Vernes SC, Myers E, Pippel M, Brown T, Hiller M, Rojas D, Dávalos LM, Lindblad-Toh K, Karlsson EK, Ray DA. Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia. Mol Biol Evol 2023; 40:msad092. [PMID: 37071810 PMCID: PMC10162687 DOI: 10.1093/molbev/msad092] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 04/20/2023] Open
Abstract
Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.
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Affiliation(s)
- Nicole S Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | | | | | - Austin B Osmanski
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | | | - Jenna R Grimshaw
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Jennifer Korstian
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Michaela Halsey
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Carlos J Garcia
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | | | - Jaquelyn Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | | | | | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- School of Biology, The University of St Andrews, Fife, United Kingdom
| | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Thomas Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
| | - Danny Rojas
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Valle del Cauca, Colombia
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University Stony Brook, NY
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
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47
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Zhou J, Hu J, Wang Y, Gao S. Induction and application of human naive pluripotency. Cell Rep 2023; 42:112379. [PMID: 37043354 DOI: 10.1016/j.celrep.2023.112379] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/18/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
Over the past few decades, many attempts have been made to capture different states of pluripotency in vitro. Naive and primed pluripotent stem cells, corresponding to the pluripotency states of pre- and post-implantation epiblasts, respectively, have been well characterized in mice and can be interconverted in vitro. Here, we summarize the recently reported strategies to generate human naive pluripotent stem cells in vitro. We discuss their applications in studies of regulatory mechanisms involved in early developmental processes, including identification of molecular features, X chromosome inactivation modeling, transposable elements regulation, metabolic characteristics, and cell fate regulation, as well as potential for extraembryonic differentiation and blastoid construction for embryogenesis modeling. We further discuss the naive pluripotency-related research, including 8C-like cell establishment and disease modeling. We also highlight limitations of current naive pluripotency studies, such as imperfect culture conditions and inadequate responsiveness to differentiation signals.
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Affiliation(s)
- Jianfeng Zhou
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jindian Hu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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48
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Lu Y, Rice E, Du K, Kneitz S, Naville M, Dechaud C, Volff JN, Boswell M, Boswell W, Hillier L, Tomlinson C, Milin K, Walter RB, Schartl M, Warren WC. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 2023; 33:557-571. [PMID: 37147111 PMCID: PMC10234306 DOI: 10.1101/gr.277434.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species, namely, X. maculatus, X. couchianus, and X. hellerii Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorus species and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten-Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA;
| | - Edward Rice
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Kremitzki Milin
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Ronald B Walter
- Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
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49
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Carotti E, Tittarelli E, Canapa A, Biscotti MA, Carducci F, Barucca M. LTR Retroelements and Bird Adaptation to Arid Environments. Int J Mol Sci 2023; 24:ijms24076332. [PMID: 37047324 PMCID: PMC10094322 DOI: 10.3390/ijms24076332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
TEs are known to be among the main drivers in genome evolution, leading to the generation of evolutionary advantages that favor the success of organisms. The aim of this work was to investigate the TE landscape in bird genomes to look for a possible relationship between the amount of specific TE types and environmental changes that characterized the Oligocene era in Australia. Therefore, the mobilome of 29 bird species, belonging to a total of 11 orders, was analyzed. Our results confirmed that LINE retroelements are not predominant in all species of this evolutionary lineage and highlighted an LTR retroelement dominance in species with an Australian-related evolutionary history. The bird LTR retroelement expansion might have happened in response to the Earth’s dramatic climate changes that occurred about 30 Mya, followed by a progressive aridification across most of Australian landmasses. Therefore, in birds, LTR retroelement burst might have represented an evolutionary advantage in the adaptation to arid/drought environments.
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50
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Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Mol Ecol 2023; 32:1381-1397. [PMID: 35561000 DOI: 10.1111/mec.16501] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
Abstract
Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John S Sproul
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Luana S F Lins
- Australian National Insect Collection, CSIRO, Canberra, Australia
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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