1
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Dayi M. Evolution of parasitism genes in the plant parasitic nematodes. Sci Rep 2024; 14:3733. [PMID: 38355886 PMCID: PMC10866927 DOI: 10.1038/s41598-024-54330-3] [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: 09/02/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
The plant-parasitic nematodes are considered as one of the most destructive pests, from which the migratory and sedentary endoparasitic plant parasitic nematodes infect more than 4000 plant species and cause over $100 billion crop losses annually worldwide. These nematodes use multiple strategies to infect their host and to establish a successful parasitism inside the host such as cell-wall degradation enzymes, inhibition of host defense proteins, and molecular mimicry. In the present study, the main parasitism-associated gene families were identified and compared between the migratory and sedentary endoparasitic nematodes. The results showed that the migratory and sedentary endoparasitic nematodes share a core conserved parasitism mechanism established throughout the evolution of parasitism. However, genes involved in pectin degradation and hydrolase activity are rapidly evolving in the migratory endoparasitic nematodes. Additionally, cell-wall degrading enzymes such as GH45 cellulases and pectate lyase and peptidase and peptidase inhibitors were expanded in the migratory endoparasitic nematodes. The molecular mimicry mechanism was another key finding that differs between the endoparasitic and sedentary parasitic nematodes. The PL22 gene family, which is believed to play a significant role in the molecular mechanisms of nematode parasitism, has been found to be present exclusively in migratory endoparasitic nematodes. Phylogenetic analysis has suggested that it was de novo born in these nematodes. This discovery sheds new light on the molecular evolution of these parasites and has significant implications for our understanding of their biology and pathogenicity. This study contributes to our understanding of core parasitism mechanisms conserved throughout the nematodes and provides unique clues on the evolution of parasitism and the direction shaped by the host.
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Affiliation(s)
- Mehmet Dayi
- Forestry Vocational School, Düzce University, Konuralp Campus, 81620, Düzce, Turkey.
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan.
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2
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Dai D, Xie C, Zhou Y, Bo D, Zhang S, Mao S, Liao Y, Cui S, Zhu Z, Wang X, Li F, Peng D, Zheng J, Sun M. Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization. Nat Commun 2023; 14:7156. [PMID: 37935661 PMCID: PMC10630426 DOI: 10.1038/s41467-023-42700-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
The formation and consequences of polyploidization in animals with clonal reproduction remain largely unknown. Clade I root-knot nematodes (RKNs), characterized by parthenogenesis and allopolyploidy, show a widespread geographical distribution and extensive agricultural destruction. Here, we generated 4 unzipped polyploid RKN genomes and identified a putative novel alternative telomeric element. Then we reconstructed 4 chromosome-level assemblies and resolved their genome structures as AAB for triploid and AABB for tetraploid. The phylogeny of subgenomes revealed polyploid RKN origin patterns as hybridization between haploid and unreduced gametes. We also observed extensive chromosomal fusions and homologous gene expression decrease after polyploidization, which might offset the disadvantages of clonal reproduction and increase fitness in polyploid RKNs. Our results reveal a rare pathway of polyploidization in parthenogenic polyploid animals and provide a large number of high-precision genetic resources that could be used for RKN prevention and control.
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Affiliation(s)
- Dadong Dai
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuanshuai Xie
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yayi Zhou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dexin Bo
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shurong Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengqiang Mao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yucheng Liao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Simeng Cui
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhaolu Zhu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueyu Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fanling Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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3
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Schvarzstein M, Alam F, Toure M, Yanowitz JL. An Emerging Animal Model for Querying the Role of Whole Genome Duplication in Development, Evolution, and Disease. J Dev Biol 2023; 11:26. [PMID: 37367480 PMCID: PMC10299280 DOI: 10.3390/jdb11020026] [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: 04/22/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Whole genome duplication (WGD) or polyploidization can occur at the cellular, tissue, and organismal levels. At the cellular level, tetraploidization has been proposed as a driver of aneuploidy and genome instability and correlates strongly with cancer progression, metastasis, and the development of drug resistance. WGD is also a key developmental strategy for regulating cell size, metabolism, and cellular function. In specific tissues, WGD is involved in normal development (e.g., organogenesis), tissue homeostasis, wound healing, and regeneration. At the organismal level, WGD propels evolutionary processes such as adaptation, speciation, and crop domestication. An essential strategy to further our understanding of the mechanisms promoting WGD and its effects is to compare isogenic strains that differ only in their ploidy. Caenorhabditis elegans (C. elegans) is emerging as an animal model for these comparisons, in part because relatively stable and fertile tetraploid strains can be produced rapidly from nearly any diploid strain. Here, we review the use of Caenorhabditis polyploids as tools to understand important developmental processes (e.g., sex determination, dosage compensation, and allometric relationships) and cellular processes (e.g., cell cycle regulation and chromosome dynamics during meiosis). We also discuss how the unique characteristics of the C. elegans WGD model will enable significant advances in our understanding of the mechanisms of polyploidization and its role in development and disease.
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Affiliation(s)
- Mara Schvarzstein
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
- Biology Department, The Graduate Center at the City University of New York, New York, NY 10016, USA
- Biochemistry Department, The Graduate Center at the City University of New York, New York, NY 10016, USA
| | - Fatema Alam
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
| | - Muhammad Toure
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
| | - Judith L. Yanowitz
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA;
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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4
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Conant GC. POInT: Modeling Polyploidy in the Era of Ubiquitous Genomics. Methods Mol Biol 2023; 2545:77-90. [PMID: 36720808 DOI: 10.1007/978-1-0716-2561-3_4] [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: 02/02/2023]
Abstract
Thirteen years ago, we described an evolutionary modeling tool that could resolve the orthology relationships among the homologous genomic regions created by a whole-genome duplication. This tool, which we subsequently named POInT (the Polyploid Orthology Inference Tool), was originally only useful for studying a genome duplication known from bakers' yeast and its relatives. Now, with hundreds of genome sequences that contain the relicts of ancient polyploidy available, POInT can be used to study dozens of different polyploidies, asking both questions about the history of individual events and about the commonalities and differences seen between those events. In this chapter, I give a brief history of the development of POInT as an illustration of the interconnected nature of computational biology research. I then further describe how POInT operates and some of the strengths and drawbacks of its structure. I close with a few examples of discoveries we have made using it.
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Affiliation(s)
- Gavin C Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
- Program in Genetics, North Carolina State University, Raleigh, NC, USA.
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5
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Rutter WB, Franco J, Gleason C. Rooting Out the Mechanisms of Root-Knot Nematode-Plant Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:43-76. [PMID: 35316614 DOI: 10.1146/annurev-phyto-021621-120943] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Root-knot nematodes (RKNs; Meloidogyne spp.) engage in complex parasitic interactions with many different host plants around the world, initiating elaborate feeding sites and disrupting host root architecture. Although RKNs have been the focus of research for many decades, new molecular tools have provided useful insights into the biological mechanisms these pests use to infect and manipulate their hosts. From identifying host defense mechanisms underlying resistance to RKNs to characterizing nematode effectors that alter host cellular functions, the past decade of research has significantly expanded our understanding of RKN-plant interactions, and the increasing number of quality parasite and host genomes promises to enhance future research efforts into RKNs. In this review, we have highlighted recent discoveries, summarized the current understanding within the field, and provided links to new and useful resources for researchers. Our goal is to offer insights and tools to support the study of molecular RKN-plant interactions.
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Affiliation(s)
- William B Rutter
- US Vegetable Laboratory, USDA Agricultural Research Service, Charleston, South Carolina, USA
| | - Jessica Franco
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA;
| | - Cynthia Gleason
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA;
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6
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Hao Y, Fleming J, Petterson J, Lyons E, Edger PP, Pires JC, Thorne JL, Conant GC. Convergent evolution of polyploid genomes from across the eukaryotic tree of life. G3 (BETHESDA, MD.) 2022; 12:jkac094. [PMID: 35451464 PMCID: PMC9157103 DOI: 10.1093/g3journal/jkac094] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/15/2022] [Indexed: 11/14/2022]
Abstract
By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts. We show that many of the events show a relative rate of duplicate gene loss before the first postpolyploidy speciation that is significantly higher than in later phases of their evolution. The relatively weak selective constraint experienced by the single-copy genes these losses produced leads us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate postpolyploid period. Nearly all of the events show strong evidence of biases in the duplicate losses, consistent with them being allopolyploidies, with 2 distinct progenitors contributing to the modern species. We also find ongoing and extensive reciprocal gene losses (alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is, therefore, possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass reciprocal gene loss barriers.
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Affiliation(s)
- Yue Hao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Jonathon Fleming
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Joanna Petterson
- Department of Biomedical Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - J Chris Pires
- International Plant Science Center, New York Botanical Garden, Bronx, NY 10458, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
- Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
- Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
- Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
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7
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HODDA M. Phylum Nematoda: trends in species descriptions, the documentation of diversity, systematics, and the species concept. Zootaxa 2022; 5114:290-317. [DOI: 10.11646/zootaxa.5114.1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/04/2022]
Abstract
This paper summarizes the trends in nematode species description and systematics emerging from a comparison of the latest comprehensive classification and census of Phylum Nematoda (Hodda 2022a, b) with earlier classifications (listed in Hodda 2007). It also offers some general observations on trends in nematode systematics emerging from the review of the voluminous literature used to produce the classification. The trends in nematodes can be compared with developments in the systematics of other organisms to shed light on many of the general issues confronting systematists now and into the future.
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8
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Abstract
Ancient polyploidy events are widely distributed across the evolutionary history of eukaryotes. Here, we describe a likelihood-based tool, POInT (the Polyploidy Orthology Inference Tool), for modeling ancient whole genome duplications and triplications, assigning homoeologous genes to subgenomes and inferring gene losses across different parental subgenomes after polyploidy.
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Affiliation(s)
- Yue Hao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
- Program in Genetics, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
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9
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Hao Y, Mabry ME, Edger PP, Freeling M, Zheng C, Jin L, VanBuren R, Colle M, An H, Abrahams RS, Washburn JD, Qi X, Barry K, Daum C, Shu S, Schmutz J, Sankoff D, Barker MS, Lyons E, Pires JC, Conant GC. The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. Genome Res 2021; 31:799-810. [PMID: 33863805 PMCID: PMC8092008 DOI: 10.1101/gr.270033.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/05/2021] [Indexed: 01/08/2023]
Abstract
The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Makenzie E Mabry
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Genetics and Genome Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
| | - Marivi Colle
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - R Shawn Abrahams
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Jacob D Washburn
- Plant Genetics Research Unit, USDA-ARS, Columbia, Missouri 65211, USA
| | - Xinshuai Qi
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
- Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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10
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Conant GC. The lasting after-effects of an ancient polyploidy on the genomes of teleosts. PLoS One 2020; 15:e0231356. [PMID: 32298330 PMCID: PMC7161988 DOI: 10.1371/journal.pone.0231356] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function. I inferred a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I then phylogenetically modeled the TGD's resolution via shared and independent gene losses and applied a new simulation-based statistical test for the presence of bias toward the preservation of genes from one parental subgenome. On the basis of that test, I argue that the TGD was likely an allopolyploidy. I find that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species' history. The tissues these ohnologs are expressed in, as well as their biological functions, lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes.
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Affiliation(s)
- Gavin C. Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
- Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States of America
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