1
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Park SJ, Silic MR, Staab PL, Chen J, Zackschewski EL, Zhang G. Evolution of two-pore domain potassium channels and their gene expression in zebrafish embryos. Dev Dyn 2024; 253:722-749. [PMID: 38270285 PMCID: PMC11269526 DOI: 10.1002/dvdy.690] [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: 09/27/2023] [Revised: 12/10/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND The two-pore domain potassium (K2P) channels are a major type of potassium channels that maintain the cell membrane potential by conducting passive potassium leak currents independent of voltage change. They play prominent roles in multiple physiological processes, including neuromodulation, perception of pain, breathing and mood control, and response to volatile anesthetics. Mutations in K2P channels have been linked to many human diseases, such as neuronal and cardiovascular disorders and cancers. Significant progress has been made to understand their protein structures, physiological functions, and pharmacological modifiers. However, their expression and function during embryonic development remain largely unknown. RESULTS We employed the zebrafish model and identified 23 k2p genes using BLAST search and gene cloning. We first analyzed vertebrate K2P channel evolution by phylogenetic and syntenic analyses. Our data revealed that the six subtypes of the K2P genes have already evolved in invertebrates long before the emergence of vertebrates. Moreover, the vertebrate K2P gene number increased, most likely due to two whole-genome duplications. Furthermore, we examined zebrafish k2p gene expression during early embryogenesis by in situ hybridization. Each subgroup's genes showed similar but distinct gene expression domains with some exceptions. Most of them were expressed in neural tissues consistent with their known function of neural excitability regulation. However, a few k2p genes were expressed temporarily in specific tissues or organs, suggesting that these K2P channels may be needed for embryonic development. CONCLUSIONS Our phylogenetic and developmental analyses of K2P channels shed light on their evolutionary history and potential roles during embryogenesis related to their physiological functions and human channelopathies.
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Affiliation(s)
- Sung Jun Park
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
| | - Martin R. Silic
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
| | - Peyton L. Staab
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
| | - Jiapei Chen
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
| | - Ethan L. Zackschewski
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
| | - GuangJun Zhang
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
- Purdue University Center for Cancer Research, Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
- Purdue Institute for Inflammation, Immunology and Infectious Diseases (PI4D), Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
- Purdue Institute for Integrative Neuroscience, Purdue University, 625 Harrison Street, West Lafayette, Indiana. 47906. USA
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2
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Qi M, Clark J, Moody ERR, Pisani D, Donoghue PCJ. Molecular Dating of the Teleost Whole Genome Duplication (3R) Is Compatible With the Expectations of Delayed Rediploidization. Genome Biol Evol 2024; 16:evae128. [PMID: 38913570 PMCID: PMC11259977 DOI: 10.1093/gbe/evae128] [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: 11/10/2023] [Revised: 05/10/2024] [Accepted: 06/05/2024] [Indexed: 06/26/2024] Open
Abstract
Vertebrate evolution has been punctuated by three whole genome duplication events that have been implicated causally in phenotypic evolution, from the origin of phenotypic novelties to explosive diversification. Arguably, the most dramatic of these is the 3R whole genome duplication event associated with the origin of teleost fishes which comprise more than half of all living vertebrate species. However, tests of a causal relationship between whole genome duplication and teleost diversification have proven difficult due to the challenge of establishing the timing of these phenomena. Here we show, based on molecular clock dating of concatenated gene alignments, that the 3R whole genome duplication event occurred in the early-middle Permian (286.18 to 267.20 million years ago; Ma), 52.02 to 12.84 million years (Myr) before the divergence of crown-teleosts in the latest Permian-earliest Late Triassic (254.36 to 234.16 Ma) and long before the major pulses of teleost diversification in Ostariophysi and Percomorpha (56.37 to 100.17 Myr and at least 139.24 to 183.29 Myr later, respectively). The extent of this temporal gap between putative cause and effect precludes 3R as a deterministic driver of teleost diversification. However, these age constraints remain compatible with the expectations of a prolonged rediploidization process following whole genome duplication which, through the effects of chromosome rearrangement and gene loss, remains a viable mechanism to explain the evolution of teleost novelties and diversification.
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Affiliation(s)
- Minbo Qi
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK
| | - James Clark
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK
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3
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Ferguson S, Jones A, Murray K, Andrew R, Schwessinger B, Borevitz J. Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence. Genome Res 2024; 34:606-619. [PMID: 38589251 PMCID: PMC11146599 DOI: 10.1101/gr.277999.123] [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: 04/19/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression and reproduction. Despite the need to conserve genome architecture, a high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing and de novo assembly of 33 phylogenetically diverse, wild and naturally evolving Eucalyptus species, covering 1-50 million years of diverging genome evolution to measure genome architectural conservation and describe architectural divergence. The investigation of these genomes revealed that following lineage divergence, genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and the subsequent divergence beyond recognition of rearrangements become the primary driver of genome divergence. The loss of syntenic regions also contribute to genome divergence but at a slower pace than that of rearrangements. We hypothesize that duplications and translocations are potentially the greatest contributors to Eucalyptus genome divergence.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- Weigel Department, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Rose Andrew
- Botany & N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
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4
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Zhou Z, Li C, Yuan Q, Chi Y, Li Y, Yan Y, Al-Farraj SA, Stover NA, Chen Z, Chen X. Single-cell transcriptomic analysis reveals genome evolution in predatory litostomatean ciliates. Eur J Protistol 2024; 93:126062. [PMID: 38368736 DOI: 10.1016/j.ejop.2024.126062] [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: 11/23/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
Many ciliated protists prey on other large microbial organisms, including other protists and microscopic metazoans. The ciliate class Litostomatea unites both predatory and endosymbiotic species. The evolution of predation ability in ciliates remains poorly understood, in part, due to a lack of genomic data. To fill this gap, we acquired the transcriptome profiles of six predatory litostomateans using single-cell sequencing technology and investigated their transcriptomic features. Our results show that: (1) in contrast to non-predatory ciliates, the predatory litostomateans have expanded gene families associated with transmembrane activity and reactive oxidative stress response pathways, potentially as a result of cellular behaviors such as fast contraction and extension; (2) the expansion of the calcium-activated BK potassium channel gene family, which hypothetically regulates cell contractility, is an ancient evolutionary event for the class Litostomatea, suggesting a rewired metabolism associated with the hunting behavior of predatory ciliates; and (3) three whole genome duplication (WGD) events have been detected in litostomateans, with genes associated with biosynthetic processes, transmembrane activity, and calcium-activated potassium channel activity being retained during the WGD events. In addition, we explored the evolutionary relationships among 17 ciliate species, including eight litostomateans, and provided a rich foundational dataset for future in-depth phylogenomic studies of Litostomatea. Our comprehensive analyses suggest that the rewired cellular metabolism via expanded gene families and WGD events might be the potential genetic basis for the predation ability of raptorial ciliates.
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Affiliation(s)
- Zhaorui Zhou
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Chao Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qingxiang Yuan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Chi
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yuqing Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria 61625, USA.
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China; Suzhou Research Institute, Shandong University, Suzhou 215123, China.
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5
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Fujimori C, Sugimoto K, Ishida M, Yang C, Kayo D, Tomihara S, Sano K, Akazome Y, Oka Y, Kanda S. Long-lasting redundant gnrh1/3 expression in GnRH neurons enabled apparent switching of paralog usage during evolution. iScience 2024; 27:109304. [PMID: 38464591 PMCID: PMC10924128 DOI: 10.1016/j.isci.2024.109304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 12/08/2023] [Accepted: 02/16/2024] [Indexed: 03/12/2024] Open
Abstract
Expressed subtype of paralogous genes in functionally homologous cells sometimes show differences across species, the reasons for which have not been explained. The present study examined hypophysiotropic gonadotropin-releasing hormone (GnRH) neurons in vertebrates to investigate this mechanism. These neurons express either gnrh1 or gnrh3 paralogs, depending on the species, and apparent switching of the expressed paralogs in them occurred at least four times in vertebrate evolution. First, we found redundant expression of gnrh1 and gnrh3 in a single neuron in piranha and hypothesized that it may represent an ancestral GnRH system. Moreover, the gnrh1/gnrh3 enhancer of piranha induced reporter RFP/GFP co-expression in a single hypophysiotropic GnRH neuron in both zebrafish and medaka, whose GnRH neurons only express either gnrh3 or gnrh1. Thus, we propose that redundant expression of gnrh1/3 of relatively recent common ancestors may be the key to apparent switching of the paralog usage among present-day species.
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Affiliation(s)
- Chika Fujimori
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Optics and Imaging Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kohei Sugimoto
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Mio Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Christopher Yang
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Daichi Kayo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Soma Tomihara
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, Sakado, Saitama, Japan
| | - Yasuhisa Akazome
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Yoshitaka Oka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shinji Kanda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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6
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Nunes WVB, Oliveira DS, Dias GDR, Carvalho AB, Caruso ÍP, Biselli JM, Guegen N, Akkouche A, Burlet N, Vieira C, Carareto CMA. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (BETHESDA, MD.) 2024; 14:jkad299. [PMID: 38156703 PMCID: PMC10917504 DOI: 10.1093/g3journal/jkad299] [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: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between Drosophila mauritiana and Drosophila simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 MYA. Evolutionary rates, expression, and transcription factor-binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, we explored the expression of OdsH in Drosophila arizonae and Drosophila mojavensis, a pair of sister species with incomplete reproductive isolation. Our data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, we have proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. Our results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans.
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Affiliation(s)
- William Vilas Boas Nunes
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Daniel Siqueira Oliveira
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Guilherme de Rezende Dias
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Antonio Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Ícaro Putinhon Caruso
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Joice Matos Biselli
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Nathalie Guegen
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Abdou Akkouche
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claudia M A Carareto
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
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7
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Ferguson S, Jones A, Murray K, Andrew RL, Schwessinger B, Bothwell H, Borevitz J. Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus. Gigascience 2024; 13:giae029. [PMID: 38869149 PMCID: PMC11170218 DOI: 10.1093/gigascience/giae029] [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: 11/05/2023] [Revised: 03/11/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Structural variations (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely related Eucalyptus species to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals of Eucalyptus melliodora and Eucalyptus sideroxylon, along with recent high-quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads in E. melliodora and E. sideroxylon, respectively. Focusing on inversions and translocations, symmetric SVs that are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076 Germany
| | - Rose L Andrew
- Botany & N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Helen Bothwell
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
- Warnell School of Forestry & Natural Resources, University of Georgia, Athens 30602 GA, United States
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
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8
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Yamanaka T, Matsui H. Modeling familial and sporadic Parkinson's disease in small fishes. Dev Growth Differ 2024; 66:4-20. [PMID: 37991125 DOI: 10.1111/dgd.12904] [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: 09/01/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
The establishment of animal models for Parkinson's disease (PD) has been challenging. Nevertheless, once established, they will serve as valuable tools for elucidating the causes and pathogenesis of PD, as well as for developing new strategies for its treatment. Following the recent discovery of a series of PD causative genes in familial cases, teleost fishes, including zebrafish and medaka, have often been used to establish genetic PD models because of their ease of breeding and gene manipulation, as well as the high conservation of gene orthologs. Some of the fish lines can recapitulate PD phenotypes, which are often more pronounced than those in rodent genetic models. In addition, a new experimental teleost fish, turquoise killifish, can be used as a sporadic PD model, because it spontaneously manifests age-dependent PD phenotypes. Several PD fish models have already made significant contributions to the discovery of novel PD pathological features, such as cytosolic leakage of mitochondrial DNA and pathogenic phosphorylation in α-synuclein. Therefore, utilizing various PD fish models with distinct degenerative phenotypes will be an effective strategy for identifying emerging facets of PD pathogenesis and therapeutic modalities.
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Affiliation(s)
- Tomoyuki Yamanaka
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
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9
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Blasweiler A, Megens HJ, Goldman MRG, Tadmor-Levi R, Lighten J, Groenen MAM, Dirks RP, Jansen HJ, Spaink HP, David L, Boudinot P, Wiegertjes GF. Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication. Genomics 2023; 115:110723. [PMID: 37804957 DOI: 10.1016/j.ygeno.2023.110723] [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: 06/13/2023] [Revised: 08/22/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023]
Abstract
Allopolyploids often experience subgenome dominance, with one subgenome showing higher levels of gene expression and greater gene retention. Here, we address the functionality of both subgenomes of allotetraploid common carp (Cyprinus carpio) by analysing a functional network of interferon-stimulated genes (ISGs) crucial in anti-viral immune defence. As an indicator of subgenome dominance we investigated retainment of a core set of ohnologous ISGs. To facilitate our functional genomic analysis a high quality genome was assembled (WagV4.0). Transcriptome data from an in vitro experiment mimicking a viral infection was used to infer ISG expression. Transcriptome analysis confirmed induction of 88 ISG ohnologs on both subgenomes. In both control and infected states, average expression of ISG ohnologs was comparable between the two subgenomes. Also, the highest expressing and most inducible gene copies of an ohnolog pair could be derived from either subgenome. We found no strong evidence of subgenome dominance for common carp.
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Affiliation(s)
- A Blasweiler
- Aquaculture and Fisheries, Wageningen University, the Netherlands; Animal Breeding and Genomics, Wageningen University, the Netherlands.
| | - H-J Megens
- Animal Breeding and Genomics, Wageningen University, the Netherlands
| | - M R G Goldman
- Aquaculture and Fisheries, Wageningen University, the Netherlands
| | - R Tadmor-Levi
- Dept. of Animal Sciences, RH Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Israel
| | - J Lighten
- Biosciences, University of Exeter, United Kingdom
| | - M A M Groenen
- Animal Breeding and Genomics, Wageningen University, the Netherlands
| | - R P Dirks
- Future Genomics Technologies B.V., the Netherlands
| | - H J Jansen
- Future Genomics Technologies B.V., the Netherlands
| | - H P Spaink
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - L David
- Dept. of Animal Sciences, RH Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Israel
| | - P Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, 78350, France
| | - G F Wiegertjes
- Aquaculture and Fisheries, Wageningen University, the Netherlands
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10
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Zhang Z, Liu Y, Zhao W, Ji M. Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers. MICROBIOME 2023; 11:228. [PMID: 37848997 PMCID: PMC10583317 DOI: 10.1186/s40168-023-01621-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/14/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood. RESULTS Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms. CONCLUSION These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.
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Affiliation(s)
- Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mukan Ji
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
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11
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Gouife M, Wang F, Ban Z, Yue X, Jiang J, Xie J. Molecular and functional characterization of two granulocyte colony stimulating factors in goldfish (Carassius auratus L.). Comp Biochem Physiol B Biochem Mol Biol 2023; 268:110879. [PMID: 37490965 DOI: 10.1016/j.cbpb.2023.110879] [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: 06/02/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023]
Abstract
Granulocyte colony-stimulating factor (GCSF) is a member of the hematopoietic growth factor family that acts primarily on neutrophils and neutrophilic precursors to promote cell proliferation and differentiation. Although multiple GCSF genes have been found in teleosts, knowledge of their functions during fish hematopoietic development is still limited. Here, we report for the first time the molecular and functional characterization of two goldfish GCSFs (gfGCSF-a and gfGCSF-b). The open reading frame (ORF) of the gfGCSF-a and gfGCSF-b cDNA transcript consisted respectively of 624 bp and 678 bp with its ORF encoding 207 and 225 amino acids (aa), with a 17 aa signal peptide for each gene and a conserved domain of the IL-6 superfamily. Treatment of goldfish head kidney leukocytes (HKLs) with LPS increased gfGCSF-a and gfGCSF-b mRNA expression levels, also exposure of HKLs to either heat-killed or live A. hydrophila, induced transcriptional upregulation of gfGCSF-a and gfGCSF-b levels. Recombinant gfGCSF-a and gfGCSF-b protein (rgGCSF-a and rgGCSF-b) induced a dose-dependent production of TNFα and IL-1β from goldfish neutrophils. In vitro experiments showed rgGCSF-a and rgGCSF-b differentially promoted the proliferation and differentiation of leukocytes in goldfish. Furthermore, treatment of HKLs with rgGCSF-a showed significant upregulation of mRNA levels of the hematopoietic transcription factor GATA2, Runx1, MafB, and cMyb, while gfGCSF-b induces not only all four transcriptional factors mentioned above but also CEBPα. Our results indicate that goldfish GCSF-a and GCSF-b are important regulators of neutrophil proliferation and differentiation, which could stimulate different stages and lineages of hematopoiesis.
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Affiliation(s)
- Moussa Gouife
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China. https://twitter.com/Mouskharim
| | - Feiyang Wang
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Ziqi Ban
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xinyuan Yue
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jianhu Jiang
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang 313001, China.
| | - Jiasong Xie
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China; National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo, Zhejiang 315211, China; Key Laboratory of Aquacultural Biotechnology, Ministry of Education, Ningbo, Zhejiang 315211, China.
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12
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Peng F, Zhou L, Lu W, Gan R, Lu M, Li Z, Zhang X, Wang Y, Gui J. Genomic and Transcriptional Profiles of Kelch-like ( klhl) Gene Family in Polyploid Carassius Complex. Int J Mol Sci 2023; 24:8367. [PMID: 37176071 PMCID: PMC10179623 DOI: 10.3390/ijms24098367] [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: 12/14/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select Kelch-like (klhl) genes to study the evolution of the duplicated genes in the polyploid Carassius complex, including amphidiploid C. auratus and amphitriploid C. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most of Carassius klhl genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during Carassius evolution. The lineage-specific expansion and biased retention/loss of klhl genes are also found in Carassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of klhls in response to Carassius herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three C. gibelio gynogenetic clones. Finally, we find that most C. gibelio klhl genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for Cgklhl genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.
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Affiliation(s)
- Fang Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijia Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruihai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaojuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Gout JF, Hao Y, Johri P, Arnaiz O, Doak TG, Bhullar S, Couloux A, Guérin F, Malinsky S, Potekhin A, Sawka N, Sperling L, Labadie K, Meyer E, Duharcourt S, Lynch M. Dynamics of Gene Loss following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex. Mol Biol Evol 2023; 40:msad107. [PMID: 37154524 PMCID: PMC10195154 DOI: 10.1093/molbev/msad107] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD-derived paralogs are maintained over long evolutionary periods, and the relative contributions of different selective pressures to their maintenance are still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliate Paramecium tetraurelia and two of its sister species from the Paramecium aurelia complex. Here, we report the genome sequence and analysis of 10 additional P. aurelia species and 1 additional out group, revealing aspects of post-WGD evolution in 13 species sharing a common ancestral WGD. Contrary to the morphological radiation of vertebrates that putatively followed two WGD events, members of the cryptic P. aurelia complex have remained morphologically indistinguishable after hundreds of millions of years. Biases in gene retention compatible with dosage constraints appear to play a major role opposing post-WGD gene loss across all 13 species. In addition, post-WGD gene loss has been slower in Paramecium than in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong in Paramecium. A near complete lack of recent single-gene duplications in Paramecium provides additional evidence for strong selective pressures against gene dosage changes. This exceptional data set of 13 species sharing an ancestral WGD and 2 closely related out group species will be a useful resource for future studies on Paramecium as a major model organism in the evolutionary cell biology.
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Affiliation(s)
- Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, IN
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
- Department of Biological Sciences, Mississippi State University, Starkville, MS
| | - Yue Hao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ
| | - Parul Johri
- Department of Biology, Indiana University, Bloomington, IN
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN
| | - Simran Bhullar
- Institut de biologie de l’ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Fréderic Guérin
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Sophie Malinsky
- Institut de biologie de l’ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, Paris, France
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Natalia Sawka
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Eric Meyer
- Institut de biologie de l’ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, Paris, France
| | | | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
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14
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Niu H, Pang Y, Xie L, Yu Q, Shen Y, Li J, Xu X. Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella). BMC Genomics 2023; 24:73. [PMID: 36782132 PMCID: PMC9926789 DOI: 10.1186/s12864-023-09159-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND A considerable fraction of microRNAs (miRNAs) are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of miRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for the loss and acquisition of miRNA and miRNA clusters. RESULTS The results demonstrated that several novel miRNAs arose throughout grass carp evolution. Duplication and de novo production were critical strategies for miRNA cluster formation. Duplicates accounted for a smaller fraction of the expansion in the grass carp miRNA than de novo creation. Clustered miRNAs are more conserved and change slower, whereas unique miRNAs usually have high evolution rates and low expression levels. The expression level of miRNA expression in clusters is strongly correlated. CONCLUSIONS This study examines the genomic distribution, evolutionary background, and expression regulation of grass carp miRNAs. Our findings provide novel insights into the genesis and development of miRNA clusters in teleost.
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Affiliation(s)
- Huiqin Niu
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yifan Pang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Lingli Xie
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Qiaozhen Yu
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
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15
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Wang H, Wan HT, Wu B, Jian J, Ng AHM, Chung CYL, Chow EYC, Zhang J, Wong AOL, Lai KP, Chan TF, Zhang EL, Wong CKC. A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization. Gigascience 2022; 11:6883318. [PMID: 36480030 PMCID: PMC9730501 DOI: 10.1093/gigascience/giac120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Japanese eels (Anguilla japonica) are commercially important species, harvested extensively for food. Currently, this and related species (American and European eels) are challenging to breed on a commercial basis. As a result, the wild stock is used for aquaculture. Moreover, climate change, habitat loss, water pollution, and altered ocean currents affect eel populations negatively. Accordingly, the International Union for Conservation of Nature lists Japanese eels as endangered and on its red list. Here we presented a high-quality genome assembly for Japanese eels and demonstrated that large chromosome reorganizations occurred in the events of third-round whole-genome duplications (3R-WRDs). Several chromosomal fusions and fissions have reduced the ancestral protochromosomal number of 25 to 19 in the Anguilla lineage. A phylogenetic analysis of the expanded gene families showed that the olfactory receptors (group δ and ζ genes) and voltage-gated Ca2+ channels expanded significantly. Both gene families are crucial for olfaction and neurophysiology. Additional tandem and proximal duplications occurred following 3R-WGD to acquire immune-related genes for an adaptive advantage against various pathogens. The Japanese eel assembly presented here can be used to study other Anguilla species relating to evolution and conservation.
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Affiliation(s)
- Hongbo Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China,Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR
| | - Hin Ting Wan
- Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Hong Kong SAR
| | - Bin Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Alice H M Ng
- Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Hong Kong SAR
| | - Claire Yik-Lok Chung
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Hong Kong SAR
| | - Eugene Yui-Ching Chow
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Hong Kong SAR
| | - Jizhou Zhang
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Hong Kong SAR
| | - Anderson O L Wong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China,School of Biological Sciences, the University of Hong Kong, Hong Kong SAR
| | - Keng Po Lai
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China,Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Ting Fung Chan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China,School of Life Sciences, State Key Laboratory of Agrobiotechnology, Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Hong Kong SAR
| | - Eric Lu Zhang
- Correspondence address. Eric Lu Zhang, Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR. E-mail:
| | - Chris Kong-Chu Wong
- Correspondence address. Chris K.C. Wong, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Hong Kong SAR. E-mail:
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16
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [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: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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17
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Parey E, Louis A, Montfort J, Guiguen Y, Crollius HR, Berthelot C. An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication. Genome Res 2022; 32:1685-1697. [PMID: 35961774 PMCID: PMC9528989 DOI: 10.1101/gr.276953.122] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
Abstract
Teleost fishes are ancient tetraploids descended from an ancestral whole-genome duplication that may have contributed to the impressive diversification of this clade. Whole-genome duplications can occur via self-doubling (autopolyploidy) or via hybridization between different species (allopolyploidy). The mode of tetraploidization conditions evolutionary processes by which duplicated genomes return to diploid meiotic pairing, and subsequent genetic divergence of duplicated genes (cytological and genetic rediploidization). How teleosts became tetraploid remains unresolved, leaving a fundamental gap in the interpretation of their functional evolution. As a result of the whole-genome duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering genome-wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes. We then leverage this atlas to investigate how rediploidization occurred in teleosts at the genome-wide level. We uncover that some duplicated regions maintained tetraploidy for more than 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families. This evidence suggests that the teleost ancestor was an autopolyploid. Further, we find evidence for biased gene retention along several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into genome evolutionary dynamics following ancient polyploidizations in vertebrates.
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Affiliation(s)
- Elise Parey
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- INRAE, LPGP, 35000, Rennes, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | | | | | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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18
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Merdrignac C, Clément AE, Montfort J, Murat F, Bobe J. auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication. Cells 2022; 11:2694. [PMID: 36078102 PMCID: PMC9454499 DOI: 10.3390/cells11172694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
The AUTS2 gene plays major roles during brain development and is associated with various neuropathologies including autism. Data in non-mammalian species are scarce, and the aim of our study was to provide a comprehensive analysis of auts2 evolution in teleost fish, which are widely used for in vivo functional analysis and biomedical purposes. Comparative genomics in 78 species showed that auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD). auts2a, which is highly similar to human AUTS2, was almost systematically retained following TGD. In contrast, auts2b, which encodes for a shorter protein similar to a short human AUTS2 isoform, was lost more frequently and independently during evolution. RNA-seq analysis in 10 species revealed a highly conserved profile with predominant expression of both genes in the embryo, brain, and gonads. Based on protein length, conserved domains, and expression profiles, we speculate that the long human isoform functions were retained by auts2a, while the short isoform functions were retained by auts2a and/or auts2b, depending on the lineage/species. auts2a showed a burst in expression during medaka brain formation, where it was expressed in areas of the brain associated with neurodevelopmental disorders. Together, our data suggest a strong conservation of auts2 functions in vertebrates despite different evolutionary scenarios in teleosts.
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Affiliation(s)
| | | | | | | | - Julien Bobe
- INRAE, LPGP UR1037, Fish Physiology and Genomics, Campus de Beaulieu, F-35000 Rennes, France
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19
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Tang SL, Liang XF, He S, Li L, Alam MS, Wu J. Comparative Study of the Molecular Characterization, Evolution, and Structure Modeling of Digestive Lipase Genes Reveals the Different Evolutionary Selection Between Mammals and Fishes. Front Genet 2022; 13:909091. [PMID: 35991544 PMCID: PMC9386070 DOI: 10.3389/fgene.2022.909091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Vertebrates need suitable lipases to digest lipids for the requirement of energy and essential nutrients; however, the main digestive lipase genes of fishes have certain controversies. In this study, two types of digestive lipase genes (pancreatic lipase (pl) and bile salt-activated lipase (bsal)) were identified in mammals and fishes. The neighborhood genes and key active sites of the two lipase genes were conserved in mammals and fishes. Three copies of PL genes were found in mammals, but only one copy of the pl gene was found in most of the fish species, and the pl gene was even completely absent in some fish species (e.g., zebrafish, medaka, and common carp). Additionally, the hydrophobic amino acid residues (Ile and Leu) which are important to pancreatic lipase activity were also absent in most of the fish species. The PL was the main digestive lipase gene in mammals, but the pl gene seemed not to be the main digestive lipase gene in fish due to the absence of the pl gene sequence and the important amino acid residues. In contrast, the bsal gene existed in all fish species, even two to five copies of bsal genes were found in most of the fishes, but only one copy of the BSAL gene was found in mammals. The amino acid residues of bile salt-binding sites and the three-dimensional (3D) structure modeling of Bsal proteins were conserved in most of the fish species, so bsal might be the main digestive lipase gene in fish. The phylogenetic analysis also indicated that pl or bsal showed an independent evolution between mammals and fishes. Therefore, we inferred that the evolutionary selection of the main digestive lipase genes diverged into two types between mammals and fishes. These findings will provide valuable evidence for the study of lipid digestion in fish.
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Affiliation(s)
- Shu-Lin Tang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
- *Correspondence: Xu-Fang Liang,
| | - Shan He
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Ling Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Muhammad Shoaib Alam
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Jiaqi Wu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
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20
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Wang L, Lee M, Sun F, Song Z, Yang Z, Yue GH. A chromosome-level genome assembly of chia provides insights into high omega-3 content and coat color variation of its seeds. PLANT COMMUNICATIONS 2022; 3:100326. [PMID: 35605203 PMCID: PMC9284293 DOI: 10.1016/j.xplc.2022.100326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/14/2022] [Accepted: 04/11/2022] [Indexed: 05/26/2023]
Abstract
Chia (Salvia hispanica) is a functional food crop for humans. Although its seeds contain high omega-3 fatty acids, the seed yield of chia is still low. Genomic resources available for this plant are limited. We report the first high-quality chromosome-level genome sequence of chia. The assembled genome size was 347.6 Mb and covered 98.1% of the estimated genome size. A total of 31 069 protein-coding genes were predicted. The absence of recent whole-genome duplication and the relatively low intensity of transposable element expansion in chia compared to its sister species contribute to its small genome size. Transcriptome sequencing and gene duplication analysis reveal that the expansion of the fab2 gene family is likely to be related to the high content of omega-3 in seeds. The white seed coat color is determined by a single locus on chromosome 4. This study provides novel insights into the evolution of Salvia species and high omega-3 content, as well as valuable genomic resources for genetic improvement of important commercial traits of chia and its related species.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Fei Sun
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Zhuojun Song
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Zituo Yang
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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21
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Xiong H, Wang D, Shao C, Yang X, Yang J, Ma T, Davis CC, Liu L, Xi Z. Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication. Syst Biol 2022; 71:1348-1361. [PMID: 35689633 PMCID: PMC9558847 DOI: 10.1093/sysbio/syac040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs–paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.]
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Affiliation(s)
- Haifeng Xiong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Danying Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Chen Shao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xuchen Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jialin Yang
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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22
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Johri P, Gout JF, Doak TG, Lynch M. A Population-Genetic Lens into the Process of Gene Loss Following Whole-Genome Duplication. Mol Biol Evol 2022; 39:msac118. [PMID: 35639978 PMCID: PMC9206413 DOI: 10.1093/molbev/msac118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Whole-genome duplications (WGDs) have occurred in many eukaryotic lineages. However, the underlying evolutionary forces and molecular mechanisms responsible for the long-term retention of gene duplicates created by WGDs are not well understood. We employ a population-genomic approach to understand the selective forces acting on paralogs and investigate ongoing duplicate-gene loss in multiple species of Paramecium that share an ancient WGD. We show that mutations that abolish protein function are more likely to be segregating in retained WGD paralogs than in single-copy genes, most likely because of ongoing nonfunctionalization post-WGD. This relaxation of purifying selection occurs in only one WGD paralog, accompanied by the gradual fixation of nonsynonymous mutations and reduction in levels of expression, and occurs over a long period of evolutionary time, "marking" one locus for future loss. Concordantly, the fitness effects of new nonsynonymous mutations and frameshift-causing indels are significantly more deleterious in the highly expressed copy compared with their paralogs with lower expression. Our results provide a novel mechanistic model of gene duplicate loss following WGDs, wherein selection acts on the sum of functional activity of both duplicate genes, allowing the two to wander in expression and functional space, until one duplicate locus eventually degenerates enough in functional efficiency or expression that its contribution to total activity is too insignificant to be retained by purifying selection. Retention of duplicates by such mechanisms predicts long times to duplicate-gene loss, which should not be falsely attributed to retention due to gain/change in function.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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23
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Bernardini A, Gallo A, Gnesutta N, Dolfini D, Mantovani R. Phylogeny of NF-YA trans-activation splicing isoforms in vertebrate evolution. Genomics 2022; 114:110390. [PMID: 35589059 DOI: 10.1016/j.ygeno.2022.110390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 11/04/2022]
Abstract
NF-Y is a trimeric pioneer Transcription Factor (TF) whose target sequence -the CCAAT box- is present in ~25% of mammalian promoters. We reconstruct the phylogenetic history of the regulatory NF-YA subunit in vertebrates. We find that in addition to the remarkable conservation of the subunits-interaction and DNA-binding parts, the Transcriptional Activation Domain (TAD) is also conserved (>90% identity among bony vertebrates). We infer the phylogeny of the alternatively spliced exon-3 and partial splicing events of exon-7 -7N and 7C- revealing independent clade-specific losses of these regions. These isoforms shape the TAD. Absence of exon-3 in basal deuterostomes, cartilaginous fishes and hagfish, but not in lampreys, suggests that the "short" isoform is primordial, with emergence of exon-3 in chordates. Exon 7N was present in the vertebrate common ancestor, while 7C is a molecular innovation of teleost fishes. RNA-seq analysis in several species confirms expression of all these isoforms. We identify 3 blocks of amino acids in the TAD shared across deuterostomes, yet structural predictions and sequence analyses suggest an evolutionary drive for maintenance of an Intrinsically Disordered Region -IDR- within the TAD. Overall, these data help reconstruct the logic for alternative splicing of this essential eukaryotic TF.
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Affiliation(s)
- Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Alberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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24
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Polyploidy as a Fundamental Phenomenon in Evolution, Development, Adaptation and Diseases. Int J Mol Sci 2022; 23:ijms23073542. [PMID: 35408902 PMCID: PMC8998937 DOI: 10.3390/ijms23073542] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/02/2023] Open
Abstract
DNA replication during cell proliferation is 'vertical' copying, which reproduces an initial amount of genetic information. Polyploidy, which results from whole-genome duplication, is a fundamental complement to vertical copying. Both organismal and cell polyploidy can emerge via premature cell cycle exit or via cell-cell fusion, the latter giving rise to polyploid hybrid organisms and epigenetic hybrids of somatic cells. Polyploidy-related increase in biological plasticity, adaptation, and stress resistance manifests in evolution, development, regeneration, aging, oncogenesis, and cardiovascular diseases. Despite the prevalence in nature and importance for medicine, agri- and aquaculture, biological processes and epigenetic mechanisms underlying these fundamental features largely remain unknown. The evolutionarily conserved features of polyploidy include activation of transcription, response to stress, DNA damage and hypoxia, and induction of programs of morphogenesis, unicellularity, and longevity, suggesting that these common features confer adaptive plasticity, viability, and stress resistance to polyploid cells and organisms. By increasing cell viability, polyploidization can provide survival under stressful conditions where diploid cells cannot survive. However, in somatic cells it occurs at the expense of specific function, thus promoting developmental programming of adult cardiovascular diseases and increasing the risk of cancer. Notably, genes arising via evolutionary polyploidization are heavily involved in cancer and other diseases. Ploidy-related changes of gene expression presumably originate from chromatin modifications and the derepression of bivalent genes. The provided evidence elucidates the role of polyploidy in evolution, development, aging, and carcinogenesis, and may contribute to the development of new strategies for promoting regeneration and preventing cardiovascular diseases and cancer.
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25
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Corkins ME, DeLay BD, Miller RK. Tissue-Targeted CRISPR-Cas9-Mediated Genome Editing of Multiple Homeologs in F 0-Generation Xenopus laevis Embryos. Cold Spring Harb Protoc 2022; 2022:pdb.prot107037. [PMID: 34911820 PMCID: PMC10829535 DOI: 10.1101/pdb.prot107037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Xenopus laevis frogs are a powerful developmental model that enables studies combining classical embryology and molecular manipulation. Because of the large embryo size, ease of microinjection, and ability to target tissues through established fate maps, X. laevis has become the predominant amphibian research model. Given that their allotetraploid genome has complicated the generation of gene knockouts, strategies need to be established for efficient mutagenesis of multiple homeologs to evaluate gene function. Here we describe a protocol to use CRISPR-Cas9-mediated genome editing to target either single alleles or multiple alloalleles in F0 X. laevis embryos. A single-guide RNA (sgRNA) is designed to target a specific DNA sequence encoding a critical protein domain. To mutagenize a gene with two alloalleles, the sgRNA is designed against a sequence that is common to both homeologs. This sgRNA, along with the Cas9 protein, is microinjected into the zygote to disrupt the genomic sequences in the whole embryo or into a specific blastomere for tissue-targeted effects. Error-prone repair of CRISPR-Cas9-generated DNA double-strand breaks leads to insertions and deletions creating mosaic gene lesions within the embryos. The genomic DNA isolated from each mosaic F0 embryo is sequenced, and software is applied to assess the nature of the mutations generated and degree of mosaicism. This protocol enables the knockout of genes within the whole embryo or in specific tissues in F0 X. laevis embryos to facilitate the evaluation of resulting phenotypes.
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Affiliation(s)
- Mark E Corkins
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030, USA;
| | - Bridget D DeLay
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030, USA
| | - Rachel K Miller
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030, USA;
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
- Program in Biochemistry and Cell Biology, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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26
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Nagasawa T, Kawaguchi M, Nishi K, Yasumasu S. Molecular evolution of hatching enzymes and their paralogous genes in vertebrates. BMC Ecol Evol 2022; 22:9. [PMID: 35109790 PMCID: PMC8812170 DOI: 10.1186/s12862-022-01966-2] [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: 09/17/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hatching is identified as one of the most important events in the reproduction of oviparous vertebrates. The genes for hatching enzymes, which are vital in the hatching process, are conserved among vertebrates. However, especially in teleost, it is difficult to trace their molecular evolution in detail due to the presence of other C6astacins, which are the subfamily to which the genes for hatching enzymes belong and are highly diverged. In particular, the hatching enzyme genes are diversified with frequent genome translocations due to retrocopy. RESULTS In this study, we took advantage of the rapid expansion of whole-genome data in recent years to examine the molecular evolutionary process of these genes in vertebrates. The phylogenetic analysis and the genomic synteny analysis revealed C6astacin genes other than the hatching enzyme genes, which was previously considered to be retained only in teleosts, was also retained in the genomes of basal ray-finned fishes, coelacanths, and cartilaginous fishes. These results suggest that the common ancestor of these genes can be traced back to at least the common ancestor of the Gnathostomata. Moreover, we also found that many of the C6astacin genes underwent multiple gene duplications during vertebrate evolution, and the results of gene expression analysis in frogs implied that genes derived from hatching enzyme genes underwent neo-functionalization. CONCLUSIONS In this study, we describe in detail the molecular evolution of the C6astacin gene in vertebrates, which has not been summarized previously. The results revealed the presence of the previously unknown C6astacin gene in the basal-lineage of jawed vertebrates and large-scale gene duplication of hatching enzyme genes in amphibians. The comprehensive investigation reported in this study will be an important basis for studying the molecular evolution of the vertebrate C6astacin genes, hatching enzyme, and its paralogous genes and for identifying these genes without the need for gene expression and functional analysis.
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Affiliation(s)
- Tatsuki Nagasawa
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Kohki Nishi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan.
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27
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Vogt G. Studying phenotypic variation and DNA methylation across development, ecology and evolution in the clonal marbled crayfish: a paradigm for investigating epigenotype-phenotype relationships in macro-invertebrates. Naturwissenschaften 2022; 109:16. [PMID: 35099618 DOI: 10.1007/s00114-021-01782-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022]
Abstract
Animals can produce different phenotypes from the same genome during development, environmental adaptation and evolution, which is mediated by epigenetic mechanisms including DNA methylation. The obligatory parthenogenetic marbled crayfish, Procambarus virginalis, whose genome and methylome are fully established, proved very suitable to study this issue in detail. Comparison between developmental stages and DNA methylation revealed low expression of Dnmt methylation and Tet demethylation enzymes from the spawned oocyte to the 256 cell embryo and considerably increased expression thereafter. The global 5-methylcytosine level was 2.78% at mid-embryonic development and decreased slightly to 2.41% in 2-year-old adults. Genetically identical clutch-mates raised in the same uniform laboratory setting showed broad variation in morphological, behavioural and life history traits and differences in DNA methylation. The invasion of diverse habitats in tropical to cold-temperate biomes in the last 20 years by the marbled crayfish was associated with the expression of significantly different phenotypic traits and DNA methylation patterns, despite extremely low genetic variation on the whole genome scale, suggesting the establishment of epigenetic ecotypes. The evolution of marbled crayfish from its parent species Procambarus fallax by autotriploidy a few decades ago was accompanied by a significant increase in body size, fertility and life span, a 20% reduction of global DNA methylation and alteration of methylation in hundreds of genes, suggesting that epigenetic mechanisms were involved in speciation and fitness enhancement. The combined analysis of phenotypic traits and DNA methylation across multiple biological contexts in the laboratory and field in marbled crayfish may serve as a blueprint for uncovering the role of epigenetic mechanisms in shaping of phenotypes in macro-invertebrates.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.
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28
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Qiu X, Wang D, Lv M, Sun H, Ren J, Wang X, Zhou H. Identification and functional characterization of interleukin-12 receptor beta 1 and 2 in grass carp (Ctenopharyngodon idella). Mol Immunol 2022; 143:58-67. [PMID: 35042118 DOI: 10.1016/j.molimm.2022.01.007] [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: 12/16/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 11/30/2022]
Abstract
Interleukin 12 (IL-12) binds its receptor complex of IL-12 receptor beta 1 (IL-12Rβ1) and IL-12Rβ2 to transduce cellular signaling in mammals. In teleosts, the function of Il-12 is drawing increasing attention, but molecular and functional features of Il-12 receptors remain obscure. Especially, the existence of multiple Il-12 isoforms in some fish species elicits the requirement to clarify their receptors. In this study, we isolated three cDNA sequences as Il-12 receptor candidates from grass carp, entitled as grass carp Il-12rβ1 (gcIl-12rβ1), gcIl-12rβ2a and gcIl-12rβ2b. In silico analysis showed that gcIl-12rβ1 and gcIl-12rβ2a shared the conserved gene locus and similar structure characteristics with their orthologues of zebrafish, frog, chicken, mouse and human, respectively. However, the Il-12rβ2b of grass carp and zebrafish was similar to IL-27Ra in non-fish species. Further locally installed BLAST and gene synteny analysis uncovered three gcIl-12 receptors being single copied genes. Tissue distribution assay revealed that gcil12rβ1 and gcil12rβ2a transcripts were predominantly expressed in head kidney, differing from the even distribution of gcil12rβ2b transcripts in all detected tissues. Subsequently, the binding ability and antagonistic effects of recombinant extracellular region of gcIl-12rβ1 with recombinant grass carp Il-12 (rgcIl-12) isoforms were explored, providing functional evidence of the newly cloned gcIl-12rβ1 being genuine orthologues of mammalian IL-12Rβ1. Moreover, our data showed that gcIl-12rβ1 and gcIl-12rβ2a but not gcIl-12rβ1 and gcIl-12rβ2b mediated the effects of rgcIl-12 isoforms on ifn-γ promoter activity, thereby revealing Il-12 receptor signaling in fish. These results identified grass carp Il-12 receptors, thereby advancing our understanding of Il-12 isoform signaling in fish.
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Affiliation(s)
- Xingyang Qiu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Dan Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Mengyuan Lv
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Hao Sun
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Jingqi Ren
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Xinyan Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Hong Zhou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.
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Gundappa MK, To TH, Grønvold L, Martin SAM, Lien S, Geist J, Hazlerigg D, Sandve SR, Macqueen DJ. Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution. Mol Biol Evol 2022; 39:msab310. [PMID: 34718723 PMCID: PMC8760942 DOI: 10.1093/molbev/msab310] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The long-term evolutionary impacts of whole-genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologs) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnolog sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent "explosion" of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnolog divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial "wave" of rediploidization in the late Cretaceous (85-106 Ma). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnolog divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
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Affiliation(s)
- Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Thu-Hien To
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Lars Grønvold
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Juergen Geist
- Aquatic Systems Biology Unit, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - David Hazlerigg
- Department of Arctic and Marine Biology, Faculty of BioSciences Fisheries & Economy, University of Tromsø, Norway
| | - Simen R Sandve
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
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30
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Dornburg A, Yoder JA. On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity. Immunogenetics 2022; 74:111-128. [PMID: 34981186 DOI: 10.1007/s00251-021-01232-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/01/2021] [Indexed: 01/17/2023]
Abstract
For over half a century, deciphering the origins of the genomic loci that form the jawed vertebrate adaptive immune response has been a major topic in comparative immunogenetics. Vertebrate adaptive immunity relies on an extensive and highly diverse repertoire of tandem arrays of variable (V), diversity (D), and joining (J) gene segments that recombine to produce different immunoglobulin (Ig) and T cell receptor (TCR) genes. The current consensus is that a recombination-activating gene (RAG)-like transposon invaded an exon of an ancient innate immune VJ-bearing receptor, giving rise to the extant diversity of Ig and TCR loci across jawed vertebrates. However, a model for the evolutionary relationships between extant non-recombining innate immune receptors and the V(D)J receptors of the jawed vertebrate adaptive immune system has only recently begun to come into focus. In this review, we provide an overview of non-recombining VJ genes, including CD8β, CD79b, natural cytotoxicity receptor 3 (NCR3/NKp30), putative remnants of an antigen receptor precursor (PRARPs), and the multigene family of signal-regulatory proteins (SIRPs), that play a wide range of roles in immune function. We then focus in detail on the VJ-containing novel immune-type receptors (NITRs) from ray-finned fishes, as recent work has indicated that these genes are at least 50 million years older than originally thought. We conclude by providing a conceptual model of the evolutionary origins and phylogenetic distribution of known VJ-containing innate immune receptors, highlighting opportunities for future comparative research that are empowered by this emerging evolutionary perspective.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, USA.
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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31
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Bolton CM, Bekaert M, Eilertsen M, Helvik JV, Migaud H. Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain. Front Physiol 2021; 12:761109. [PMID: 34925060 PMCID: PMC8674837 DOI: 10.3389/fphys.2021.761109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/09/2021] [Indexed: 12/28/2022] Open
Abstract
To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.
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Affiliation(s)
- Charlotte M Bolton
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Mariann Eilertsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Jon Vidar Helvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
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32
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Inoue J. ORTHOSCOPE*: a phylogenetic pipeline to infer gene histories from genome-wide data. Mol Biol Evol 2021; 39:6400256. [PMID: 34662403 PMCID: PMC8763121 DOI: 10.1093/molbev/msab301] [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] [Indexed: 11/13/2022] Open
Abstract
Comparative genome-scale analyses of protein-coding gene sequences are employed to examine evidence for whole-genome duplication and horizontal gene transfer. For this purpose, an orthogroup should be delineated to infer evolutionary history regarding each gene, and results of all orthogroup analyses need to be integrated to infer a genome-scale history. An orthogroup is a set of genes descended from a single gene in the last common ancestor of all species under consideration. However, such analyses confront several problems: (1) analytical pipelines to infer all gene histories with methods comparing species and gene trees are not fully developed, and (2) without detailed analyses within orthogroups, evolutionary events of paralogous genes in the same orthogroup cannot be distinguished for genome-wide integration of results derived from multiple orthogroup analyses. Here I present an analytical pipeline, ORTHOSCOPE* (star), to infer evolutionary histories of animal/plant genes from genome-scale data. ORTHOSCOPE* estimates a tree for a specified gene, detects speciation/gene duplication events that occurred at nodes belonging to only one lineage leading to a species of interest, and then integrates results derived from gene trees estimated for all query genes in genome-wide data. Thus, ORTHOSCOPE* can be used to detect species nodes just after whole genome duplications as a first step of comparative genomic analyses. Moreover, by examining the presence or absence of genes belonging to species lineages with dense taxon sampling available from the ORTHOSCOPE web version, ORTHOSCOPE* can detect genes lost in specific lineages and horizontal gene transfers. This pipeline is available at https://github.com/jun-inoue/ORTHOSCOPE_STAR.
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Affiliation(s)
- Jun Inoue
- Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Japan
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33
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Yang L, Naylor GJP, Mayden RL. Deciphering reticulate evolution of the largest group of polyploid vertebrates, the subfamily cyprininae (Teleostei: Cypriniformes). Mol Phylogenet Evol 2021; 166:107323. [PMID: 34634450 DOI: 10.1016/j.ympev.2021.107323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 02/04/2023]
Abstract
Despite the rarity of polyploidy in animals, some groups with polyploid species exhibit complicated and interesting patterns of reticulate evolution. Here we focus on fishes in the subfamily Cyprininae, the largest polyploid group of vertebrates. The large number of polyploid taxa poses significant challenges for phylogenetic and evolutionary studies on this subfamily. In this study, we cloned and sequenced three single-copy nuclear loci to investigate the evolution of polyploidy in the Cyprininae. Topologies of nuclear gene trees were compared with a newly reconstructed mitochondrial tree. The data provided herein corroborate the hybrid origins of the tribes Torini, Cyprinini, Spinibarbini, Barbini, and also Probarbini. Based on results from this study and previous studies, we hypothesize that at least 13 independent polyploidization events have occurred during the evolution of the Cyprininae. We offer hypotheses on the origin of each polyploid group and show that a diploid group or the diploid ancestor of a polyploid group might have served as progenitor of one or two other polyploid groups. The evolutionary history of Cyprinine (since its first divergence) can be divided into three stages: the "Diploid stage" (69.2-43.4 Ma or million years ago), the "Tetraploidization stage" (43.4-18.9 Ma), and the "Hexaploidization stage" (18.9 Ma to present). The second stage is when all tetraploidization events happened, while the last stage is when all hexaploidization events and most genus- or species-specific polyploidization events occurred. The post-polyploidization dynamics of polyploid groups are complicated and warrant more genomic level studies. We showed that the subfamily Cyprininae may represent a more complicated polyploid system than most, if not all, other vertebrates and some plants, if one or more of the following factors are considered: number of polyploid species, number of different ploidy levels, and number and type of independent polyploidization events.
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Affiliation(s)
- Lei Yang
- Florida Museum of Natural History, 1659 Museum Rd. University of Florida, Gainesville, FL 32611, USA.
| | - Gavin J P Naylor
- Florida Museum of Natural History, 1659 Museum Rd. University of Florida, Gainesville, FL 32611, USA
| | - Richard L Mayden
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA
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34
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Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system. Immunogenetics 2021; 73:479-497. [PMID: 34510270 DOI: 10.1007/s00251-021-01225-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/06/2021] [Indexed: 01/16/2023]
Abstract
Over 99% of ray-finned fishes (Actinopterygii) are teleosts, a clade that comprises half of all living vertebrate species that have diversified across virtually all fresh and saltwater ecosystems. This ecological breadth raises the question of how the immunogenetic diversity required to persist under heterogeneous pathogen pressures evolved. The teleost genome duplication (TGD) has been hypothesized as the evolutionary event that provided the substrate for rapid genomic evolution and innovation. However, studies of putative teleost-specific innate immune receptors have been largely limited to comparisons either among teleosts or between teleosts and distantly related vertebrate clades such as tetrapods. Here we describe and characterize the receptor diversity of two clustered innate immune gene families in the teleost sister lineage: Holostei (bowfin and gars). Using genomic and transcriptomic data, we provide a detailed investigation of the phylogenetic history and conserved synteny of gene clusters encoding diverse immunoglobulin domain-containing proteins (DICPs) and novel immune-type receptors (NITRs). These data demonstrate an ancient linkage of DICPs to the major histocompatibility complex (MHC) and reveal an evolutionary origin of NITR variable-joining (VJ) exons that predate the TGD by at least 50 million years. Further characterizing the receptor diversity of Holostean DICPs and NITRs illuminates a sequence diversity that rivals the diversity of these innate immune receptor families in many teleosts. Taken together, our findings provide important historical context for the evolution of these gene families that challenge prevailing expectations concerning the consequences of the TGD during actinopterygiian evolution.
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35
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Fukunaga T, Iwasaki W. Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families. BIOINFORMATICS ADVANCES 2021; 1:vbab014. [PMID: 36700099 PMCID: PMC9710636 DOI: 10.1093/bioadv/vbab014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 01/28/2023]
Abstract
Motivation Reconstruction of gene copy number evolution is an essential approach for understanding how complex biological systems have been organized. Although various models have been proposed for gene copy number evolution, existing evolutionary models have not appropriately addressed the fact that different gene families can have very different gene gain/loss rates. Results In this study, we developed Mirage (MIxtuRe model for Ancestral Genome Estimation), which allows different gene families to have flexible gene gain/loss rates. Mirage can use three models for formulating heterogeneous evolution among gene families: the discretized Γ model, probability distribution-free model and pattern mixture (PM) model. Simulation analysis showed that Mirage can accurately estimate heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that the PM model fits genome data from various taxonomic groups better than the other heterogeneous models. Using Mirage, we revealed that metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated. Availability and implementation The source code of Mirage is freely available at https://github.com/fukunagatsu/Mirage. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Tsukasa Fukunaga
- Waseda Institute for Advanced Study, Waseda University, Tokyo 1690051, Japan,Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 1130032, Japan,To whom correspondence should be addressed. or
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 2770882, Japan,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 1130032, Japan,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 2770882, Japan,Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 2770882, Japan,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 1130032, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 1130032, Japan,To whom correspondence should be addressed. or
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36
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Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication. Proc Natl Acad Sci U S A 2021; 118:2101780118. [PMID: 34301898 DOI: 10.1073/pnas.2101780118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Teleost fishes comprise one-half of all vertebrate species and possess a duplicated genome. This whole-genome duplication (WGD) occurred on the teleost stem lineage in an ancient common ancestor of all living teleosts and is hypothesized as a trigger of their exceptional evolutionary radiation. Genomic and phylogenetic data indicate that WGD occurred in the Mesozoic after the divergence of teleosts from their closest living relatives but before the origin of the extant teleost groups. However, these approaches cannot pinpoint WGD among the many extinct groups that populate this 50- to 100-million-y lineage, preventing tests of the evolutionary effects of WGD. We infer patterns of genome size evolution in fossil stem-group teleosts using high-resolution synchrotron X-ray tomography to measure the bone cell volumes, which correlate with genome size in living species. Our findings indicate that WGD occurred very early on the teleost stem lineage and that all extinct stem-group teleosts known so far possessed duplicated genomes. WGD therefore predates both the origin of proposed key innovations of the teleost skeleton and the onset of substantial morphological diversification in the clade. Moreover, the early occurrence of WGD allowed considerable time for postduplication reorganization prior to the origin of the teleost crown group. This suggests at most an indirect link between WGD and evolutionary success, with broad implications for the relationship between genomic architecture and large-scale evolutionary patterns in the vertebrate Tree of Life.
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Capillo G, Lauriano ER, Icardo JM, Siriyappagouder P, Kuciel M, Karapanagiotis S, Zaccone G, Fernandes JMO. Structural Identification of the Pacemaker Cells and Expression of Hyperpolarization-Activated Cyclic Nucleotide-Gated (HCN) Channels in the Heart of the Wild Atlantic Cod, Gadus morhua (Linnaeus, 1758). Int J Mol Sci 2021; 22:7539. [PMID: 34299159 PMCID: PMC8307021 DOI: 10.3390/ijms22147539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/05/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are proteins that contain highly conserved functional domains and sequence motifs that are correlated with their unique biophysical activities, to regulate cardiac pacemaker activity and synaptic transmission. These pacemaker proteins have been studied in mammalian species, but little is known now about their heart distribution in lower vertebrates and c-AMP modulation. Here, we characterized the pacemaker system in the heart of the wild Atlantic cod (Gadus morhua), with respect to primary pacemaker molecular markers. Special focus is given to the structural, ultrastructural and molecular characterization of the pacemaker domain, through the expression of HCN channel genes and the immunohistochemistry of HCN isoforms, including the location of intracardiac neurons that are adjacent to the sinoatrial region of the heart. Similarly to zebrafish and mammals, these neurons are immunoreactive to ChAT, VAChT and nNOS. It has been shown that cardiac pacemaking can be modulated by sympathetic and parasympathetic pathways, and the existence of intracardiac neurons projecting back to the central nervous system provide a plausible link between them.
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Affiliation(s)
- Gioele Capillo
- Department of Veterinary Sciences, Polo Universitario dell’Annunziata, University of Messina, 98168 Messina, Italy;
- Institute of Marine Biological Resources and Biotechnology—National Research Council (IRBIM, CNR), Spianata S. Raineri, 98122 Messina, Italy
| | - Eugenia R. Lauriano
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98168 Messina, Italy;
| | - Jose M. Icardo
- Department of Anatomy and Cell Biology, Poligono de Cazona, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain
| | | | - Michal Kuciel
- Poison Information Centre, Department of Toxicology and Environmental Disease, Faculty of Medicine, Jagiellonian University, Kopernika 15, 30-501 Cracow, Poland;
| | - Stelios Karapanagiotis
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway; (P.S.); (S.K.)
| | - Giacomo Zaccone
- Department of Veterinary Sciences, Polo Universitario dell’Annunziata, University of Messina, 98168 Messina, Italy;
| | - Jorge M. O. Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway; (P.S.); (S.K.)
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38
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Takei Y. The digestive tract as an essential organ for water acquisition in marine teleosts: lessons from euryhaline eels. ZOOLOGICAL LETTERS 2021; 7:10. [PMID: 34154668 PMCID: PMC8215749 DOI: 10.1186/s40851-021-00175-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/16/2021] [Indexed: 05/17/2023]
Abstract
Adaptation to a hypertonic marine environment is one of the major topics in animal physiology research. Marine teleosts lose water osmotically from the gills and compensate for this loss by drinking surrounding seawater and absorbing water from the intestine. This situation is in contrast to that in mammals, which experience a net osmotic loss of water after drinking seawater. Water absorption in fishes is made possible by (1) removal of monovalent ions (desalinization) by the esophagus, (2) removal of divalent ions as carbonate (Mg/CaCO3) precipitates promoted by HCO3- secretion, and (3) facilitation of NaCl and water absorption from diluted seawater by the intestine using a suite of unique transporters. As a result, 70-85% of ingested seawater is absorbed during its passage through the digestive tract. Thus, the digestive tract is an essential organ for marine teleost survival in the hypertonic seawater environment. The eel is a species that has been frequently used for osmoregulation research in laboratories worldwide. The eel possesses many advantages as an experimental animal for osmoregulation studies, one of which is its outstanding euryhalinity, which enables researchers to examine changes in the structure and function of the digestive tract after direct transfer from freshwater to seawater. In recent years, the molecular mechanisms of ion and water transport across epithelial cells (the transcellular route) and through tight junctions (the paracellular route) have been elucidated for the esophagus and intestine. Thanks to the rapid progress in analytical methods for genome databases on teleosts, including the eel, the molecular identities of transporters, channels, pumps and junctional proteins have been clarified at the isoform level. As 10 y have passed since the previous reviews on this subject, it seems relevant and timely to summarize recent progress in research on the molecular mechanisms of water and ion transport in the digestive tract in eels and to compare the mechanisms with those of other teleosts and mammals from comparative and evolutionary viewpoints. We also propose future directions for this research field to achieve integrative understanding of the role of the digestive tract in adaptation to seawater with regard to pathways/mechanisms including the paracellular route, divalent ion absorption, metabolon formation and cellular trafficking of transporters. Notably, some of these have already attracted practical attention in laboratories.
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Affiliation(s)
- Yoshio Takei
- Laboratory of Physiology, Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan.
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Functional Domains and Evolutionary History of the PMEL and GPNMB Family Proteins. Molecules 2021; 26:molecules26123529. [PMID: 34207849 PMCID: PMC8273697 DOI: 10.3390/molecules26123529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
The ancient paralogs premelanosome protein (PMEL) and glycoprotein nonmetastatic melanoma protein B (GPNMB) have independently emerged as intriguing disease loci in recent years. Both proteins possess common functional domains and variants that cause a shared spectrum of overlapping phenotypes and disease associations: melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma. Surprisingly, these proteins have yet to be shown to physically or genetically interact within the same cellular pathway. This juxtaposition inspired us to compare and contrast this family across a breadth of species to better understand the divergent evolutionary trajectories of two related, but distinct, genes. In this study, we investigated the evolutionary history of PMEL and GPNMB in clade-representative species and identified TMEM130 as the most ancient paralog of the family. By curating the functional domains in each paralog, we identified many commonalities dating back to the emergence of the gene family in basal metazoans. PMEL and GPNMB have gained functional domains since their divergence from TMEM130, including the core amyloid fragment (CAF) that is critical for the amyloid potential of PMEL. Additionally, the PMEL gene has acquired the enigmatic repeat domain (RPT), composed of a variable number of imperfect tandem repeats; this domain acts in an accessory role to control amyloid formation. Our analyses revealed the vast variability in sequence, length and repeat number in homologous RPT domains between craniates, even within the same taxonomic class. We hope that these analyses inspire further investigation into a gene family that is remarkable from the evolutionary, pathological and cell biology perspectives.
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40
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Wang Y, Guo B. The divergence of alternative splicing between ohnologs in teleost fishes. BMC Ecol Evol 2021; 21:98. [PMID: 34034651 PMCID: PMC8146666 DOI: 10.1186/s12862-021-01833-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene duplication and alternative splicing (AS) are two distinct mechanisms generating new materials for genetic innovations. The evolutionary link between gene duplication and AS is still controversial, due to utilizing duplicates from inconsistent ages of duplication events in earlier studies. With the aid of RNA-seq data, we explored evolutionary scenario of AS divergence between duplicates with ohnologs that resulted from the teleost genome duplication event in zebrafish, medaka, and stickleback. RESULTS Ohnologs in zebrafish have fewer AS forms compared to their singleton orthologs, supporting the function-sharing model of AS divergence between duplicates. Ohnologs in stickleback have more AS forms compared to their singleton orthologs, which supports the accelerated model of AS divergence between duplicates. The evolution of AS in ohnologs in medaka supports a combined scenario of the function-sharing and the accelerated model of AS divergence between duplicates. We also found a small number of ohnolog pairs in each of the three teleosts showed significantly asymmetric AS divergence. For example, the well-known ovary-factor gene cyp19a1a has no AS form but its ohnolog cyp19a1b has multiple AS forms in medaka, suggesting that functional divergence between duplicates might have result from AS divergence. CONCLUSIONS We found that a combined scenario of function-sharing and accelerated models for AS evolution in ohnologs in teleosts and rule out the independent model that assumes a lack of correlation between gene duplication and AS. Our study thus provided insights into the link between gene duplication and AS in general and ohnolog divergence in teleosts from AS perspective in particular.
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Affiliation(s)
- Yuwei Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China.
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41
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Desvignes T, Sydes J, Montfort J, Bobe J, Postlethwait JH. Evolution after Whole-Genome Duplication: Teleost MicroRNAs. Mol Biol Evol 2021; 38:3308-3331. [PMID: 33871629 PMCID: PMC8321539 DOI: 10.1093/molbev/msab105] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole-genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the teleost genome duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than nonclustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3'-complementary regions, compared with minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multispecies analysis of the mechanisms influencing metazoan miRNA evolution after whole-genome duplication.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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Czimer D, Porok K, Csete D, Gyüre Z, Lavró V, Fülöp K, Chen Z, Gyergyák H, Tusnády GE, Burgess SM, Mócsai A, Váradi A, Varga M. A New Zebrafish Model for Pseudoxanthoma Elasticum. Front Cell Dev Biol 2021; 9:628699. [PMID: 33768091 PMCID: PMC7985086 DOI: 10.3389/fcell.2021.628699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/16/2021] [Indexed: 11/30/2022] Open
Abstract
Calcification of various tissues is a significant health issue associated with aging, cancer and autoimmune diseases. There are both environmental and genetic factors behind this phenomenon and understanding them is essential for the development of efficient therapeutic approaches. Pseudoxanthoma elasticum (PXE) is a rare genetic disease, a prototype for calcification disorders, resulting from the dysfunction of ABCC6, a transport protein found in the membranes of cells. It is identified by excess calcification in a variety of tissues (e.g., eyes, skin, arteries) and currently it has no cure, known treatments target the symptoms only. Preclinical studies of PXE have been successful in mice, proving the usefulness of animal models for the study of the disease. Here, we present a new zebrafish (Danio rerio) model for PXE. By resolving some ambiguous assemblies in the zebrafish genome, we show that there are two functional and one non-functional paralogs for ABCC6 in zebrafish (abcc6a, abcc6b.1, and abcc6b.2, respectively). We created single and double mutants for the functional paralogs and characterized their calcification defects with a combination of techniques. Zebrafish deficient in abcc6a show defects in their vertebral calcification and also display ectopic calcification foci in their soft tissues. Our results also suggest that the impairment of abcc6b.1 does not affect this biological process.
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Affiliation(s)
- Dávid Czimer
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Klaudia Porok
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Csete
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Gyüre
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Viktória Lavró
- Division of Biosciences, University College London, London, United Kingdom
| | - Krisztina Fülöp
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zelin Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hella Gyergyák
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor E. Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, United States
| | - Attila Mócsai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - András Váradi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
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Vogt G. Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance. J Biosci 2021. [DOI: 10.1007/s12038-021-00138-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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44
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Genome-wide identification and characterization of olfactory receptor genes in common carp (Cyprinus carpio). Gene 2021; 777:145468. [PMID: 33539942 DOI: 10.1016/j.gene.2021.145468] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 11/21/2022]
Abstract
The environment contains a large extent of chemical information, which could be detected as olfactory sense. Olfactory in vertebrates plays important roles on many aspects during life time, including localizing prey or food, avoiding predators, mating behavior and social communication. Considering the essential role of olfactory receptors in the specific recognition of diverse stimuli, understanding the evolutionary dynamics of olfactory receptors in teleost means a lot, especially in the allotetraploid common carp, who has undergone the fourth whole-genome duplication event. Here, we identified the whole set of olfactory receptor genes in representative teleosts and found a significant contraction in common carp when compared with other teleosts. Odorant receptor genes (OR) occupy the most among four groups of olfactory receptors, including 33 functional genes and 16 pseudogenes. Furthermore, 6 trace amine-associated receptor (TAAR) genes (including 1 pseudogene), 7 odorant-related-A receptor genes, and 10 olfactory C family receptor genes (including 3 pseudogenes) were identified in common carp. Phylogenetic and motif analysis were performed to illustrate the phylogenetic relationship and structural conservation of teleost olfactory receptors. Selection pressure analysis suggested that olfactory receptor groups in common carp were all under relaxed purifying-selection. Additionally, gene expression divergences for olfactory receptor genes were investigated during embryonic development stages of common carp. We aim to determine the abundance of common carp olfactory receptor genes, explore the evolutionary fate and expression dynamics, and provide some genomic clues for the evolution of polyploid olfactory after whole-genome duplication and for future studies of teleost olfactory.
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Shi T, Chen J. A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication. Genome Biol 2020; 21:295. [PMID: 33292440 PMCID: PMC7722308 DOI: 10.1186/s13059-020-02212-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/23/2020] [Indexed: 11/25/2022] Open
Abstract
The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-specific rather than shared by all eudicots.
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Affiliation(s)
- Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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Draft Genome of the Common Snapping Turtle, Chelydra serpentina, a Model for Phenotypic Plasticity in Reptiles. G3-GENES GENOMES GENETICS 2020; 10:4299-4314. [PMID: 32998935 PMCID: PMC7718744 DOI: 10.1534/g3.120.401440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Turtles are iconic reptiles that inhabit a range of ecosystems from oceans to deserts and climates from the tropics to northern temperate regions. Yet, we have little understanding of the genetic adaptations that allow turtles to survive and reproduce in such diverse environments. Common snapping turtles, Chelydra serpentina, are an ideal model species for studying adaptation to climate because they are widely distributed from tropical to northern temperate zones in North America. They are also easy to maintain and breed in captivity and produce large clutch sizes, which makes them amenable to quantitative genetic and molecular genetic studies of traits like temperature-dependent sex determination. We therefore established a captive breeding colony and sequenced DNA from one female using both short and long reads. After trimming and filtering, we had 209.51Gb of Illumina reads, 25.72Gb of PacBio reads, and 21.72 Gb of Nanopore reads. The assembled genome was 2.258 Gb in size and had 13,224 scaffolds with an N50 of 5.59Mb. The longest scaffold was 27.24Mb. BUSCO analysis revealed 97.4% of core vertebrate genes in the genome. We identified 3.27 million SNPs in the reference turtle, which indicates a relatively high level of individual heterozygosity. We assembled the transcriptome using RNA-Seq data and used gene prediction software to produce 22,812 models of protein coding genes. The quality and contiguity of the snapping turtle genome is similar to or better than most published reptile genomes. The genome and genetic variants identified here provide a foundation for future studies of adaptation to climate.
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Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour 2020; 21:816-833. [PMID: 33084200 DOI: 10.1111/1755-0998.13287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hadeel Saad
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Chenhong Li
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - William T White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA
| | - Dahiana Arcila
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA.,Department of Biology, University of Oklahoma, Norman, OK, USA
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Lu Y, Boswell M, Boswell W, Salinas RY, Savage M, Reyes J, Walter S, Marks R, Gonzalez T, Medrano G, Warren WC, Schartl M, Walter RB. Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns. BMC Genomics 2020; 21:787. [PMID: 33176680 PMCID: PMC7659085 DOI: 10.1186/s12864-020-07202-9] [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: 01/27/2020] [Accepted: 10/28/2020] [Indexed: 11/25/2022] Open
Abstract
Background Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period. Results Our results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs. Conclusions These observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Raquel Ybanez Salinas
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.,The University of Texas MD Anderson Cancer Center, Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Jose Reyes
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Sean Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Rebecca Marks
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Trevor Gonzalez
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Geraldo Medrano
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.,Developmental Biochemistry, Theodor-Boveri-Institute, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
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Wang X, Yan J. Directional divergence of Ep300 duplicates in teleosts and its implications. BMC Evol Biol 2020; 20:140. [PMID: 33129255 PMCID: PMC7603692 DOI: 10.1186/s12862-020-01712-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023] Open
Abstract
Background EP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy. Danio rerio is a promising model organism to study EP300 related diseases and drugs; however, the effect of EP300 duplicates derived from teleost-specific whole genome duplication should not just be neglected. Results In this study, we obtained EP300 protein sequences of representative teleosts, mammals and sauropsids, with which we inferred a highly supported maximum likelihood tree. We observed that Ep300 duplicates (Ep300a and Ep300b) were widely retained in teleosts and universally expressed in a variety of tissues. Consensus sequences of Ep300a and Ep300b had exactly the same distribution of conserved domains, suggesting that their functions should still be largely overlapped. We analyzed the molecular evolution of Ep300 duplicates in teleosts, using branch-site models, clade models and site models. The results showed that both duplicates were subject to strong positive selection; however, for an extant species, generally at most one copy was under positive selection. At the clade level, there were evident positive correlations between evolutionary rates, the number of positively selected sites and gene expression levels. In Ostariophysi, Ep300a were under stronger positive selection than Ep300b; in Neoteleostei, another species-rich teleost clade, the contrary was the case. We also modeled 3D structures of zf-TAZ domain and its flanking regions of Ep300a and Ep300b of D. rerio and Oryzias latipes and found that in either species the faster evolving copy had more short helixes. Conclusions Collectively, the two copies of Ep300 have undoubtedly experienced directional divergence in main teleost clades. The divergence of EP300 between teleosts and mammals should be greater than the divergence between different teleost clades. Further studies are needed to clarify to what extent the EP300 involved regulatory network has diverged between teleosts and mammals, which would also help explain the huge success of teleosts.
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Affiliation(s)
- Xianzong Wang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China.
| | - Junli Yan
- College of Urban and Rural Construction, Shanxi Agricultural University, Taigu, 030801, China
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50
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Parey E, Louis A, Cabau C, Guiguen Y, Roest Crollius H, Berthelot C. Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications. Mol Biol Evol 2020; 37:3324-3337. [DOI: 10.1093/molbev/msaa149] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Abstract
Whole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here, we present Synteny-guided CORrection of Paralogies and Orthologies (SCORPiOs), a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-My-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.
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Affiliation(s)
- Elise Parey
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cédric Cabau
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | | | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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