1
|
Graham LA, Davies PL. Fish antifreeze protein origin in sculpins by frameshifting within a duplicated housekeeping gene. FEBS J 2024; 291:4043-4061. [PMID: 38923815 DOI: 10.1111/febs.17205] [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: 11/13/2023] [Revised: 03/25/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Antifreeze proteins (AFPs) are found in a variety of marine cold-water fishes where they prevent freezing by binding to nascent ice crystals. Their diversity (types I, II, III and antifreeze glycoproteins), as well as their scattered taxonomic distribution hint at their complex evolutionary history. In particular, type I AFPs appear to have arisen in response to the Late Cenozoic Ice Age that began ~ 34 million years ago via convergence in four different groups of fish that diverged from lineages lacking this AFP. The progenitor of the alanine-rich α-helical type I AFPs of sculpins has now been identified as lunapark, an integral membrane protein of the endoplasmic reticulum. Following gene duplication and loss of all but three of the 15 exons, the final exon, which encoded a glutamate- and glutamine-rich segment, was converted to an alanine-rich sequence by a combination of frameshifting and mutation. Subsequent gene duplications produced numerous isoforms falling into four distinct groups. The origin of the flounder type I AFP is quite different. Here, a small segment from the original antiviral protein gene was amplified and the rest of the coding sequence was lost, while the gene structure was largely retained. The independent origins of type I AFPs with up to 83% sequence identity in flounder and sculpin demonstrate strong convergent selection at the level of protein sequence for alanine-rich single alpha helices that bind to ice. Recent acquisition of these AFPs has allowed sculpins to occupy icy seawater niches with reduced competition and predation from other teleost species.
Collapse
Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| |
Collapse
|
2
|
Rives N, Lamba V, Cheng CHC, Zhuang X. Diverse origins of near-identical antifreeze proteins in unrelated fish lineages provide insights into evolutionary mechanisms of new gene birth and protein sequence convergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584730. [PMID: 38559027 PMCID: PMC10980009 DOI: 10.1101/2024.03.12.584730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Determining the origins of novel genes and the genetic mechanisms underlying the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. The convergently evolved fish antifreeze proteins provide excellent opportunities to investigate evolutionary origins and pathways of new genes. Particularly notable is the near-identical type I antifreeze proteins (AFPI) in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages, revealing different paths by which a similar protein arose from diverse genomic resources. Comprehensive comparative analyses of de novo sequenced genome of the winter flounder and grubby sculpin, available high-quality genome of the cunner and 14 other relevant species found that the near-identical AFPI originated from a distinct genetic precursor in each lineage. Each independently evolved a coding region for the novel ice-binding protein while retaining sequence identity in the regulatory regions with their respective ancestor. The deduced evolutionary processes and molecular mechanisms are consistent with the Innovation-Amplification-Divergence (IAD) model applicable to AFPI formation in all three lineages, a new Duplication-Degeneration-Divergence (DDD) model we propose for the sculpin lineage, and a DDD model with gene fission for the cunner lineage. This investigation illustrates the multiple ways by which a novel functional gene with sequence convergence at the protein level could evolve across divergent species, advancing our understanding of the mechanistic intricacies in new gene formation.
Collapse
|
3
|
Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024; 19:1623-1678. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [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: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
Collapse
Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
| |
Collapse
|
4
|
Mazloum A, Karagyaur M, Chernyshev R, van Schalkwyk A, Jun M, Qiang F, Sprygin A. Post-genomic era in agriculture and veterinary science: successful and proposed application of genetic targeting technologies. Front Vet Sci 2023; 10:1180621. [PMID: 37601766 PMCID: PMC10434572 DOI: 10.3389/fvets.2023.1180621] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Gene editing tools have become an indispensable part of research into the fundamental aspects of cell biology. With a vast body of literature having been generated based on next generation sequencing technologies, keeping track of this ever-growing body of information remains challenging. This necessitates the translation of genomic data into tangible applications. In order to address this objective, the generated Next Generation Sequencing (NGS) data forms the basis for targeted genome editing strategies, employing known enzymes of various cellular machinery, in generating organisms with specifically selected phenotypes. This review focuses primarily on CRISPR/Cas9 technology in the context of its advantages over Zinc finger proteins (ZNF) and Transcription activator-like effector nucleases (TALEN) and meganucleases mutagenesis strategies, for use in agricultural and veterinary applications. This review will describe the application of CRISPR/Cas9 in creating modified organisms with custom-made properties, without the undesired non-targeted effects associated with virus vector vaccines and bioactive molecules produced in bacterial systems. Examples of the successful and unsuccessful applications of this technology to plants, animals and microorganisms are provided, as well as an in-depth look into possible future trends and applications in vaccine development, disease resistance and enhanced phenotypic traits will be discussed.
Collapse
Affiliation(s)
- Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
| | - Maxim Karagyaur
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
| | | | - Antoinette van Schalkwyk
- Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort, South Africa
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Ma Jun
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Fu Qiang
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | | |
Collapse
|
5
|
Widen SA, Bes IC, Koreshova A, Pliota P, Krogull D, Burga A. Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities. Science 2023; 380:eade0705. [PMID: 37384706 DOI: 10.1126/science.ade0705] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 05/17/2023] [Indexed: 07/01/2023]
Abstract
Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.
Collapse
Affiliation(s)
- Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Israel Campo Bes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| |
Collapse
|
6
|
Gilbert C, Maumus F. Sidestepping Darwin: horizontal gene transfer from plants to insects. CURRENT OPINION IN INSECT SCIENCE 2023; 57:101035. [PMID: 37061183 DOI: 10.1016/j.cois.2023.101035] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/06/2023]
Abstract
Horizontal transfer of genetic material (HT) is the passage of DNA between organisms by means other than reproduction. Increasing numbers of HT are reported in insects, with bacteria, fungi, plants, and insects acting as the main sources of these transfers. Here, we provide a detailed account of plant-to-insect HT events. At least 14 insect species belonging to 6 orders are known to have received plant genetic material through HT. One of them, the whitefly Bemisia tabaci (Middle East Asia Minor 1), concentrates most of these transfers, with no less than 28 HT events yielding 55 plant-derived genes in this species. Several plant-to-insect HT events reported so far involve gene families known to play a role in plant-parasite interactions. We highlight methodological approaches that may further help characterize these transfers. We argue that plant-to-insect HT is likely more frequent than currently appreciated and that in-depth studies of these transfers will shed new light on plant-insect interactions.
Collapse
Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Evolution, Génomes, Comportement et Ecologie, Gif-sur-Yvette, France.
| | - Florian Maumus
- Université Paris-Saclay, INRAE, URGI, Versailles, France
| |
Collapse
|
7
|
Burns JA, Gruber DF, Gaffney JP, Sparks JS, Brugler MR. Transcriptomics of a Greenlandic Snailfish Reveals Exceptionally High Expression of Antifreeze Protein Transcripts. Evol Bioinform Online 2022; 18:11769343221118347. [PMID: 35991949 PMCID: PMC9386813 DOI: 10.1177/11769343221118347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/08/2022] [Indexed: 11/15/2022] Open
Abstract
Polar fishes have evolved antifreeze proteins (AFPs) that allow them to survive in subzero temperatures. We performed deep transcriptomic sequencing on a postlarval/juvenile variegated snailfish, Liparis gibbus (Actinopterygii: Scorpaeniformes: Cottoidei: Liparidae), living in an iceberg habitat (-2°C) in Eastern Greenland and report detection of highly expressed transcripts that code for putative AFPs from 2 gene families, Type I and LS-12-like proteins (putative Type IV AFPs). The transcripts encoding both proteins have expression levels among the top <1% of expressed genes in the fish. The Type I AFP sequence is different from a reported Type I AFP from the same species, possibly expressed from a different genetic locus. While prior findings from related adult sculpins suggest that LS-12-like/Type IV AFPs may not have a role in antifreeze protection, our finding of very high relative gene expression of the LS-12-like gene suggests that highly active transcription of the gene is important to the fish in the iceberg habitat and raises the possibility that weak or combinatorial antifreeze activity could be beneficial. These findings highlight the physiological importance of antifreeze proteins to the survival of fishes living in polar habitats.
Collapse
Affiliation(s)
- John A Burns
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - David F Gruber
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY, USA
- The Graduate Center, Program in Biology, City University of New York, New York, NY, USA
| | - Jean P Gaffney
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY, USA
- The Graduate Center, Program in Biology, City University of New York, New York, NY, USA
| | - John S Sparks
- Department of Ichthyology, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
| |
Collapse
|
8
|
Bartha L, Mandáková T, Kovařík A, Bulzu PA, Rodde N, Mahelka V, Lysak MA, Fustier MA, Šafář J, Cápal P, Keresztes L, Banciu HL. Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer. THE NEW PHYTOLOGIST 2022; 235:1246-1259. [PMID: 35460285 DOI: 10.1111/nph.18171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.
Collapse
Affiliation(s)
- László Bartha
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeş-Bolyai University, 400271, Cluj-Napoca, Romania
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265, Brno, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, 370 05, České Budějovice, Czech Republic
| | - Nathalie Rodde
- French Plant Genomic Resource Center, INRAE-CNRGV, 31320, Castanet Tolosan, France
| | - Václav Mahelka
- Institute of Botany, Czech Academy of Sciences, 25243, Průhonice, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | | | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 779 00, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 779 00, Olomouc, Czech Republic
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
- Centre of Systems Biology, Biodiversity and Bioresources (3B), Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
| | - Horia L Banciu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeş-Bolyai University, 400271, Cluj-Napoca, Romania
- Centre of Systems Biology, Biodiversity and Bioresources (3B), Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
| |
Collapse
|
9
|
Béliveau C, Gagné P, Picq S, Vernygora O, Keeling CI, Pinkney K, Doucet D, Wen F, Spencer Johnston J, Maaroufi H, Boyle B, Laroche J, Dewar K, Juretic N, Blackburn G, Nisole A, Brunet B, Brandão M, Lumley L, Duan J, Quan G, Lucarotti CJ, Roe AD, Sperling FAH, Levesque RC, Cusson M. The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins. Genome Biol Evol 2022; 14:evac087. [PMID: 35668612 PMCID: PMC9210311 DOI: 10.1093/gbe/evac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce "antifreeze proteins" (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a "zonadhesin-like" protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the "zonadhesin-like" protein as precursor of tortricid AFPs.
Collapse
Affiliation(s)
- Catherine Béliveau
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Patrick Gagné
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Sandrine Picq
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Oksana Vernygora
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Christopher I Keeling
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, Quebec, Canada
| | - Kristine Pinkney
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Daniel Doucet
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Fayuan Wen
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington DC, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, 2475 College Station, Texas, USA
| | - Halim Maaroufi
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Brian Boyle
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Jérôme Laroche
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Ken Dewar
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - Nikoleta Juretic
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Gwylim Blackburn
- Pacific Forestry Centre, Natural Resources Canada, Victoria, British Columbia, Canada
| | - Audrey Nisole
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Bryan Brunet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Marcelo Brandão
- Laboratório de Biologia Integrativa e Sistêmica - CBMEG/UNICAMP, Campinas, Brazil
| | - Lisa Lumley
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jun Duan
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Guoxing Quan
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | | | - Amanda D Roe
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Michel Cusson
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, Quebec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| |
Collapse
|
10
|
Graham LA, Gauthier SY, Davies PL. Origin of an antifreeze protein gene in response to Cenozoic climate change. Sci Rep 2022; 12:8536. [PMID: 35595816 PMCID: PMC9122973 DOI: 10.1038/s41598-022-12446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Antifreeze proteins (AFPs) inhibit ice growth within fish and protect them from freezing in icy seawater. Alanine-rich, alpha-helical AFPs (type I) have independently (convergently) evolved in four branches of fishes, one of which is a subsection of the righteye flounders. The origin of this gene family has been elucidated by sequencing two loci from a starry flounder, Platichthys stellatus, collected off Vancouver Island, British Columbia. The first locus had two alleles that demonstrated the plasticity of the AFP gene family, one encoding 33 AFPs and the other allele only four. In the closely related Pacific halibut, this locus encodes multiple Gig2 (antiviral) proteins, but in the starry flounder, the Gig2 genes were found at a second locus due to a lineage-specific duplication event. An ancestral Gig2 gave rise to a 3-kDa "skin" AFP isoform, encoding three Ala-rich 11-a.a. repeats, that is expressed in skin and other peripheral tissues. Subsequent gene duplications, followed by internal duplications of the 11 a.a. repeat and the gain of a signal sequence, gave rise to circulating AFP isoforms. One of these, the "hyperactive" 32-kDa Maxi likely underwent a contraction to a shorter 3.3-kDa "liver" isoform. Present day starry flounders found in Pacific Rim coastal waters from California to Alaska show a positive correlation between latitude and AFP gene dosage, with the shorter allele being more prevalent at lower latitudes. This study conclusively demonstrates that the flounder AFP arose from the Gig2 gene, so it is evolutionarily unrelated to the three other classes of type I AFPs from non-flounders. Additionally, this gene arose and underwent amplification coincident with the onset of ocean cooling during the Cenozoic ice ages.
Collapse
Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Sherry Y Gauthier
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.
| |
Collapse
|
11
|
Davies PL. Reflections on antifreeze proteins and their evolution. Biochem Cell Biol 2022; 100:282-291. [PMID: 35580352 DOI: 10.1139/bcb-2022-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The discovery of radically different antifreeze proteins (AFPs) in fishes during the 1970s and 1980s suggested that these proteins had recently and independently evolved to protect teleosts from freezing in icy seawater. Early forays into the isolation and characterization of AFP genes in these fish showed they were massively amplified, often in long tandem repeats. The work of many labs in the 1980s onward led to the discovery and characterization of AFPs in other kingdoms, such as insects, plants, and many different microorganisms. The distinct ice-binding property that these ice-binding proteins (IBPs) share has facilitated their purification through adsorption to ice, and the ability to produce recombinant versions of IBPs has enabled their structural characterization and the mapping of their ice-binding sites (IBSs) using site-directed mutagenesis. One hypothesis for their ice affinity is that the IBS organizes surface waters into an ice-like pattern that freezes the protein onto ice. With access now to a rapidly expanding database of genomic sequences, it has been possible to trace the origins of some fish AFPs through the process of gene duplication and divergence, and to even show the horizontal transfer of an AFP gene from one species to another.
Collapse
Affiliation(s)
- Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| |
Collapse
|
12
|
Han Z, Xu S, Gao T. Unexpected complex horizontal gene transfer in teleost fish. Curr Zool 2022; 69:222-223. [PMID: 37092000 PMCID: PMC10120958 DOI: 10.1093/cz/zoac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316002, China
| | - Shengyong Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316002, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316002, China
| |
Collapse
|
13
|
Kejnovsky E, Jedlicka P. Nucleic acids movement and its relation to genome dynamics of repetitive DNA: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components?: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components? Bioessays 2022; 44:e2100242. [PMID: 35112737 DOI: 10.1002/bies.202100242] [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: 10/14/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 11/07/2022]
Abstract
There is growing evidence of evolutionary genome plasticity. The evolution of repetitive DNA elements, the major components of most eukaryotic genomes, involves the amplification of various classes of mobile genetic elements, the expansion of satellite DNA, the transfer of fragments or entire organellar genomes and may have connections with viruses. In addition to various repetitive DNA elements, a plethora of large and small RNAs migrate within and between cells during individual development as well as during evolution and contribute to changes of genome structure and function. Such migration of DNA and RNA molecules often results in horizontal gene transfer, thus shaping the whole genomic network of interconnected species. Here, we propose that a high evolutionary dynamism of repetitive genome components is often related to the migration/movement of DNA or RNA molecules. We speculate that the cytoplasm is probably an ideal compartment for such evolutionary experiments.
Collapse
Affiliation(s)
- Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| |
Collapse
|
14
|
Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA. Why sequence all eukaryotes? Proc Natl Acad Sci U S A 2022; 119:e2115636118. [PMID: 35042801 PMCID: PMC8795522 DOI: 10.1073/pnas.2115636118] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
Collapse
Affiliation(s)
- Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Anna K Childers
- Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Jennifer A M Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia
- University of Canberra, Bruce, ACT 2617, Australia
| | - Kevin J Hackett
- Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - W John Kress
- Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Nancy A Moran
- Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
| |
Collapse
|
15
|
Plant to Insect Horizontal Gene Transfer: Empowering Whiteflies. Trends Genet 2021; 37:688-690. [PMID: 33941397 DOI: 10.1016/j.tig.2021.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/16/2021] [Indexed: 11/24/2022]
Abstract
Horizontal gene transfer (HGT) is a well-documented evolutionary driving phenomenon in prokaryotes and eukaryotes, but its impact on the plant kingdom has remained elusive. A recent study provides compelling evidences, which support the idea that a plant-derived gene allows for the detoxification of plant defense metabolites in a polyphagous arthropod herbivore.
Collapse
|