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Zhang X, Chen J, Luo H, Chen X, Zhong J, Ji X. Climate-driven mitochondrial selection in lacertid lizards. Ecol Evol 2024; 14:e11176. [PMID: 38529027 PMCID: PMC10961475 DOI: 10.1002/ece3.11176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
The mitochondrion, which is an intracellular organelle responsible for most of the energy-producing pathways, can have its genome targeted for climate-driven selection. However, climate-driven mitochondrial selection remains a sparsely studied area in reptiles. Here, we reported the complete mitochondrial genome sequence of a lacertid lizard (Takydromus intermedius) and used mitogenomes from 54 species of lacertid lizards to study their phylogenetic relationships and to identify the mitochondrial genes under positive selection by climate. The length of the complete mitochondrial genome sequence of T. intermedius was 17,713 bp, which was within the range of lengths (17,224-18,943) ever reported for Takydromus species. The arrangement of mitochondrial genes in T. intermedius was the same as in other congeneric species. The 54 lacertid species could be divided into three geographically and climatically different clades. We identified three mitochondrial genes (ATP6, ATP8, and ND3) under positive selection by climate, and found that isothermality, temperature seasonality, precipitation of wettest month, and precipitation seasonality were the most important climatic variables contributing to the gene selection.
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Affiliation(s)
- Xiang Zhang
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Jian Chen
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Hong‐Yu Luo
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Xin Chen
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Jun Zhong
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
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Ramos E, Selleghin-Veiga G, Magpali L, Daros B, Silva F, Picorelli A, Freitas L, Nery MF. Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians. J Mol Evol 2023; 91:865-881. [PMID: 38010516 DOI: 10.1007/s00239-023-10141-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 10/29/2023] [Indexed: 11/29/2023]
Abstract
The genetic basis underlying adaptive physiological mechanisms has been extensively explored in mammals after colonizing the seas. However, independent lineages of aquatic mammals exhibit complex patterns of secondary colonization in freshwater environments. This change in habitat represents new osmotic challenges, and additional changes in key systems, such as the osmoregulatory system, are expected. Here, we studied the selective regime on coding and regulatory regions of 20 genes related to the osmoregulation system in strict aquatic mammals from independent evolutionary lineages, cetaceans, and sirenians, with representatives in marine and freshwater aquatic environments. We identified positive selection signals in genes encoding the protein vasopressin (AVP) in mammalian lineages with secondary colonization in the fluvial environment and in aquaporins for lineages inhabiting the marine and fluvial environments. A greater number of sites with positive selection signals were found for the dolphin species compared to the Amazonian manatee. Only the AQP5 and AVP genes showed selection signals in more than one independent lineage of these mammals. Furthermore, the vasopressin gene tree indicates greater similarity in river dolphin sequences despite the independence of their lineages based on the species tree. Patterns of distribution and enrichment of Transcription Factors in the promoter regions of target genes were analyzed and appear to be phylogenetically conserved among sister species. We found accelerated evolution signs in genes ACE, AQP1, AQP5, AQP7, AVP, NPP4, and NPR1 for the fluvial mammals. Together, these results allow a greater understanding of the molecular bases of the evolution of genes responsible for osmotic control in aquatic mammals.
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Affiliation(s)
- Elisa Ramos
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Giovanna Selleghin-Veiga
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Letícia Magpali
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Beatriz Daros
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Felipe Silva
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Agnello Picorelli
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Lucas Freitas
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Mariana F Nery
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil.
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Lorente-Martínez H, Agorreta A, Irisarri I, Zardoya R, Edwards SV, San Mauro D. Multiple Instances of Adaptive Evolution in Aquaporins of Amphibious Fishes. BIOLOGY 2023; 12:846. [PMID: 37372131 DOI: 10.3390/biology12060846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
Aquaporins (AQPs) are a highly diverse family of transmembrane proteins involved in osmotic regulation that played an important role in the conquest of land by tetrapods. However, little is known about their possible implication in the acquisition of an amphibious lifestyle in actinopterygian fishes. Herein, we investigated the molecular evolution of AQPs in 22 amphibious actinopterygian fishes by assembling a comprehensive dataset that was used to (1) catalogue AQP paralog members and classes; (2) determine the gene family birth and death process; (3) test for positive selection in a phylogenetic framework; and (4) reconstruct structural protein models. We found evidence of adaptive evolution in 21 AQPs belonging to 5 different classes. Almost half of the tree branches and protein sites that were under positive selection were found in the AQP11 class. The detected sequence changes indicate modifications in molecular function and/or structure, which could be related to adaptation to an amphibious lifestyle. AQP11 orthologues appear to be the most promising candidates to have facilitated the processes of the water-to-land transition in amphibious fishes. Additionally, the signature of positive selection found in the AQP11b stem branch of the Gobiidae clade suggests a possible case of exaptation in this clade.
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Affiliation(s)
- Héctor Lorente-Martínez
- Department of Biodiversity, Ecology, and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Ainhoa Agorreta
- Department of Biodiversity, Ecology, and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Iker Irisarri
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature Hamburg, 20146 Hamburg, Germany
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Diego San Mauro
- Department of Biodiversity, Ecology, and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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Rajput S, Gautam D, Vats A, Rana C, Behera M, Roshan M, Ludri A, De S. Adaptive Selection in the Evolution of Aquaglyceroporins in Mammals. J Mol Evol 2023:10.1007/s00239-023-10112-5. [PMID: 37149832 DOI: 10.1007/s00239-023-10112-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 04/10/2023] [Indexed: 05/08/2023]
Abstract
Aquaporins (AQPs) are integral membrane proteins responsible for water transport across cellular membranes in both prokaryotes and eukaryotes. A subfamily of AQPs, known as aquaglyceroporins (AQGPs), facilitate the transport of small solutes such as glycerol, water, and other solutes across cellular membranes. These proteins are involved in a variety of physiological processes, such as organogenesis, wound healing, and hydration. Although AQPs have been studied extensively in different species, their conservation patterns, phylogenetic relationships, and evolution in mammals remain unexplored. In the present study, 119 AQGP coding sequences from 31 mammalian species were analysed to identify conserved residues, gene organisation, and most importantly, the nature of AQGP gene selection. Repertoire analysis revealed the absence of AQP7, 9, and 10 genes in certain species of Primates, Rodentia, and Diprotodontia, although not all three genes were absent in a single species. Two Asparagine-Proline-Alanine (NPA) motifs located at the N- and C-terminal ends, aspartic acid (D) residues, and the ar/R region were conserved in AQP3, 9, and 10. Six exons encoding the functional MIP domain of AQGP genes were found to be conserved across mammalian species. Evolutionary analysis indicated signatures of positive selection in AQP7, 9, and 10 amongst different mammalian lineages. Furthermore, substitutions of certain amino acids located close to critical residues may alter AQGP functionality, which is crucial for substrate selectivity, pore formation, and transport efficiency required for the maintenance of homeostasis in different mammalian species.
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Affiliation(s)
- Shiveeli Rajput
- Animal Biotechnology Centre, Animal Genomics Lab, ICAR-National Dairy Research Institute (NDRI), AGL, Karnal, Haryana, 132001, India
| | - Devika Gautam
- Animal Biotechnology Centre, Animal Genomics Lab, ICAR-National Dairy Research Institute (NDRI), AGL, Karnal, Haryana, 132001, India
| | - Ashutosh Vats
- Animal Biotechnology Centre, Animal Genomics Lab, ICAR-National Dairy Research Institute (NDRI), AGL, Karnal, Haryana, 132001, India
| | - Chanchal Rana
- Animal Biotechnology Centre, Animal Genomics Lab, ICAR-National Dairy Research Institute (NDRI), AGL, Karnal, Haryana, 132001, India
| | - Manisha Behera
- Department of Zoology, Hindu College, University of Delhi, Delhi, 110007, India
| | - Mayank Roshan
- Animal Biotechnology Centre, Animal Genomics Lab, ICAR-National Dairy Research Institute (NDRI), AGL, Karnal, Haryana, 132001, India
| | - Ashutosh Ludri
- Department of Animal Physiology, ICAR-National Dairy Research Institute (NDRI), Karnal, Haryana, 132001, India
| | - Sachinandan De
- Animal Biotechnology Centre, Animal Genomics Lab, ICAR-National Dairy Research Institute (NDRI), AGL, Karnal, Haryana, 132001, India.
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Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [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: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
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Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
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Lorente-Martínez H, Agorreta A, Torres-Sánchez M, San Mauro D. Evidence of positive selection suggests possible role of aquaporins in the water-to-land transition of mudskippers. ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0382-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
Abstract
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.
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Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
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Functional characterization of an aquaporin from a microsporidium, Nosema bombycis. PLoS One 2017; 12:e0181703. [PMID: 28749993 PMCID: PMC5531513 DOI: 10.1371/journal.pone.0181703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/04/2017] [Indexed: 11/19/2022] Open
Abstract
Microsporidia are a diverse group of eukaryotic organisms, capable of causing parasitic infections in both vertebrates and invertebrates. During the germination process, there is an increase in the osmotic pressure of microsporidian spores. As part of this study, we cloned a homologous aquaporin gene in Nosema bombycis, and named it Nosema bombycis aquaporin (NbAQP). Sequence analysis revealed that the NbAQP contains an open reading frame with a length of 750 bp and encodes a polypeptide of 249 amino acids. Amino acid sequence homology was greater than 50% that of five aquaporins from other microsporidian species. Indirect immunofluorescence (IFA) and immunogold electron microscopy showed NbAQP to be located predominantly in the spore wall of N. bombycis spores. The results of qRT-PCR analysis revealed that NbAQP expression remained high 0 h after inoculation and decreased sharply to 24 h, increased gradually from 2 days and peaked at 6 days. After expression of NbAQP in Xenopus laevis oocytes, it was observed that NbAQP can promote rapid penetration of water into oocytes. The associated permeation rate was 2–3 times that of the water-injected and uninjected oocytes. Antibody blocking experiments showed that the inhibition rate of spore germination was approximately 28% after antibody blocking. The difference in germination rate between the control group and the NbAQP group was significant (P < 0.05). This study shows for the first time that N. bombycis contains functional water channel proteins and provides a platform suitable for further research into the mechanisms underlying the regulation of NbAQP protein expression. Further study of NbAQP and their inhibitors may have significance for prevention of microsporidiosis.
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