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Chen B, Dai W, Li X, Mao T, Liu Y, Pie MR, Yang J, Meegaskumbura M. Wall-following - Phylogenetic context of an enhanced behaviour in stygomorphic Sinocyclocheilus (Cypriniformes: Cyprinidae) cavefishes. Ecol Evol 2024; 14:e11575. [PMID: 38932953 PMCID: PMC11199845 DOI: 10.1002/ece3.11575] [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: 11/06/2023] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
With 75 known species, the freshwater fish genus Sinocyclocheilus is the largest cavefish radiation in the world and shows multiple adaptations for cave-dwelling (stygomorphic adaptations), which include a range of traits such as eye degeneration (normal-eyed, micro-eyed and eyeless), depigmentation of skin, and in some species, the presence of "horns". Their behavioural adaptations to subterranean environments, however, are poorly understood. Wall-following (WF) behaviour, where an organism remains in close contact with the boundary demarcating its habitat when in the dark, is a peculiar behaviour observed in a wide range of animals and is enhanced in cave dwellers. Hence, we hypothesise that wall-following is also present in Sinocyclocheilus, possibly enhanced in eyeless species compared to eye bearing (normal-/micro-eyed species). Using 13 species representative of Sinocyclocheilus radiation and eye morphs, we designed a series of assays, based on pre-existing methods for Astyanax mexicanus behavioural experiments, to examine wall-following behaviour under three conditions. Our results indicate that eyeless species exhibit significantly enhanced intensities of WF compared to normal-eyed species, with micro-eyed forms demonstrating intermediate intensities in the WF distance. Using a mtDNA based dated phylogeny (chronogram with four clades A-D), we traced the degree of WF of these forms to outline common patterns. We show that the intensity of WF behaviour is higher in the subterranean clades compared to clades dominated by normal-eyed free-living species. We also found that eyeless species are highly sensitive to vibrations, whereas normal-eyed species are the least sensitive. Since WF behaviour is presented to some degree in all Sinocyclocheilus species, and given that these fishes evolved in the late Miocene, we identify this behaviour as being ancestral with WF enhancement related to cave occupation. Results from this diversification-scale study of cavefish behaviour suggest that enhanced wall-following behaviour may be a convergent trait across all stygomorphic lineages.
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Affiliation(s)
- Bing Chen
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of ForestryGuangxi UniversityNanningChina
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life SciencesFudan UniversityShanghaiChina
| | - Wen‐Zhang Dai
- School of Life Science and Institute of Wetland EcologyNanjing UniversityNanjingChina
| | - Xiang‐Lin Li
- State Key Laboratory of Efficient Production of Forest ResourcesSchool of Ecology and Nature Conservation, Beijing Forestry UniversityBeijingChina
| | - Ting‐Ru Mao
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of ForestryGuangxi UniversityNanningChina
| | - Ye‐Wei Liu
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of ForestryGuangxi UniversityNanningChina
| | - Marcio R. Pie
- Biology DepartmentEdge Hill UniversityOrmskirkLancashireUK
| | - Jian Yang
- Key Laboratory of Environment Change and Resource Use, Beibu GulfNanning Normal UniversityNanningGuangxiChina
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of ForestryGuangxi UniversityNanningChina
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2
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Wang K, Wang J, Liang B, Chang J, Zhu Y, Chen J, Agnarsson I, Li D, Peng Y, Liu J. Eyeless cave-dwelling Leptonetela spiders still rely on light. SCIENCE ADVANCES 2023; 9:eadj0348. [PMID: 38117895 PMCID: PMC10732526 DOI: 10.1126/sciadv.adj0348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Subterranean animals living in perpetual darkness may maintain photoresponse. However, the evolutionary processes behind the conflict between eye loss and maintenance of the photoresponse remain largely unknown. We used Leptonetela spiders to investigate the driving forces behind the maintenance of the photoresponse in cave-dwelling spiders. Our behavioral experiments showed that all eyeless/reduced-eyed cave-dwelling species retained photophobic response and that they had substantially decreased survival at cave entrances due to weak drought resistance. The transcriptomic analysis demonstrated that nearly all phototransduction pathway genes were present and that all tested phototransduction pathway genes were subjected to strong functional constraints in cave-dwelling species. Our results suggest that cave-dwelling eyeless spiders still use light and that light detection likely plays a role in avoiding the cave entrance habitat. This study confirms that some eyeless subterranean animals have retained their photosensitivity due to natural selection and provides a case of mismatch between phenotype and genotype or physiological function in a long-term evolutionary process.
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Affiliation(s)
- Kai Wang
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jinhui Wang
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Bing Liang
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jian Chang
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yang Zhu
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jian Chen
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ingi Agnarsson
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102 Reykjavik, Iceland
| | - Daiqin Li
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yu Peng
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jie Liu
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
- School of Nuclear Technology and Chemistry and Biology, Hubei University of Science and Technology, Xianning, Hubei 437100, China
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3
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Sifuentes-Romero I, Aviles AM, Carter JL, Chan-Pong A, Clarke A, Crotty P, Engstrom D, Meka P, Perez A, Perez R, Phelan C, Sharrard T, Smirnova MI, Wade AJ, Kowalko JE. Trait Loss in Evolution: What Cavefish Have Taught Us about Mechanisms Underlying Eye Regression. Integr Comp Biol 2023; 63:393-406. [PMID: 37218721 PMCID: PMC10445413 DOI: 10.1093/icb/icad032] [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: 02/27/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered, as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic, and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of the evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.
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Affiliation(s)
- Itzel Sifuentes-Romero
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Ari M Aviles
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Joseph L Carter
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Allen Chan-Pong
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Anik Clarke
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Patrick Crotty
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - David Engstrom
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Pranav Meka
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Alexandra Perez
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Riley Perez
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Christine Phelan
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Taylor Sharrard
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Maria I Smirnova
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Stiles–Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL 33458, USA
- Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Amanda J Wade
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Johanna E Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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4
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Carruthers M, Edgley DE, Saxon AD, Gabagambi NP, Shechonge A, Miska EA, Durbin R, Bridle JR, Turner GF, Genner MJ. Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes. Mol Biol Evol 2022; 39:msac251. [PMID: 36376993 PMCID: PMC10101686 DOI: 10.1093/molbev/msac251] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.
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Affiliation(s)
- Madeleine Carruthers
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Duncan E Edgley
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Andrew D Saxon
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Nestory P Gabagambi
- Tanzanian Fisheries Research Institute, Kyela Research
Centre, P.O. Box 98, Kyela, Mbeya, Tanzania
| | - Asilatu Shechonge
- Tanzanian Fisheries Research Institute, Dar es Salaam Research
Centre, P.O. Box 9750, Dar es Salaam, Tanzania
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge,
Cambridge CB2 1QN, United
Kingdom
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - George F Turner
- School of Natural Sciences, Bangor University,
Bangor, Wales LL57 2UW, United
Kingdom
| | - Martin J Genner
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
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5
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Zhao Q, Shao F, Li Y, Yi SV, Peng Z. Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes. Mol Ecol 2022; 31:5831-5845. [PMID: 36125323 PMCID: PMC9828065 DOI: 10.1111/mec.16700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Department of Laboratory Animal Science, College of Basic Medical SciencesArmy Medical University (Third Military Medical University)ChongqingChina
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Key Laboratory of Sichuan Province for Fish Conservation and Utilization in the Upper Reaches of the Yangtze RiverNeijiang Normal University College of Life SciencesNeijiangChina
| | - Soojin V. Yi
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Academy of Plateau Science and SustainabilityQinghai Normal UniversityXiningChina
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6
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Lam SM, Li J, Sun H, Mao W, Liu Z, Zhao Q, Han C, Gong X, Jiang B, Chua GH, Zhao Z, Meng F, Shui G. Quantitative lipidomics and spatial MS-Imaging uncovered neurological and systemic lipid metabolic pathways underlying troglomorphic adaptations in cave-dwelling fish. Mol Biol Evol 2022; 39:6547622. [PMID: 35277964 PMCID: PMC9011034 DOI: 10.1093/molbev/msac050] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Sinocyclocheilus represents a rare, freshwater teleost genus endemic to China that comprises the river-dwelling surface fish and the cave-dwelling cavefish. Using a combinatorial approach of quantitative lipidomics and mass-spectrometry imaging (MSI), we demonstrated that neural compartmentalization of lipid distribution and lipid metabolism are associated with the evolution of troglomorphic traits in Sinocyclocheilus. Attenuated DHA biosynthesis via the Δ4 desaturase pathway led to reductions in docosahexaenoic acid (DHA)-phospholipids in cavefish cerebellum. Instead, cavefish accumulates arachidonic acid (ARA)-phospholipids that may disfavor retinotectal arbor growth. Importantly, MSI of sulfatides, coupled with immunostaining of myelin basic protein and transmission electron microscopy images of hindbrain axons revealed demyelination in cavefish raphe serotonergic neurons. Demyelination in cavefish parallels the loss of neuroplasticity governing social behavior such as aggressive dominance. Outside the brain, quantitative lipidomics and qRT-PCR revealed systemic reductions in membrane esterified DHAs in the liver, attributed to suppression of genes along the Sprecher pathway (elovl2, elovl5, acox1). Development of fatty livers was observed in cavefish, likely mediated by an impeded mobilization of storage lipids, as evident in the diminished expressions of pnpla2, lipea, lipeb, dagla and mgll; and suppressed β-oxidation of fatty acyls via both mitochondria and peroxisomes, reflected in the reduced expressions of cpt1ab, hadhaa, cpt2, decr1 and acox1. These neurological and systemic metabolic adaptations serve to reduce energy expenditure, forming the basis of recessive evolution that eliminates non-essential morphological and behavioral traits, giving cavefish a selective advantage to thrive in caves where proper resource allocation becomes a major determinant of survival.
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Affiliation(s)
- Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,LipidALL Technologies Company Limited, Changzhou 213022, Jiangsu Province, China
| | - Jie Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weining Mao
- Qujing Aquaculture Station, Qujing 655000, Yunan Province, China
| | - Zongmin Liu
- Qujing Aquaculture Station, Qujing 655000, Yunan Province, China
| | - Qingshuo Zhao
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Han
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry Chinese Academy of Sciences, Beijing Mass Spectrum Center, Beijing, China
| | - Xia Gong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Binhua Jiang
- LipidALL Technologies Company Limited, Changzhou 213022, Jiangsu Province, China
| | - Gek Huey Chua
- LipidALL Technologies Company Limited, Changzhou 213022, Jiangsu Province, China
| | - Zhenwen Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry Chinese Academy of Sciences, Beijing Mass Spectrum Center, Beijing, China
| | - Fanwei Meng
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Mao T, Liu Y, Vasconcellos MM, Pie MR, Ellepola G, Fu C, Yang J, Meegaskumbura M. Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity. Mol Phylogenet Evol 2022; 168:107400. [PMID: 35031467 DOI: 10.1016/j.ympev.2022.107400] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 01/19/2023]
Abstract
Troglomorphism-any morphological adaptation enabling life to the constant darkness of caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and olfactory organs-has long intrigued biologists. However, inferring the proximate and ultimate mechanisms driving the evolution of troglomorphism (stygomorphism) in freshwater fish requires a sound understanding of the evolutionary relationships between surface and stygomorphic lineages. We use Restriction Site Associated DNA Sequencing (RADseq) to better understand the evolution of the Sinocyclocheilus fishes of China. With a remarkable array of derived stygomorphic traits, they comprise the largest cavefish diversification in the world, emerging as a multi-species model system to study evolutionary novelty. We sequenced a total of 120 individuals throughout the Sinocyclocheilus distribution. The data comprised a total of 646,497 bp per individual, including 4378 loci and 67,983 SNPs shared across a minimum of 114 individuals at a given locus. Phylogenetic analyses using either the concatenated RAD loci (RAxML) or the SNPs under a coalescent model (SVDquartets, SNAPP) showed a high degree of congruence with similar topologies and high node support (>95 for most nodes in the phylogeny). The major clades recovered conform to a pattern previously established using Sanger-based mt-DNA sequences, with a few notable exceptions. We now recognize six major clades in this group, elevating the blind cavefish S. tianlinensis and the micro-eyed S. microphthalmus as two new distinct clades due to their deep divergence from other clades. PCA plots of the SNP data also support the recognition of six major clusters of species congruent with the identified clades in ordination space. A Bayes factor delimitation (BFD) analysis showed support for 21 species, recognizing 19 previously described species and two putative new cryptic ones. Two species whose identities were previously disputed, S. furcodorsalis and S. tianeensis, are supported here as distinct species. In addition, our multi-species calibrated tree in SNAPP suggests that the genus Sinocyclocheilus originated around 10.16 Mya, with most speciation events occurring in the last 2 Mya, likely favored by the uplift of the Qinghai-Tibetan Plateau and cave occupation induced by climate-driven aridification during this period. These results provide a firm basis for future comparative studies on the evolution of Sinocyclocheilus and its adaptations to cave life.
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Affiliation(s)
- Tingru Mao
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Yewei Liu
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Mariana M Vasconcellos
- Programa de Pós-Graduação em Ecologia. Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcio R Pie
- Biology Department, Edge Hill University, Ormskirk, Lancashire L39 4QP, United Kingdom
| | - Gajaba Ellepola
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Chenghai Fu
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Jian Yang
- Key Laboratory of Environment Change and Resource Use, Beibu Gulf, Nanning Normal University, Nanning, Guangxi, PR China
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China.
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8
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Sadier A, Sears KE, Womack M. Unraveling the heritage of lost traits. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:107-118. [PMID: 33528870 DOI: 10.1002/jez.b.23030] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 12/22/2022]
Abstract
We synthesize ontogenetic work spanning the past century that show evolutionarily lost structures are rarely entirely absent from earlier developmental stages. We discuss morphological and genetic insights from developmental studies reveal about the evolution of trait loss and regain.
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Affiliation(s)
- Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Molly Womack
- Department of Biology, Utah State University, Logan, Utah, USA
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9
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Harper A, Baudouin Gonzalez L, Schönauer A, Janssen R, Seiter M, Holzem M, Arif S, McGregor AP, Sumner-Rooney L. Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates. G3 (BETHESDA, MD.) 2021; 11:jkab299. [PMID: 34849767 PMCID: PMC8664421 DOI: 10.1093/g3journal/jkab299] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 01/12/2023]
Abstract
Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.
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Affiliation(s)
- Amber Harper
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Luis Baudouin Gonzalez
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Geocentrum, 752 36 Uppsala, Sweden
| | - Michael Seiter
- Department of Evolutionary Biology, Unit Integrative Zoology, University of Vienna, 1090 Vienna, Austria
| | - Michaela Holzem
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Division of Signalling and Functional Genomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 69120 Heidelberg, Germany
| | - Saad Arif
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Lauren Sumner-Rooney
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK
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10
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Tovar RU, Cantu V, Fremaux B, Gonzalez Jr P, Spikes A, García DM. Comparative development and ocular histology between epigean and subterranean salamanders ( Eurycea) from central Texas. PeerJ 2021; 9:e11840. [PMID: 34395082 PMCID: PMC8325428 DOI: 10.7717/peerj.11840] [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: 10/20/2018] [Accepted: 07/01/2021] [Indexed: 11/24/2022] Open
Abstract
The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes-the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni.
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Affiliation(s)
- Ruben U. Tovar
- Department of Biology, Texas State University, San Marcos, TX, United States of America
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Valentin Cantu
- San Marcos Aquatic Resources Center, U.S. Fish and Wildlife Service, San Marcos, TX, United States of America
- Uvalde National Fish Hatchery, U.S. Fish and Wildlife Service, Uvalde, TX, United States of America
| | - Brian Fremaux
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Pedro Gonzalez Jr
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Amanda Spikes
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Dana M. García
- Department of Biology, Texas State University, San Marcos, TX, United States of America
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11
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Zheng S, Shao F, Tao W, Liu Z, Long J, Wang X, Zhang S, Zhao Q, Carleton KL, Kocher TD, Jin L, Wang Z, Peng Z, Wang D, Zhang Y. Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles. Mol Ecol Resour 2021; 21:1575-1592. [PMID: 33503304 DOI: 10.1111/1755-0998.13338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 01/07/2023]
Abstract
The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.
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Affiliation(s)
- Shuqing Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhilong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Juan Long
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Xiaoshuang Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Shuai Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
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12
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Secutti S, Trajano E. Reproduction, development, asymmetry and late eye regression in the Brazilian cave catfish Ituglanis passensis (Siluriformes, Trichomycteridae): evidence contributing to the neutral mutation theory. SUBTERRANEAN BIOLOGY 2021. [DOI: 10.3897/subtbiol.31.60691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The troglobitic (exclusively subterranean source population) catfish Ituglanis passensis (Siluriformes, Trichomycteridae) is endemic to the Passa Três Cave, São Domingos karst area, Rio Tocantins basin, Central Brazil. This unique population presents variably reduced eyes and melanic pigmentation. We describe reproduction and early development in this species based on a spontaneous (non-induced) reproductive-event that occurred in the laboratory in January–February, 2009, while simultaneously comparing with data from the cave-habitat and a previous reproductive event. Egg laying was parceled. Egg-size and number were within variations observed in epigean congeners. Larvae behavior and growth is described. A single surviving specimen was monitored over two years. Eye-regression started late, one year after birth, and followed a pattern of stasis phases intercalated with slow growth and fluctuating asymmetric rates. Late eye regression, associated with asymmetry in eye development and intra-population variability of troglomorphic traits, as shown by several Brazilian subterranean fishes, provide support for the Neutral Mutation Theory.
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13
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Li C, Chen H, Zhao Y, Chen S, Xiao H. Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes. Ecol Evol 2020; 10:14256-14271. [PMID: 33391713 PMCID: PMC7771137 DOI: 10.1002/ece3.7024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 07/28/2020] [Accepted: 10/28/2020] [Indexed: 11/13/2022] Open
Abstract
Cave-dwelling animals evolve distinct troglomorphic traits, such as loss of eyes, skin pigmentation, and augmentation of senses following long-term adaptation to perpetual darkness. However, the molecular genetic mechanisms underlying these phenotypic variations remain unclear. In this study, we conducted comparative histology and comparative transcriptomics study of the skin of eight Sinocyclocheilus species (Cypriniformes: Cyprinidae) that included surface- and cave-dwelling species. We analyzed four surface and four cavefish species by using next-generation sequencing, and a total of 802,798,907 clean reads were generated and assembled into 505,495,009 transcripts, which contributed to 1,037,334 unigenes. Bioinformatic comparisons revealed 10,629 and 6,442 significantly differentially expressed unigenes between four different surface-cave fish groups. Further, tens of differentially expressed genes (DEGs) potentially related to skin pigmentation were identified. Most of these DEGs (including GNAQ, PKA, NRAS, and p38) are downregulated in cavefish species. They are involved in key signaling pathways of pigment synthesis, such as the melanogenesis, Wnt, and MAPK pathways. This trend of downregulation was confirmed through qPCR experiments. This study will deepen our understanding of the formation of troglomorphic traits in cavefishes.
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Affiliation(s)
- Chunqing Li
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded EnvironmentsSchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Hongyu Chen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded EnvironmentsSchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
- School of Life SciencesYunnan UniversityKunmingChina
| | - Yinchen Zhao
- School of Life SciencesYunnan UniversityKunmingChina
| | - Shanyuan Chen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded EnvironmentsSchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Heng Xiao
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded EnvironmentsSchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
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14
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Zhao Y, Chen H, Li C, Chen S, Xiao H. Comparative Transcriptomics Reveals the Molecular Genetic Basis of Cave Adaptability in Sinocyclocheilus Fish Species. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.589039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cavefish evolved a series of distinct survival mechanisms for adaptation to cave habitat. Such mechanisms include loss of eyesight and pigmentation, sensitive sensory organs, unique dietary preferences, and predation behavior. Thus, it is of great interest to understand the mechanisms underlying these adaptability traits of troglobites. The teleost genus Sinocyclocheilus (Cypriniformes: Cyprinidae) is endemic to China and has more than 70 species reported (including over 30 cavefish species). High species diversity and diverse phenotypes make the Sinocyclocheilus as an outstanding model for studying speciation and adaptive evolution. In this study, we conducted a comparative transcriptomics study on the brain tissues of two Sinocyclocheilus species (surface-dwelling species – Sinocyclocheilus malacopterus and semi-cave-dwelling species – Sinocyclocheilus rhinocerous living in the same water body. A total of 425,188,768 clean reads were generated, which contributed to 102,839 Unigenes. Bioinformatic analysis revealed a total of 3,289 differentially expressed genes (DEGs) between two species Comparing to S. malacopterus, 2,598 and 691 DEGs were found to be respectively, down-regulated and up-regulated in S. rhinocerous. Furthermore, it is also found tens of DEGs related to cave adaptability such as insulin secretion regulation (MafA, MafB, MafK, BRSK, and CDK16) and troglomorphic traits formation (CEP290, nmnat1, coasy, and pqbp1) in the cave-dwelling S. rhinocerous. Interestingly, most of the DEGs were found to be down-regulated in cavefish species and this trend of DEGs expression was confirmed through qPCR experiments. This study would provide an appropriate genetic basis for future studies on the formation of troglomorphic traits and adaptability characters of troglobites, and improve our understanding of mechanisms of cave adaptation.
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15
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Zhao Y, Huang Z, Huang J, Zhang C, Meng F. Phylogenetic analysis and expression differences of eye-related genes in cavefish genus Sinocyclocheilus. Integr Zool 2020; 16:354-367. [PMID: 32652757 DOI: 10.1111/1749-4877.12466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The adaptive evolution of visual systems has been observed in many cavefish. However, little is known about the molecular mechanisms underlying these adaptations, which include regressive changes such as eye degeneration. Here, we analyzed phylogenetic and expression patterns of 6 eye-related genes (crx, foxg1b, opn1sw2, otx2, rho and sox2) in 12 Sinocyclocheilus species from China, including 8 stygobionts and 4 stygophiles, and examined photoreceptor cell morphology of these species. Those eye-degenerated species of Sinocyclocheilus were polyphyletic and showed different degrees of photoreceptor defects in responses to cave environments. The eye loss and degeneration are the result of convergent evolution. Although S. anophthalmus grouped with the eye-normal species, it displayed not only a high degree of eye degeneration but also significant expression differences in eye-related genes compared with the eye-normal species. The gene foxg1b, which was determined to be under positive selection, might play an important role in the process of eye degeneration in S. anophthalmus based on differential expression. Eye-related gene expression and selection may have contributed to the polyphyly of the cave species. We examined gene expression and duplication in 6 eye-related genes and revealed that these genes displayed considerable diversity in relative expression in Sinocyclocheilus fishes. Otx2 and sox2 were significantly up-regulated in individual cave species, while the other 4 genes (crx, foxg1b, opn1sw2 and rho) were significantly down-regulated. These findings provide a valuable resource for elucidating molecular mechanisms associated with visual system evolution in cavefish.
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Affiliation(s)
- Yahui Zhao
- State Key Laboratory of Membrane Biology, State Key Laboratory of Integrated Pest Management, Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zushi Huang
- State Key Laboratory of Membrane Biology, State Key Laboratory of Integrated Pest Management, Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jinqing Huang
- State Key Laboratory of Membrane Biology, State Key Laboratory of Integrated Pest Management, Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Faculty of Basic Medical Sciences, Guilin Medical University, Guilin, China
| | - Chunguang Zhang
- State Key Laboratory of Membrane Biology, State Key Laboratory of Integrated Pest Management, Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fanwei Meng
- State Key Laboratory of Membrane Biology, State Key Laboratory of Integrated Pest Management, Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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16
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Aardema ML, Stiassny MLJ, Alter SE. Genomic Analysis of the Only Blind Cichlid Reveals Extensive Inactivation in Eye and Pigment Formation Genes. Genome Biol Evol 2020; 12:1392-1406. [PMID: 32653909 PMCID: PMC7502198 DOI: 10.1093/gbe/evaa144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
Trait loss represents an intriguing evolutionary problem, particularly when it occurs across independent lineages. Fishes in light-poor environments often evolve “troglomorphic” traits, including reduction or loss of both pigment and eyes. Here, we investigate the genomic basis of trait loss in a blind and depigmented African cichlid, Lamprologus lethops, and explore evolutionary forces (selection and drift) that may have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower Congo River. Available evidence suggests that it inhabits deep, low-light habitats. Using genome sequencing, we show that genes related to eye formation and pigmentation, as well as other traits associated with troglomorphism, accumulated inactivating mutations rapidly after speciation. A number of the genes affected in L. lethops are also implicated in troglomorphic phenotypes in Mexican cavefish (Astyanax mexicanus) and other species. Analysis of heterozygosity patterns across the genome indicates that L. lethops underwent a significant population bottleneck roughly 1 Ma, after which effective population sizes remained low. Branch-length tests on a subset of genes with inactivating mutations show little evidence of directional selection; however, low overall heterozygosity may reduce statistical power to detect such signals. Overall, genome-wide patterns suggest that accelerated genetic drift from a severe bottleneck, perhaps aided by directional selection for the loss of physiologically expensive traits, caused inactivating mutations to fix rapidly in this species.
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Affiliation(s)
- Matthew L Aardema
- Department of Biology, Montclair State University.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, New York
| | - S Elizabeth Alter
- Department of Ichthyology, American Museum of Natural History, New York, New York.,The Graduate Center, City University of New York.,Department of Biology, York College/The City University of New York
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17
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Sears CR, Boggs TE, Gross JB. Dark-rearing uncovers novel gene expression patterns in an obligate cave-dwelling fish. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:518-529. [PMID: 32372488 DOI: 10.1002/jez.b.22947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 03/31/2020] [Accepted: 04/04/2020] [Indexed: 01/01/2023]
Abstract
Extreme environments often result in the evolution of dramatic adaptive features. The Mexican tetra, Astyanax mexicanus, includes 30 different populations of cave-dwelling forms that live in perpetual darkness. As a consequence, many populations have evolved eye loss, reduced pigmentation, and amplification of nonvisual sensory systems. Closely-related surface-dwelling morphs demonstrate typical vision, pigmentation, and sensation. Transcriptomic assessments in this system have revealed important developmental changes associated with the cave morph, however, they have not accounted for photic rearing conditions. Prior studies reared individuals under a 12:12 hr light/dark (LD) cycle. Here, we reared cavefish under constant darkness (DD) for 5+ years. From these experimental individuals, we performed mRNA sequencing and compared gene expression of surface fish reared under LD conditions to cavefish reared under DD conditions to identify photic-dependent gene expression differences. Gene Ontology enrichment analyses revealed a number of previously underappreciated cave-associated changes impacting blood physiology and olfaction. We further evaluated the position of differentially expressed genes relative to QTL positions from prior studies and found several candidate genes associated with these ecologically relevant lighting conditions. In sum, this work highlights photic conditions as a key environmental factor impacting gene expression patterns in blind cave-dwelling fish.
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Affiliation(s)
- Connor R Sears
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Tyler E Boggs
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
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18
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Chen H, Li C, Liu T, Chen S, Xiao H. A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species. MICROBIAL ECOLOGY 2020; 79:299-311. [PMID: 31280331 DOI: 10.1007/s00248-019-01409-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.
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Affiliation(s)
- Hongyu Chen
- School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Chunqing Li
- School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Tao Liu
- School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Shanyuan Chen
- School of Life Sciences, Yunnan University, Kunming, 650500, China.
- National Demonstration Center for Experimental Life Sciences Education (Yunnan University), Yunnan University, Kunming, China.
| | - Heng Xiao
- School of Life Sciences, Yunnan University, Kunming, 650500, China.
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19
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Zhao Q, Zhang R, Xiao Y, Niu Y, Shao F, Li Y, Peng Z. Comparative Transcriptome Profiling of the Loaches Triplophysa bleekeri and Triplophysa rosa Reveals Potential Mechanisms of Eye Degeneration. Front Genet 2020; 10:1334. [PMID: 32010191 PMCID: PMC6977438 DOI: 10.3389/fgene.2019.01334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Eye degeneration is one of the most obvious characteristics of organisms restricted to subterranean habitats. In cavefish, eye degeneration has evolved independently numerous times and each process is associated with different genetic mechanisms. To gain a better understanding of these mechanisms, we compared the eyes of adult individuals of the cave loach Triplophysa rosa and surface loach Triplophysa bleekeri. Compared with the normal eyes of the surface loach, those of the cave loach were found to possess a small abnormal lens and a defective retina containing photoreceptor cells that lack outer segments. Sequencing of the transcriptomes of both species to identify differentially expressed genes (DEGs) and genes under positive selection revealed 4,802 DEGs and 50 genes under positive selection (dN/dS > 1, FDR < 0.1). For cave loaches, we identified one Gene Ontology category related to vision that was significantly enriched in downregulated genes. Specifically, we found that many of the downregulated genes, including pitx3, lim2, crx, gnat2, rx1, rho, prph2, and β|γ-crystallin are associated with lens/retinal development and maintenance. However, compared with those in the surface loach, the lower dS rates but higher dN rates of the protein-coding sequences in T. rosa indicate that changes in amino acid sequences might be involved in the adaptation and visual degeneration of cave loaches. We also found that genes associated with light perception and light-stimulated vision have evolved at higher rates (some genes dN/dS > 1 but FDR > 0.1). Collectively, the findings of this study indicate that the degradation of cavefish vision is probably associated with both gene expression and amino acid changes and provide new insights into the mechanisms underlying the degeneration of cavefish eyes.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yingqi Xiao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yabing Niu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
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20
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Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus. Genes (Basel) 2019; 11:genes11010042. [PMID: 31905778 PMCID: PMC7016750 DOI: 10.3390/genes11010042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/18/2022] Open
Abstract
Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.
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21
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McGowan KL, Passow CN, Arias-Rodriguez L, Tobler M, Kelley JL. Expression analyses of cave mollies ( Poecilia mexicana) reveal key genes involved in the early evolution of eye regression. Biol Lett 2019; 15:20190554. [PMID: 31640527 DOI: 10.1098/rsbl.2019.0554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Eye regression occurs across cave-dwelling populations of many species and is often coupled with a decrease or loss in eye function. Teleost fishes are among the few vertebrates to undergo widespread colonization of caves and often exhibit eye regression with blindness. Cave populations of the poeciliid fish Poecilia mexicana (cave molly) exhibit reduced-albeit functional-eyes, offering the opportunity to investigate partial eye regression. We sequenced eye transcriptomes of cave and surface populations of P. mexicana to identify differentially expressed genes that potentially underlie eye regression in cave mollies. We identified 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signaling. Twenty-six of these genes were downregulated in cave compared to surface populations. Functional enrichment analysis revealed eye-related gene ontologies that were under-represented in cave mollies. In addition, a set of co-expressed genes related to vision and circadian rhythm was correlated with habitat type (cave versus surface). Our study suggests that differential gene expression plays a key role in the beginning evolutionary stages of eye regression in P. mexicana, shedding further light on regressive evolution in cavefish.
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Affiliation(s)
- Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Courtney N Passow
- Department of Ecology, Evolution and Behavior, University of Minnesota-Twin Cities, St. Paul, MN 55108, USA.,Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco 86150, Mexico
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
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22
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Huang Z, Titus T, Postlethwait JH, Meng F. Eye Degeneration and Loss of otx5b Expression in the Cavefish Sinocyclocheilus tileihornes. J Mol Evol 2019; 87:199-208. [PMID: 31332479 PMCID: PMC6711879 DOI: 10.1007/s00239-019-09901-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/13/2019] [Indexed: 12/17/2022]
Abstract
Cave animals possess remarkable phenotypes associated with existence in their dark environments. The Chinese cavefish Sinocyclocheilus tileihornes shows substantial eye degeneration, a trait shared by most cave species. The extent to which independent evolution of troglomorphic traits uses convergent molecular genetic mechanisms is as yet unknown. We performed transcriptome-wide gene expression profiling in S. tileihornes eyes and compared results with those from the closely related surface species S. angustiporus and an independently derived congeneric cavefish, S. anophthalmus. In total, 52.85 million 100 bp long paired-end clean reads were generated for S. tileihornes, and we identified differentially expressed genes between the three possible pairs of species. Functional analysis of genes differentially expressed between S. tileihornes and S. angustiporus revealed that phototransduction (KEGG id: dre04744) was the most significantly enriched pathway, indicating the obvious differences in response to captured photons between the cavefish S. tileihornes and the surface species S. angustiporus. Analysis of key genes regulating eye development showed complete absence of otx5b (orthodenticle homolog 5) expression in S. tileihornes eyes, probably related to degradation of rods, but normal expression of crx (cone-rod homeobox). The enriched pathways and Otx5 are involved in phototransduction, photoreceptor formation, and regulation of photoreceptor-related gene expression. Unlike the S. tileihornes reported here, S. anophthalmus has reduced crx and otx5 expression. These results show that different species of cavefish within the same genus that independently evolved troglodyte characteristics can have different genetic mechanisms of eye degeneration.
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Affiliation(s)
- Zushi Huang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | | | - Fanwei Meng
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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23
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Stern DB, Crandall KA. The Evolution of Gene Expression Underlying Vision Loss in Cave Animals. Mol Biol Evol 2019; 35:2005-2014. [PMID: 29788330 PMCID: PMC6063295 DOI: 10.1093/molbev/msy106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the nature of convergent loss of complex traits. Advances in evolutionary developmental biology have illuminated the significant role of heritable gene expression variation in the evolution of new forms. Here, we analyze gene expression variation in adult eye tissue across the freshwater crayfish, representing four independent vision-loss events in caves. Species and individual expression patterns cluster by eye function rather than phylogeny, suggesting convergence in transcriptome evolution in independently blind animals. However, this clustering is not greater than what is observed in surface species with conserved eye function after accounting for phylogenetic expectations. Modeling expression evolution suggests that there is a common increase in evolutionary rates in the blind lineages, consistent with a relaxation of selective constraint maintaining optimal expression levels. This is evidence for a repeated loss of expression constraint in the transcriptomes of blind animals and that convergence occurs via a similar trajectory through genetic drift.
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Affiliation(s)
- David B Stern
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC
| | - Keith A Crandall
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC
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24
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Sumner-Rooney L. The Kingdom of the Blind: Disentangling Fundamental Drivers in the Evolution of Eye Loss. Integr Comp Biol 2019; 58:372-385. [PMID: 29873729 DOI: 10.1093/icb/icy047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Light is a fundamentally important biological cue used by almost every animal on earth, to maintain daily rhythms, navigate, forage, find mates, or avoid predators. But an enormous number of species live in darkness: in subterranean caves, deep oceans, underground burrows, and within parasitic host bodies, and the loss of eyes appears consistently across these ecosystems. However, the evolutionary mechanisms that lead to the reduction of the visual system remain the subject of great interest and debate more than 150 years after Darwin tackled the issue. Studies of model taxa have discovered significant roles for natural selection, neutral evolution, and pleiotropy, but the interplay between them remains unclear. To nail down unifying concepts surrounding the evolution of eye loss, we must embrace the enormous range of affected animals and habitats. The fine developmental details of model systems such as the Mexican cave tetra Astyanax mexicanus have transformed and enriched the field, but these should be complemented by wider studies to identify truly overarching patterns that apply throughout animals. Here, the major evolutionary drivers are placed within a conceptual cost-benefit framework that incorporates the fundamental constraints and forces that influence evolution in the dark. Major physiological, ecological, and environmental factors are considered within the context of this framework, which appears faithful to observed patterns in deep-sea and cavernicolous animals. To test evolutionary hypotheses, a comparative phylogenetic approach is recommended, with the goal of studying large groups exhibiting repeated reduction, and then comparing these across habitats, taxa, and lifestyles. Currently, developmental and physiological methods cannot feasibly be used on such large scales, but penetrative imaging techniques could provide detailed morphological data non-invasively and economically for large numbers of species. Comprehensive structural datasets can then be contextualized phylogenetically to examine recurrent trends and associations, and to reconstruct character histories through multiple independent transitions into darkness. By assessing these evolutionary trajectories within an energetic cost-benefit framework, the relationships between fundamental influences can be inferred and compared across different biological and physical parameters. However, substantial numbers of biological and environmental factors affect the evolutionary trajectory of loss, and it is critical that researchers make fair and reasonable comparisons between objectively similar groups.
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25
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Stern DB, Crandall KA. Phototransduction Gene Expression and Evolution in Cave and Surface Crayfishes. Integr Comp Biol 2019; 58:398-410. [PMID: 29762661 DOI: 10.1093/icb/icy029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the absence of light in caves, animals have repeatedly evolved reduced eyes and visual systems. Whether the underlying genetic components remain intact in blind species remains unanswered across taxa. The freshwater crayfish have evolved to live in caves multiple times throughout their history; therefore, this system provides an opportunity to probe the genetic patterns and processes underlying repeated vision loss. Using transcriptomic data from the eyes of 14 species of cave and surface crayfishes, we identify the expression of 17 genes putatively related to visual phototransduction. We find a similarly complete repertoire of phototransduction gene families expressed in cave and surface species, but that the expression levels of those transcripts are consistently lower in cave species. We find statistical support for episodic positive selection, increased and decreased selection strength in caves, depending on the gene family. Analyses of gene expression evolution suggest convergent and possibly adaptive downregulation of these genes across eye-reduction events. Our results reveal a combination of evolutionary processes acting on the sequences and gene expression levels of vision-related genes underlying the loss of vision in caves.
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Affiliation(s)
- David B Stern
- The George Washington University, Milken Institute School of Public Health, Computational Biology Institute, 800 22nd St NW, Washington, DC 20052, USA.,Birge Hall, Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Keith A Crandall
- The George Washington University, Milken Institute School of Public Health, Computational Biology Institute, 800 22nd St NW, Washington, DC 20052, USA
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26
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Meng F, Zhao Y, Titus T, Zhang C, Postlethwait JH. Brain of the blind: transcriptomics of the golden-line cavefish brain. Curr Zool 2018; 64:765-773. [PMID: 30538736 PMCID: PMC6280103 DOI: 10.1093/cz/zoy005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/09/2018] [Indexed: 11/14/2022] Open
Abstract
The genus Sinocyclocheilus (golden-line barbel) includes 25 species of cave-dwelling blind fish (cavefish) and more than 30 surface-dwelling species with normal vision. Cave environments are dark and generally nutrient-poor with few predators. Cavefish of several genera evolved convergent morphological adaptations in visual, pigmentation, brain, olfactory, and digestive systems. We compared brain morphology and gene expression patterns in a cavefish Sinocyclocheilus anophthalmus with those of a closely related surface-dwelling species S. angustiporus. Results showed that cavefish have a longer olfactory tract and a much smaller optic tectum than surface fish. Transcriptomics by RNA-seq revealed that many genes upregulated in cavefish are related to lysosomes and the degradation and metabolism of proteins, amino acids, and lipids. Genes downregulated in cavefish tended to involve "activation of gene expression in cholesterol biosynthesis" and cholesterol degradation in the brain. Genes encoding Srebfs (sterol regulatory element-binding transcription factors) and Srebf targets, including enzymes in cholesterol synthesis, were downregulated in cavefish brains compared with surface fish brains. The gene encoding Cyp46a1, which eliminates cholesterol from the brain, was also downregulated in cavefish brains, while the total level of cholesterol in the brain remained unchanged. Cavefish brains misexpressed several genes encoding proteins in the hypothalamus-pituitary axis, including Trh, Sst, Crh, Pomc, and Mc4r. These results suggest that the rate of lipid biosynthesis and breakdown may both be depressed in golden-line cavefish brains but that the lysosome recycling rate may be increased in cavefish; properties that might be related to differences in nutrient availability in caves.
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Affiliation(s)
- Fanwei Meng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Chunguang Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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27
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Mojaddidi H, Fernandez FE, Erickson PA, Protas ME. Embryonic origin and genetic basis of cave associated phenotypes in the isopod crustacean Asellus aquaticus. Sci Rep 2018; 8:16589. [PMID: 30409988 PMCID: PMC6224564 DOI: 10.1038/s41598-018-34405-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/16/2018] [Indexed: 12/14/2022] Open
Abstract
Characteristics common to animals living in subterranean environments include the reduction or absence of eyes, lessened pigmentation and enhanced sensory systems. How these characteristics have evolved is poorly understood for the majority of cave dwelling species. In order to understand the evolution of these changes, this study uses an invertebrate model system, the freshwater isopod crustacean, Asellus aquaticus, to examine whether adult differences between cave and surface dwelling individuals first appear during embryonic development. We hypothesized that antennal elaboration, as well as eye reduction and pigment loss, would be apparent during embryonic development. We found that differences in pigmentation, eye formation, and number of segments of antenna II were all present by the end of embryonic development. In addition, we found that cave and surface hatchlings do not significantly differ in the relative size of antenna II and the duration of embryonic development. To investigate whether the regions responsible for eye and pigment differences could be genetically linked to differences in article number, we genotyped F2 hybrids for the four previously mapped genomic regions associated with eye and pigment differences and phenotyped these F2 hybrids for antenna II article number. We found that the region previously known to be responsible for both presence versus absence of pigment and eye size also was significantly associated with article number. Future experiments will address whether pleiotropy and/or genetic linkage play a role in the evolution of cave characteristics in Asellus aquaticus.
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Affiliation(s)
- Hafasa Mojaddidi
- Dominican University of California, 50 Acacia Ave, San Rafael, CA, 94901, USA
| | - Franco E Fernandez
- Dominican University of California, 50 Acacia Ave, San Rafael, CA, 94901, USA
| | | | - Meredith E Protas
- Dominican University of California, 50 Acacia Ave, San Rafael, CA, 94901, USA.
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28
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Weng MP, Liao BY. modPhEA: model organism Phenotype Enrichment Analysis of eukaryotic gene sets. Bioinformatics 2018; 33:3505-3507. [PMID: 28666356 DOI: 10.1093/bioinformatics/btx426] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/28/2017] [Indexed: 12/26/2022] Open
Abstract
Motivation Genome-scale phenotypic data are available for many model organisms, yet existing tools to functionally interpret gene sets from these phenotypic data are largely based on mutagenesis-derived phenotypes observed in mouse or human. Results Data from both mutagenesis and knockdown experiments are incorporated into modPhEA to allow users to perform enrichment analyses based on phenotypes observed in budding yeast (Saccharomyces cerevisiae), roundworm (Caenorhabditis elegans), fruit fly (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus) and humans (Homo sapiens). The phenotypes analysed can be customized to investigate complex traits and gene sets from any fully sequenced animal or fungal genome are also supported by modPhEA. Availability and implementation Freely available on the web at http://evol.nhri.org.tw/modPhEA/. Contact liaoby@nhri.org.tw. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan, ROC
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan, ROC
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29
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Tierney SM, Langille B, Humphreys WF, Austin AD, Cooper SJB. Massive Parallel Regression: A Précis of Genetic Mechanisms for Vision Loss in Diving Beetles. Integr Comp Biol 2018; 58:465-479. [DOI: 10.1093/icb/icy035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Simon M Tierney
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Barbara Langille
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - William F Humphreys
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, WA 6986, Australia
- School of Animal Biology, The University of Western Australia, Nedlands, WA 6907, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
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30
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Re C, Fišer Ž, Perez J, Tacdol A, Trontelj P, Protas ME. Common Genetic Basis of Eye and Pigment Loss in Two Distinct Cave Populations of the Isopod Crustacean Asellus aquaticus. Integr Comp Biol 2018; 58:421-430. [DOI: 10.1093/icb/icy028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Cassandra Re
- Dominican University of California, 50 Acacia Avenue, San Rafael, CA 94901, USA
| | - Žiga Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Justin Perez
- Dominican University of California, 50 Acacia Avenue, San Rafael, CA 94901, USA
| | - Allyson Tacdol
- Dominican University of California, 50 Acacia Avenue, San Rafael, CA 94901, USA
| | - Peter Trontelj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Meredith E Protas
- Dominican University of California, 50 Acacia Avenue, San Rafael, CA 94901, USA
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31
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Chou CH, Huang HY, Huang WC, Hsu SD, Hsiao CD, Liu CY, Chen YH, Liu YC, Huang WY, Lee ML, Chen YC, Huang HD. The aquatic animals' transcriptome resource for comparative functional analysis. BMC Genomics 2018; 19:103. [PMID: 29764375 PMCID: PMC5954267 DOI: 10.1186/s12864-018-4463-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. Results To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. Conclusion In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/. Electronic supplementary material The online version of this article (10.1186/s12864-018-4463-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsi-Yuan Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli, 320, Taiwan
| | - Chia-Yu Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Hung Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Chen Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Yun Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Meng-Lin Lee
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yi-Chang Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
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32
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The transcriptomes of cave and surface populations of Gammarus minus (Crustacea: Amphipoda) provide evidence for positive selection on cave downregulated transcripts. PLoS One 2017; 12:e0186173. [PMID: 29016667 PMCID: PMC5633187 DOI: 10.1371/journal.pone.0186173] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/26/2017] [Indexed: 11/23/2022] Open
Abstract
Gammarus minus, a freshwater amphipod living in the cave and surface streams in the eastern USA, is an excellent model for investigating evolutionary adaptation to the subterranean environment. RNA-Seq was conducted on one pair of morphologically distinct sister populations inhabiting surface and cave habitats to identify genes that were differentially expressed in the two populations, as well as to compare levels and patterns of genetic variation within and between populations. Of the 104,630 transcripts identified in the transcriptome assembly, 57% had higher average levels of expression in the cave population. After Benjamini-Hochberg correction for multiple tests, 1517 and 551 transcripts were significantly upregulated or downregulated, respectively, in the cave population, indicating an almost three-fold enrichment of cave-upregulated genes. The average level of nucleotide diversity across all transcripts was significantly lower in the cave population. Within the cave population, where the average nucleotide diversity of cave-downregulated transcripts was 75% that of the cave-upregulated transcripts, a highly significant difference, whereas within the spring population the nucleotide diversities of cave-downregulated and cave-upregulated transcripts was virtually identical. Three lines of evidence suggest that the reduced variation in cave downregulated transcripts is due to positive selection in the cave population: 1) the average neutrality index of cave-downregulated genes was < 1, consistent with positive selection, and significantly less than that of cave-upregulated genes; 2) Tajima’s D was positively correlated with the cave:surface expression ratio, and 3) cave-downregulated transcripts were significantly more likely to be highly diverged from their surface homologs than cave-upregulated transcripts. Five transcripts had fixed premature termination codons in the cave population. The expression patterns and sequence variation in one such transcript, encoding the DNA repair protein photolyase, were examined in more detail and provide the first evidence for the relaxation of functional constraint in this light-dependent protein in a subterranean population.
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33
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Passow CN, Brown AP, Arias-Rodriguez L, Yee MC, Sockell A, Schartl M, Warren WC, Bustamante C, Kelley JL, Tobler M. Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Mol Ecol 2017; 26:4211-4225. [PMID: 28598519 PMCID: PMC5731456 DOI: 10.1111/mec.14198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 12/31/2022]
Abstract
Variation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA-sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulphide (H2 S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors. We analysed organ-specific transcriptome-wide data from four ecotypes of Poecilia mexicana (nonsulphidic surface, sulphidic surface, nonsulphidic cave and sulphidic cave). The majority of variation in gene expression was correlated with organ type, and the presence of specific environmental stressors elicited unique expression differences among organs. Shared patterns of gene expression between populations exposed to the same environmental stressors increased with levels of organismal organization (from transcript to gene to physiological pathway). In addition, shared patterns of gene expression were more common between populations from sulphidic than populations from cave habitats, potentially indicating that physiochemical stressors with clear biochemical consequences can constrain the diversity of adaptive solutions that mitigate their adverse effects. Overall, our analyses provided insights into transcriptional variation in a unique system, in which adaptation to H2 S and darkness coincide. Functional annotations of differentially expressed genes provide a springboard for investigating physiological mechanisms putatively underlying adaptation to extreme environments.
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Affiliation(s)
| | - Anthony P. Brown
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - Muh-Ching Yee
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
- Texas A&M Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Wesley C. Warren
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Joanna L. Kelley
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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Exploring the molecular basis of adaptive evolution in hydrothermal vent crab Austinograea alayseae by transcriptome analysis. PLoS One 2017; 12:e0178417. [PMID: 28552991 PMCID: PMC5446156 DOI: 10.1371/journal.pone.0178417] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/12/2017] [Indexed: 12/12/2022] Open
Abstract
Elucidating the genetic mechanisms of adaptation to the hydrothermal vent in organisms at genomic level is significant for understanding the adaptive evolution process in the extreme environment. We performed RNA-seq on four different tissues of a vent crab species, Austinograea alayseae, producing 725,461 unigenes and 134,489 annotated genes. Genes related to sensory, circadian rhythm, hormone, hypoxia stress, metal detoxification and immunity were identified. It was noted that in the degenerated eyestalk, transcription of phototransduction related genes which are important for retinal function was greatly reduced; three crucial neuropeptide hormones, one molt-inhibiting and two crustacean hyperglycemic hormone precursors were characterized with conserved domains; hypoxia-inducible factor 1 and two novel isoforms of metallothioneins in the vent crabs were discovered. An analysis of 6,932 orthologs among three crabs A. alayseae, Portunus trituberculutus and Eriocheir sinensis revealed 19 positive selected genes (PSGs). Most of the PSGs were involved in immune responses, such as crustins and anti-lipopolysaccharide factor, suggesting their function in the adaptation to environment. The characterization of the first vent crab transcriptome provides abundant resources for genetic and evolutionary studies of this species, and paves the way for further investigation of vent adaptation process in crabs.
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Chi W, Ma X, Niu J, Zou M. Genome-wide identification of genes probably relevant to the adaptation of schizothoracins (Teleostei: Cypriniformes) to the uplift of the Qinghai-Tibet Plateau. BMC Genomics 2017; 18:310. [PMID: 28427344 PMCID: PMC5397779 DOI: 10.1186/s12864-017-3703-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 04/12/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Molecular adaptation to the severe environments present during the uplift of the Qinghai-Tibet Plateau has attracted the attention of researchers. The divergence of the three specialization groups of schizothoracins (Primitive, Specialized and Highly Specialized) may correspond to the three phases of plateau uplift. Based on the transcripts of representative species of the three specialized groups and an outgroup, genes in schizothoracins that may have played important roles during the adaptation to new environments were investigated. RESULTS The contigs of Gymnodiptychus dybowskii and Schizothorax pseudaksaiensis were compared with those of Gymnocypris przewalskii ganzihonensis and the outgroup Sinocyclocheilus angustiporus, and 5,894 ortholog groups with an alignment length longer than 90 nt after deleting gaps were retained. Evolutionary analyses indicated that the average evolutionary rate of the branch leading to the Specialized group was faster than that of the branch leading to the Highly Specialized group. Moreover, the numbers of gene categories in which more than half of the genes evolved faster than the average values of the genome were 117 and 15 along the branches leading to the Specialized and Highly Specialized groups, respectively. A total of 40, 36, and 55 genes were likely subject to positive selection along the branches leading to the Primitive, Specialized and Highly Specialized groups, respectively, and many of these genes are likely relevant to adaptation to the cold temperatures, low oxygen concentrations, and strong ultraviolet radiation that result from elevation. CONCLUSIONS By selecting representative species of the three groups of schizothoracins and applying next-generation sequencing technology, several candidate genes corresponding to adaptation to the three phases of plateau uplift were identified. Some of the genes identified in this report that were likely subject to positive selection are good candidates for subsequent evolutionary and functional analyses of adaptation to high altitude.
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Affiliation(s)
- Wei Chi
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Xufa Ma
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Jiangong Niu
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Fisheries Research Institute of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Ming Zou
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
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Luo F, Huang J, He A, Luo T, Zhou H, Wen Y. Complete mitochondrial genome of a cavefish Sinocyclocheilus ronganensis (Cypriniformes: Cyprinidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:117-118. [PMID: 33473736 PMCID: PMC7800113 DOI: 10.1080/23802359.2017.1280696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
In this study, we report the complete mitochondrial genome of Sinocyclocheilus ronganensis. The whole mitochondrial genome is 16,587 bp with an accession number KX778473, and consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs genes, and a 936 bp control region. Phylogenetic analysis shows that S. ronganensis is close to cave-restricted S. anophthalmus and surface-dwelling S. grahami. The complete mitogenome of S. ronganensis may provide useful information for studying the genetic mechanism of cavefish, and enrich the fish mitochondrial genome resource for further research.
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Affiliation(s)
- Fuguang Luo
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Jie Huang
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Anyou He
- Lab of Fishery and Ecological environment, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Tong Luo
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Huanjia Zhou
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Yanhong Wen
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
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Krishnan J, Rohner N. Cavefish and the basis for eye loss. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150487. [PMID: 27994128 PMCID: PMC5182419 DOI: 10.1098/rstb.2015.0487] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 11/12/2022] Open
Abstract
Animals have colonized the entire world from rather moderate to the harshest environments, some of these so extreme that only few animals are able to survive. Cave environments present such a challenge and obligate cave animals have adapted to perpetual darkness by evolving a multitude of traits. The most common and most studied cave characteristics are the regression of eyes and the overall reduction in pigmentation. Studying these traits can provide important insights into how evolutionary forces drive convergent and regressive adaptation. The blind Mexican cavefish (Astyanax mexicanus) has emerged as a useful model to study cave evolution owing to the availability of genetic and genomic resources, and the amenability of embryonic development as the different populations remain fertile with each other. In this review, we give an overview of our current knowledge underlying the process of regressive and convergent evolution using eye degeneration in cavefish as an example.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Jaya Krishnan
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
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Ishikawa A, Kusakabe M, Yoshida K, Ravinet M, Makino T, Toyoda A, Fujiyama A, Kitano J. Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes. Evolution 2017; 71:565-581. [PMID: 28075479 DOI: 10.1111/evo.13175] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/21/2016] [Indexed: 12/12/2022]
Abstract
Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus). We identified both local and distant eQTLs, some of which constitute hotspots, regions with a disproportionate number of significant eQTLs relative to the genomic background. The majority of local eQTLs including those in the hotspots caused expression changes consistent with the direction of transcriptomic divergence between ecotypes. Genome scan analysis showed that many local eQTLs overlapped with genomic regions of high differentiation. In contrast, nearly half of the distant eQTLs including those in the hotspots caused opposite expression changes, and few overlapped with regions of high differentiation, indicating that distant eQTLs may act as a constraint of transcriptome evolution. Finally, a comparison between two salinity conditions revealed that nearly half of eQTL hotspots were environment specific, suggesting that analysis of genetic architecture in multiple conditions is essential for predicting response to selection.
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Affiliation(s)
- Asano Ishikawa
- Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Makoto Kusakabe
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.,Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Kohta Yoshida
- Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Mark Ravinet
- Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan.,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Takashi Makino
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jun Kitano
- Division of Ecological Genetics, National Institute of Genetics, Shizuoka, Japan
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Stout CC, Tan M, Lemmon AR, Lemmon EM, Armbruster JW. Resolving Cypriniformes relationships using an anchored enrichment approach. BMC Evol Biol 2016; 16:244. [PMID: 27829363 PMCID: PMC5103605 DOI: 10.1186/s12862-016-0819-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). RESULTS Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. CONCLUSIONS Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.
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Affiliation(s)
- Carla C. Stout
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Milton Tan
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306 USA
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 USA
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
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Casane D, Rétaux S. Evolutionary Genetics of the Cavefish Astyanax mexicanus. ADVANCES IN GENETICS 2016; 95:117-59. [PMID: 27503356 DOI: 10.1016/bs.adgen.2016.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Blind and depigmented fish belonging to the species Astyanax mexicanus are outstanding models for evolutionary genetics. During their evolution in the darkness of caves, they have undergone a number of changes at the morphological, physiological, and behavioral levels, but they can still breed with their river-dwelling conspecifics. The fertile hybrids between these two morphotypes allow forward genetic approaches, from the search of quantitative trait loci to the identification of the mutations underlying the evolution of troglomorphism. We review here the past 30years of evolutionary genetics on Astyanax: from the first crosses and the discovery of convergent evolution of different Astyanax cavefish populations to the most recent evolutionary transcriptomics and genomics studies that have provided researchers with potential candidate genes to be tested using functional genetic approaches. Although significant progress has been made and some genes have been identified, cavefish have not yet fully revealed the secret of their adaptation to the absence of light. In particular, the genetic determinism of their loss of eyes seems complex and still puzzles researchers. We also discuss future research directions, including searches for the origin of cave alleles and searches for selection genome-wide, as well as the necessary but missing information on the timing of cave colonization by surface fish.
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Affiliation(s)
- D Casane
- Laboratory EGCE, CNRS and University of Paris-Sud, Gif-sur-Yvette, France; Paris Diderot University, Sorbonne Paris Cité, France
| | - S Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Sud, Gif-sur-Yvette, France
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Hulsey CD, Fraser GJ, Meyer A. Biting into the Genome to Phenome Map: Developmental Genetic Modularity of Cichlid Fish Dentitions. Integr Comp Biol 2016; 56:373-88. [DOI: 10.1093/icb/icw059] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Abstract
The Genetics Society of America’s George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers and who exemplify the qualities of its namesake as a respected academic, administrator, and public servant. The 2015 recipient is John Postlethwait. He has made groundbreaking contributions in developing the zebrafish as a molecular genetic model and in understanding the evolution of new gene functions in vertebrates. He built the first zebrafish genetic map and showed that its genome, along with that of distantly related teleost fish, had been duplicated. Postlethwait played an integral role in the zebrafish genome-sequencing project and elucidated the genomic organization of several fish species. Postlethwait is also honored for his active involvement with the zebrafish community, advocacy for zebrafish as a model system, and commitment to driving the field forward.
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Wei S, Shang H, Cao Y, Wang Q. The coiled-coil domain containing protein Ccdc136b antagonizes maternal Wnt/β-catenin activity during zebrafish dorsoventral axial patterning. J Genet Genomics 2016; 43:431-8. [PMID: 27477027 DOI: 10.1016/j.jgg.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/05/2016] [Accepted: 05/09/2016] [Indexed: 01/09/2023]
Abstract
The coiled-coil domain containing protein CCDC136 is a putative tumor suppressor and significantly down-regulated in gastric and colorectal cancer tissues. However, little is known about its biological functions during vertebrate embryo development. Zebrafish has two CCDC136 orthologs, ccdc136a and ccdc136b, but only ccdc136b is highly expressed during early embryonic development. In this study, we demonstrate that ccdc136b is required for dorsal-ventral axial patterning in zebrafish embryos. ccdc136b morphants display strongly dorsalized phenotypes. Loss- and gain-of-function experiments in zebrafish embryos and mammalian cells show that Ccdc136b is a crucial negative regulator of the Wnt/β-catenin signaling pathway, and plays a critical role in the establishment of the dorsal-ventral axis. We further find that Ccdc136b interacts with APC, promotes the binding affinity of APC with β-catenin and then facilitates the turnover of β-catenin. These results provide the first evidence that CCDC136 regulates zebrafish dorsal-ventral patterning by antagonizing Wnt/β-catenin signal transduction and suggest a potential mechanism underlying its suppressive activity in carcinogenesis.
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Affiliation(s)
- Shi Wei
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hanqiao Shang
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Cao
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Wang
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Rispe C, Legeai F, Papura D, Bretaudeau A, Hudaverdian S, Le Trionnaire G, Tagu D, Jaquiéry J, Delmotte F. De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms. BMC Genomics 2016; 17:219. [PMID: 26968158 PMCID: PMC4787006 DOI: 10.1186/s12864-016-2530-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/24/2016] [Indexed: 11/28/2022] Open
Abstract
Background Grapevine phylloxera, an insect related to true aphids, is a major historic pest of viticulture only controlled through the selection of resistant rootstocks or through quarantine regulations where grapevine is cultivated own-rooted. Transcriptomic data could help understand the bases of its original life-traits, including a striking case of polyphenism, with forms feeding on roots and forms feeding in leaf-galls. Comparisons with true aphids (for which complete genomes have been sequenced) should also allow to link differences in life-traits of the two groups with changes in gene repertoires or shifts in patterns of expression. Results We sequenced transcriptomes of the grapevine phylloxera (Illumina technology), choosing three life-stages (adults on roots or on leaf galls, and eggs) to cover a large catalogue of transcripts, and performed a de novo assembly. This resulted in 105,697 contigs, which were annotated: most contigs had a best blastx hit to the pea aphid (phylogenetically closest complete genome), while very few bacterial hits were recorded (except for Probionibacterium acnes). Coding sequences were predicted from this data set (17,372 sequences), revealing an extremely high AT-bias (at the third codon position). Differential expression (DE) analysis among root-feeding and gall-feeding showed that i) the root-feeding form displayed a much larger number of differentially expressed transcripts ii) root-feeding biased genes were enriched in some categories, for example cuticular proteins and genes associated with cell-cell signaling iii) leaf-galling-biased genes were enriched in genes associated with the nucleus and DNA-replication, suggesting a metabolism more oriented towards fast and active multiplication. We also identified a gene family with a very high expression level (copies totaling nearly 10 % of the reads) in the grapevine phylloxera (both in root and leaf galling forms), but usually expressed at very low levels in true aphids (except in sexual oviparous females). These transcripts thus appear to be associated with oviparity. Conclusions Our study illustrated major intraspecific changes in transcriptome profiles, related with different life-styles (and the feeding on roots versus in leaf-galls). At a different scale, we could also illustrate one major shift in expression levels associated with changes in life-traits that occurred along evolution and that respectively characterize (strictly oviparous) grapevine phylloxera and (mostly viviparous) true aphids. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2530-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claude Rispe
- Present Address: BIOEPAR, INRA, Oniris, La Chantrerie, F-44307, Nantes, France. .,IGEPP, INRA, F-35653, Le Rheu cedex, France.
| | - Fabrice Legeai
- IGEPP, BIPAA, INRA, Campus Beaulieu, Rennes, France.,Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes, France
| | | | - Anthony Bretaudeau
- IGEPP, BIPAA, INRA, Campus Beaulieu, Rennes, France.,Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genouest, Campus Beaulieu, Rennes, France
| | | | | | - Denis Tagu
- IGEPP, INRA, F-35653, Le Rheu cedex, France
| | - Julie Jaquiéry
- IGEPP, INRA, F-35653, Le Rheu cedex, France.,Present address: University of Rennes 1, UMR CNRS 6553 EcoBio, 35042, Rennes, France
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Wilkens H. Genetics and hybridization in surface and caveAstyanax(Teleostei): a comparison of regressive and constructive traits. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Horst Wilkens
- University of Hamburg; Centrum für Naturkunde - CeNak; Zoological Museum; Martin-Luther-King-Platz 3 20146 Hamburg Germany
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Yang J, Chen X, Bai J, Fang D, Qiu Y, Jiang W, Yuan H, Bian C, Lu J, He S, Pan X, Zhang Y, Wang X, You X, Wang Y, Sun Y, Mao D, Liu Y, Fan G, Zhang H, Chen X, Zhang X, Zheng L, Wang J, Cheng L, Chen J, Ruan Z, Li J, Yu H, Peng C, Ma X, Xu J, He Y, Xu Z, Xu P, Wang J, Yang H, Wang J, Whitten T, Xu X, Shi Q. The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biol 2016; 14:1. [PMID: 26728391 PMCID: PMC4698820 DOI: 10.1186/s12915-015-0223-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/17/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.
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Affiliation(s)
- Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | | | - Jie Bai
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,Fauna & Flora International, Cambridge, CB1 2JD, UK.
| | - Dongming Fang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Ying Qiu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,China National Genebank, Shenzhen, 518083, China.
| | - Wansheng Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Hui Yuan
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Chao Bian
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Jiang Lu
- BGI-Shenzhen, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shiyang He
- BGI-Shenzhen, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Yaolei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xinxin You
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | | | - Ying Sun
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National Genebank, Shenzhen, 518083, China.
| | | | - Yong Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | | | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiaoyong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xinhui Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Lanping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | | | - Le Cheng
- China National Genebank, Shenzhen, 518083, China. .,BGI-Yunnan, Kunming, 650106, China.
| | - Jieming Chen
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Zhiqiang Ruan
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Jia Li
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hui Yu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chao Peng
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Xingyu Ma
- Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
| | - Junmin Xu
- Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
| | - You He
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China.
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210029, China.
| | - Pao Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China. .,James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - Tony Whitten
- Fauna & Flora International, Cambridge, CB1 2JD, UK.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Qiong Shi
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
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47
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He S, Lu J, Jiang W, Yang S, Yang J, Shi Q. The complete mitochondrial genome sequence of a cavefish Sinocyclocheilus anshuiensis (Cypriniformes: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4256-4258. [PMID: 26539745 DOI: 10.3109/19401736.2015.1046127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Sinocyclocheilus anshuiensis is a special cavefish that lives in the Southwestern China with many specific regressive features, such as rudimentary eyes and scales, and loss of pigmentation. In this study, we performed sequencing and assembly of its complete mitochondrial genome. We confirmed that total length of the mitochondrion is 16 618 bp with an AT ratio of 55.4%. The complete mitochondrial genome contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a 963 bp control region. Our current data provide important resources for the research of cavefish mitochondrial evolution and energy metabolism.
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Affiliation(s)
- Shiyang He
- a College of Life Sciences, University of Chinese Academy of Sciences , Beijing , China
| | - Jiang Lu
- a College of Life Sciences, University of Chinese Academy of Sciences , Beijing , China
| | - Wansheng Jiang
- b State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
| | | | - Junxing Yang
- b State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
| | - Qiong Shi
- c BGI-Shenzhen , Shenzhen , China.,d Shenzhen Key Lab of Marine Genomics , Shenzhen , China , and.,e State Key Laboratory of Agricultural Genomics , Shenzhen , China
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48
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Stahl BA, Gross JB, Speiser DI, Oakley TH, Patel NH, Gould DB, Protas ME. A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus. PLoS One 2015; 10:e0140484. [PMID: 26462237 PMCID: PMC4604090 DOI: 10.1371/journal.pone.0140484] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/25/2015] [Indexed: 12/14/2022] Open
Abstract
Cave animals, compared to surface-dwelling relatives, tend to have reduced eyes and pigment, longer appendages, and enhanced mechanosensory structures. Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. An excellent system for exploring these questions is the isopod, Asellus aquaticus. This species includes multiple cave and surface populations that have numerous morphological differences between them. A key feature is that hybrids between cave and surface individuals are viable, which enables genetic crosses and linkage analyses. Here, we advance this system by analyzing single animal transcriptomes of Asellus aquaticus. We use high throughput sequencing of non-normalized cDNA derived from the head of a surface-dwelling male, the head of a cave-dwelling male, the head of a hybrid male (produced by crossing a surface individual with a cave individual), and a pooled sample of surface embryos and hatchlings. Assembling reads from surface and cave head RNA pools yielded an integrated transcriptome comprised of 23,984 contigs. Using this integrated assembly as a reference transcriptome, we aligned reads from surface-, cave- and hybrid- head tissue and pooled surface embryos and hatchlings. Our approach identified 742 SNPs and placed four new candidate genes to an existing linkage map for A. aquaticus. In addition, we examined SNPs for allele-specific expression differences in the hybrid individual. All of these resources will facilitate identification of genes and associated changes responsible for cave adaptation in A. aquaticus and, in concert with analyses of other species, will inform our understanding of the evolutionary processes accompanying adaptation to the subterranean environment.
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Affiliation(s)
- Bethany A. Stahl
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, 33458, United States of America
| | - Joshua B. Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Daniel I. Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, United States of America
| | - Nipam H. Patel
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Douglas B. Gould
- Departments of Ophthalmology and Anatomy, Institute for Human Genetics, UCSF School of Medicine, San Francisco, CA, United States of America
| | - Meredith E. Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, United States of America
- * E-mail:
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49
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Macias-Muñoz A, Smith G, Monteiro A, Briscoe AD. Transcriptome-Wide Differential Gene Expression in Bicyclus anynana Butterflies: Female Vision-Related Genes Are More Plastic. Mol Biol Evol 2015; 33:79-92. [PMID: 26371082 DOI: 10.1093/molbev/msv197] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Vision is energetically costly to maintain. Consequently, over time many cave-adapted species downregulate the expression of vision genes or even lose their eyes and associated eye genes entirely. Alternatively, organisms that live in fluctuating environments, with different requirements for vision at different times, may evolve phenotypic plasticity for expression of vision genes. Here, we use a global transcriptomic and candidate gene approach to compare gene expression in the heads of a polyphenic butterfly. Bicyclus anynana have two seasonal forms that display sexual dimorphism and plasticity in eye morphology, and female-specific plasticity in opsin gene expression. Nonchoosy dry season females downregulate opsin expression, consistent with the high physiological cost of vision. To identify other genes associated with sexually dimorphic and seasonally plastic differences in vision, we analyzed RNA-sequencing data from whole head tissues. We identified two eye development genes (klarsicht and warts homologs) and an eye pigment biosynthesis gene (henna) differentially expressed between seasonal forms. By comparing sex-specific expression across seasonal forms, we found that klarsicht, warts, henna, and another eye development gene (domeless) were plastic in a female-specific manner. In a male-only analysis, white (w) was differentially expressed between seasonal forms. Reverse transcription polymerase chain reaction confirmed that warts and white are expressed in eyes only, whereas klarsicht, henna and domeless are expressed in both eyes and brain. We find that differential expression of eye development and eye pigment genes is associated with divergent eye phenotypes in B. anynana seasonal forms, and that there is a larger effect of season on female vision-related genes.
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Affiliation(s)
- Aide Macias-Muñoz
- Ecology and Evolutionary Biology, University of California, Irvine BEACON Center for the Study of Evolution in Action
| | - Gilbert Smith
- Ecology and Evolutionary Biology, University of California, Irvine BEACON Center for the Study of Evolution in Action
| | - Antónia Monteiro
- Biological Sciences, National University of Singapore, Singapore Yale-NUS College, Singapore
| | - Adriana D Briscoe
- Ecology and Evolutionary Biology, University of California, Irvine BEACON Center for the Study of Evolution in Action
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50
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Zhang X, Wang S, Chen S, Chen Y, Liu Y, Shao C, Wang Q, Lu Y, Gong G, Ding S, Sha Z. Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2015; 43:209-218. [PMID: 25543033 DOI: 10.1016/j.fsi.2014.11.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/15/2014] [Accepted: 11/16/2014] [Indexed: 06/04/2023]
Abstract
Half-smooth tongue sole (Cynoglossus semilaevis) is one of the most valuable marine aquatic species in Northern China. Given to the rapid development of aquaculture industry, the C. semilaevis was subjected to disease-causing bacteria Vibrio anguillarum. It therefore is indispensable and urgent to understand the mechanism of C. semilaevis host defense against V. anguillarum infection. In the present study, the extensively analysis at the transcriptome level for V. Anguillarum disease in tongue sole was carried out. In total, 94,716 high quality contigs were generated from 75,884,572 clean reads in three libraries (HOSG, NOSG, and CG). 22,746 unigenes were identified when compared with SwissProt, an NR protein database and NT nucleotide database. 954 genes exhibiting the differentially expression at least one pair of comparison in all three libraries were identified. GO enrichment for these genes revealed gene response to biotic stimulus, immune system regulation, and immune response and cytokine production. Further, the pathways such as complement and coagulation cascades and Vibrio cholerae infection pathways were enriched in defensing of pathogen. Besides, 13,428 SSRs and 118,239 SNPs were detected in tongue sole, providing further support for genetic variation and marker-assisted selection in future. In summary, this study identifies several putative immune pathways and candidate genes deserving further investigation in the context of development of therapeutic regimens and lays the foundation for selecting resistant lines of C. semilaevis against V. anguillarum.
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Affiliation(s)
- Xiang Zhang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China; Laboratory of Marine Biodiversity and Global Change, College of Oceanography and Environmental Science, Xiamen University, 182 Daxue Road, Xiamen 361005, Fujian, China
| | - Shaolin Wang
- Department of Psychiatry & Neurobiology Science, University of Virginia, 1670 Discovery Drive, Suite 110, Charlottesville 22911, VA, USA
| | - Songlin Chen
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yadong Chen
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yang Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Changwei Shao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Qilong Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yang Lu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Guangye Gong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Shaoxiong Ding
- Laboratory of Marine Biodiversity and Global Change, College of Oceanography and Environmental Science, Xiamen University, 182 Daxue Road, Xiamen 361005, Fujian, China
| | - Zhenxia Sha
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China.
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