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Wang Y, Shang P, Dai Y, Xu D, Dong Y, Huang Z. The complete mitochondrial genome of a new species of the genus Schizothorax from Sichuan, China (Cypriniformes: Cyprinidae). Mitochondrial DNA B Resour 2023; 8:1356-1359. [PMID: 38196799 PMCID: PMC10776055 DOI: 10.1080/23802359.2023.2288437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/21/2023] [Indexed: 01/11/2024] Open
Abstract
Schizothorax gulinensis sp. nov. is a new species of the genus Schizothorax from Sichuan, China (Cypriniformes: Cyprinidae). In this study, we have first reported the complete mitochondrial genome of S. gulinensis with Illumina sequencing. There were 16,587 nucleotide pairs in the mitochondrial genome (mitogenome) of S. gulinensis, including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs), as well as one non-coding control region (CR). The proportion of nucleotides in mitochondrial genome was 29.67% (A), 25.45% (T), 17.84% (G), 27.05% (C), and A + T content was 55.12%. All PCGs have the same start codon of the standard ATG, excepting for that of NADH dehydrogenase subunit 1 (nad1) which was the ATC, NADH dehydrogenase subunit 5 (nad5) which was the ATT and cytochrome c oxidase 1 (cox1) which was the ATC. Phylogenetic analysis results supported that S. gulinensis was closely related to Schizothorax grahami. The complete mitochondrial sequence of S. gulinensis will contribute to mitochondrial genome database and provide useful resources for population genetics and evolution analyses.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Pan Shang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, PR China
| | - Yuanxing Dai
- Gulin County Bureau of Agriculture and Rural Affairs, Luzhou, PR China
| | - Dayong Xu
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Yanzhen Dong
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Zhiqiu Huang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
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Regmi B, Douglas MR, Wangchuk K, Zbinden ZD, Edds DR, Tshering S, Douglas ME. The Himalayan uplift and evolution of aquatic biodiversity across Asia: Snowtrout (Cyprininae: Schizothorax) as a test case. PLoS One 2023; 18:e0289736. [PMID: 37874844 PMCID: PMC10597529 DOI: 10.1371/journal.pone.0289736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 07/26/2023] [Indexed: 10/26/2023] Open
Abstract
Global biodiversity hotspots are often remote, tectonically active areas undergoing climatic fluctuations, such as the Himalaya Mountains and neighboring Qinghai-Tibetan Plateau (QTP). They provide biogeographic templates upon which endemic biodiversity can be mapped to infer diversification scenarios. Yet, this process can be somewhat opaque for the Himalaya, given substantial data gaps separating eastern and western regions. To help clarify, we evaluated phylogeographic and phylogenetic hypotheses for a widespread fish (Snowtrout: Cyprininae; Schizothorax) by sequencing 1,140 base pair of mtDNA cytochrome-b (cytb) from Central Himalaya samples (Nepal: N = 53; Bhutan: N = 19), augmented with 68 GenBank sequences (N = 60 Schizothorax/N = 8 outgroups). Genealogical relationships (N = 132) were analyzed via maximum likelihood (ML), Bayesian (BA), and haplotype network clustering, with clade divergence estimated via TimeTree. Snowtrout seemingly originated in Central Asia, dispersed across the QTP, then into Bhutan via southward-flowing tributaries of the east-flowing Yarlung-Tsangpo River (YLTR). Headwaters of five large Asian rivers provided dispersal corridors from Central into eastern/southeastern Asia. South of the Himalaya, the YLTR transitions into the Brahmaputra River, facilitating successive westward colonization of Himalayan drainages first in Bhutan, then Nepal, followed by far-western drainages subsequently captured by the (now) westward-flowing Indus River. Two distinct Bhutanese phylogenetic groups were recovered: Bhutan-1 (with three subclades) seemingly represents southward dispersal from the QTP; Bhutan-2 apparently illustrates northward colonization from the Lower Brahmaputra. The close phylogenetic/phylogeographic relationships between the Indus River (Pakistan) and western tributaries of the Upper Ganges (India/Nepal) potentially implicate an historic, now disjunct connection. Greater species-divergences occurred across rather than within-basins, suggesting vicariance as a driver. The Himalaya is a component of the Earth's largest glacial reservoir (i.e., the "third-pole") separate from the Arctic/Antarctic. Its unique aquatic biodiversity must be defined and conserved through broad, trans-national collaborations. Our study provides an initial baseline for this process.
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Affiliation(s)
- Binod Regmi
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Marlis R. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Karma Wangchuk
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
- National Research & Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture & Forests, Royal Government of Bhutan, Thimphu, Bhutan
| | - Zachery D. Zbinden
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - David R. Edds
- Department of Biological Sciences, Emporia State University, Emporia, Kansas, United States of America
| | - Singye Tshering
- National Research & Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture & Forests, Royal Government of Bhutan, Thimphu, Bhutan
| | - Michael E. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
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Purohit S, Sharma P, Kothiyal S, Singh U, Nautiyal P, Singh M, Bhattacharya I. Resolving the phylogenetic relationship of Himalayan snow trout Schizothorax plagiostomus with other species of Schizothoracine using mitochondrial CO-I and Cyt b genes. Mol Biol Rep 2023; 50:3927-3933. [PMID: 36680623 DOI: 10.1007/s11033-023-08274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND The classification of the sub-family Schizothoracinae has been debatable due to the overlap in morphological characters. There are discrepancies between classical taxonomy and molecular taxonomy, as well. In the present study, mitochondrial genes CO-I and Cyt b were sequenced to elucidate the phylogenetic status of three species of the genus Schizothorax. METHODS AND RESULTS In total, 29 samples of three species viz., S. plagiostomus, S. progastus, and S. richardsonii, were collected from rivers of Uttarakhand, India. For phylogenetic analyses, 40 sequences of CO-I and 41 sequences of Cyt b of Schizothoracinae species were downloaded from NCBI. The highest genetic divergence based on CO-I (16.08%) is between S. plagiostomus and Ptychobarbus dipogon, while the lowest divergence (0.00%) is between 10 pairs of species. The highest divergence based on Cyt b (19.43%), is between S. niger and Gymnocypris eckloni, while the lowest divergence (0.00%) is between four pairs of species. The divergence (0.00% for CO-I and 2.38% for Cyt b) between S. chongi and S. kozlovi, seems a case of convergent molecular evolution of the CO-I gene and in this case, CO-I alone cannot be used to differentiate these two species. CONCLUSION The simultaneous use of two molecular markers along with morphomeristic data is a better strategy for the classification of the sub-family Schizothoracinae. These results will be a resource dataset for determining the taxonomical status of Schizothoracine species and will help in the conservation and commercial production of these commercially important fish species.
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Affiliation(s)
- Shriya Purohit
- Department of Zoology, HNB Garhwal University, Srinagar Campus, Pauri Garhwal, Uttarakhand, 246174, India
| | - Partigya Sharma
- Department of Zoology, HNB Garhwal University, Srinagar Campus, Pauri Garhwal, Uttarakhand, 246174, India
| | - Sachin Kothiyal
- Department of Zoology, HNB Garhwal University, Srinagar Campus, Pauri Garhwal, Uttarakhand, 246174, India
| | - Upendra Singh
- Department of Zoology, HNB Garhwal University, Srinagar Campus, Pauri Garhwal, Uttarakhand, 246174, India
| | - Prakash Nautiyal
- Department of Zoology, HNB Garhwal University, Srinagar Campus, Pauri Garhwal, Uttarakhand, 246174, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, 226002, India.
| | - Indrashis Bhattacharya
- Department of Zoology, HNB Garhwal University, Srinagar Campus, Pauri Garhwal, Uttarakhand, 246174, India.
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Wang F, Wang L, Liu D, Gao Q, Nie M, Zhu S, Chao Y, Yang C, Zhang C, Yi R, Ni W, Tian F, Zhao K, Qi D. Chromosome-level assembly of Gymnocypris eckloni genome. Sci Data 2022; 9:464. [PMID: 35918339 PMCID: PMC9346132 DOI: 10.1038/s41597-022-01595-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022] Open
Abstract
Gymnocypris eckloni is widely distributed in isolated lakes and the upper reaches of the Yellow River and play significant roles in the trophic web of freshwater communities. In this study, we generated a chromosome-level genome of G. eckloni using PacBio, Illumina and Hi-C sequencing data. The genome consists of 23 pseudo-chromosomes that contain 918.68 Mb of sequence, with a scaffold N50 length of 43.54 Mb. In total, 23,157 genes were annotated, representing 94.80% of the total predicted protein-coding genes. The phylogenetic analysis showed that G. eckloni was most closely related to C. carpio with an estimated divergence time of ~34.8 million years ago. For G. eckloni, we identified a high-quality genome at the chromosome level. This genome will serve as a valuable genomic resource for future research on the evolution and ecology of the schizothoracine fish in the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Fayan Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Lihan Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Dan Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Miaomiao Nie
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Shihai Zhu
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Chaojie Yang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Rigui Yi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Weilin Ni
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
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Li J, Chen S, Lahm T, Peng Y, Shen H, Zhang K, Huang W, Liang X, Liu B, Chen M. Characterization of the complete mitogenome of Gymnocypris dobula (Günther, 1868) (Cypriniformes: Cyprinidae). Mitochondrial DNA B Resour 2022; 7:297-299. [PMID: 35128057 PMCID: PMC8812766 DOI: 10.1080/23802359.2021.1972051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Gymnocypris dobula, classified into the highly specialized Schizothoracine fish, is endemic to Tibet, China. The complete mitochondrial DNA sequence of G. dobula was 16,728 base pairs in length and comprised 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes as well as one control region as in a typical vertebrate mitochondrial DNA gene. The ML and BI trees showed that G. dobula was most closely related to Gymnocypris scleracanthus within the highly specialized group. This mitogenome provides new molecular data for further taxonomic and phylogenetic studies of Schizothoracine fish.
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Affiliation(s)
- Jiasheng Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Shiyi Chen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Tashi Lahm
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Ying Peng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Haodi Shen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Kun Zhang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Wenhua Huang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Xudong Liang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Bingjian Liu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Meiqun Chen
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
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Zhou J, Wang W, Li Z, Zhang C, Wan Z, Sun S, Zeng B, Li M, Sun G. Metabolome and Transcriptome Analysis of Liver and Oocytes of Schizothorax o'connori Raised in Captivity. Front Genet 2021; 12:677066. [PMID: 34691140 PMCID: PMC8531413 DOI: 10.3389/fgene.2021.677066] [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: 03/11/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Schizothorax o’connori (S. o’connori) is a representative tetraploid species in the subfamily Schizothoracinae and an important endemic fish in the Qinghai-Tibet Plateau. However, the domestication of S. o’connori remains challenging due to the lack of basic research. Here, we investigated the effects of artificial feeding on the oocytes and liver of S. o’connori by comparing the histological, metabolomic, and transcriptomic data. Histological results showed that the oocytes and liver of captive-reared S. o’connori had abnormal cell morphology. After comparison with the self-built database, a total of 233 metabolites were annotated. In oocytes, a total of 37 differentially accumulated metabolites (DAMs) were detected and two pathways were significantly enriched. There were obvious differences in the metabolites related to ovarian development, including pregnenolone and arachidonic acid. In liver, a total of 70 DAMs were detected and five pathways were significantly enriched. Based on the transcriptomic data, a total of 159 differentially expressed genes (DEGs) were significantly related with cell growth and death pathway in oocytes, while a total of 2841 DEGs were significantly related with 102 pathways in liver. Comparing the metabolomic and transcriptomic data showed that there were three common significant enrichment pathways in liver, including biosynthesis of unsaturated fatty acids, starch and sucrose metabolism, and fatty acid biosynthesis. These results showed that special attention should be given to the composition and intake of fatty acids during the artificial breeding of S. o’connori. In addition, many of metabolite-gene pairs were related to adenosine 5′-diphosphate, adenosine monophosphate, and pregnenolone. In summary, these data provide an overview of global metabolic and transcriptomic resources and broaden our understanding of captive-reared S. o’connori.
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Affiliation(s)
- Jianshe Zhou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Wanliang Wang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Zhichao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Zhiyi Wan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Shuaijie Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Benhe Zeng
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
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Chafin TK, Regmi B, Douglas MR, Edds DR, Wangchuk K, Dorji S, Norbu P, Norbu S, Changlu C, Khanal GP, Tshering S, Douglas ME. Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210727. [PMID: 34729207 PMCID: PMC8548808 DOI: 10.1098/rsos.210727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological 'ecotypes' observed in polyploid snowtrout (Cyprinidae: Schizothorax). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq (N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples (N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational 'ecotypes' were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively 'masks' previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder 80309, USA
| | - Binod Regmi
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Marlis R. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - David R. Edds
- Department of Biological Sciences, Emporia State University, Emporia, KS 66801, USA
| | - Karma Wangchuk
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sonam Dorji
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Pema Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sangay Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Changlu Changlu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Gopal Prasad Khanal
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Singye Tshering
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Michael E. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
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8
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Sidlauskas BL, Assega FM, Melo BF, Oliveira C, Birindelli JLO. Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The nearly 150 species of Anostomidae comprise one of the most diverse and taxonomically dynamic families of Neotropical freshwater fishes. A recent revision of the enigmatic and poorly diagnosed genus Anostomoides demonstrated that it contains two valid species, each with complicated taxonomic histories; however, that study did not address their phylogenetic placement. Herein, we integrate molecular and morphological data to demonstrate their distant evolutionary relationship, and thus the polyphyly of Anostomoides. While we reconstruct one of the species in a previously hypothesized placement within a clade also containing Laemolyta, Rhytiodus and Schizodon, the other represents a morphologically and genetically distinctive lineage that diverged early in the history of the family. We describe and illustrate the osteology of this remarkable species, discuss the evolutionary implications of its unique suite of features, and use those characteristics to diagnose a new genus that evolved independently of all other known members of the family for approximately 37 Myr.
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Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Fernando M Assega
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Estadual de Londrina, Centro de Ciencias Biologicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, Londrina, PR, Brazil
| | - Bruno F Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antonio C. W. Zanin, Rubião Jr, Botucatu, SP, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antonio C. W. Zanin, Rubião Jr, Botucatu, SP, Brazil
| | - José L O Birindelli
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Estadual de Londrina, Centro de Ciencias Biologicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, Londrina, PR, Brazil
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9
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Tong C, Li M, Tang Y, Zhao K. Genomic Signature of Shifts in Selection and Alkaline Adaptation in Highland Fish. Genome Biol Evol 2021; 13:evab086. [PMID: 33892511 PMCID: PMC8126726 DOI: 10.1093/gbe/evab086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed primarily related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species, and four alkaline intolerant species. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of shared genes associated with ion transport, apoptosis, immune response, and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.
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Affiliation(s)
- Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Miao Li
- Center for Advanced Retinal and Ocular Therapeutics, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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10
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Riedel J, Zozaya SM, Hoskin CJ, Schwarzkopf L. Parallel evolution of toepads in rock-dwelling lineages of a terrestrial gecko (Gekkota: Gekkonidae: Heteronotia binoei). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Abstract
Selection for effective locomotion can lead to specialized morphological structures. Adhesive toepads, which have arisen independently in different lizard clades, facilitate the use of vertical and inverted substrates. Their evolution is poorly understood because functionally intermediate morphological configurations between padless and pad-bearing forms are rare. To shed light on toepad evolution, we assessed the subdigital morphology of phylogenetically distinct lineages of the Bynoe’s gecko species complex (Heteronotia binoei). Most populations of H. binoei are terrestrial, but two relatively distantly related saxicoline (rock-dwelling) lineages have enlarged terminal subdigital scales resembling toepads. We reconstructed the ancestral terminal subdigital scale size of nine lineages of H. binoei in eastern Australia, including these two saxicoline lineages. Additionally, we compared the subdigital microstructures of four lineages: the two saxicoline lineages and their respective terrestrial sister-lineages. Surprisingly, all four lineages had fully developed setae, but the setae of the two saxicoline lineages were significantly longer, branched more often and were more widely spaced than the terrestrial sister-lineages. We conclude that the saxicoline lineages represent examples of parallel evolution of enlarged adhesive structures in response to vertical substrate use, and their morphology represents a useful model as an intermediate state in toepad evolution.
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Affiliation(s)
- Jendrian Riedel
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Stephen M Zozaya
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Lin Schwarzkopf
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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11
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Xiao S, Mou Z, Fan D, Zhou H, Zou M, Zou Y, Zhou C, Yang R, Liu J, Zhu S, Li Y, Liu Y, Liu F, Wang W, Zeng B, Li H, Wang D, Liu H. Genome of Tetraploid Fish Schizothorax o'connori Provides Insights into Early Re-diploidization and High-Altitude Adaptation. iScience 2020; 23:101497. [PMID: 32905880 PMCID: PMC7486454 DOI: 10.1016/j.isci.2020.101497] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 06/10/2020] [Accepted: 08/19/2020] [Indexed: 12/26/2022] Open
Abstract
Whole-genome duplications (WGDs) of Schizothoracinae are believed to have played a significant role in speciation and environmental adaptation on the Qinghai-Tibet Plateau (QTP). Here, we present a genome for Schizothorax o'connori, a QTP endemic fish and showed the species as a young tetraploid with a recent WGD later than ∼1.23 mya. We exhibited that massive insertions between duplicated genomes caused by transposon bursts could induce mutagenesis in adjacent sequences and alter the expression of neighboring genes, representing an early re-diploidization process in a polyploid genome after WGD. Meanwhile, we found that many genes involved in DNA repair and folate transport/metabolism experienced natural selection and might contribute to the environmental adaptation of this species. Therefore, the S. o'connori genome could serve as a young tetraploid model for investigations of early re-diploidization in polyploid genomes and offers an invaluable genetic resource for environmental adaptation studies of the endemic fish of the QTP.
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Affiliation(s)
- Shijun Xiao
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Department of Computer Science, Wuhan University of Technology, Wuhan, China
- College of Plant Protection, Jilin Agriculture University, Changchun, Jilin, China
| | - Zhenbo Mou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Dingding Fan
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - He Zhou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Ming Zou
- Department of Computer Science, Wuhan University of Technology, Wuhan, China
| | - Yu Zou
- Department of Computer Science, Wuhan University of Technology, Wuhan, China
| | - Chaowei Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Department of Aquaculture, College of Animal Science, Southwest University, Chongqing, China
| | - Ruibin Yang
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jiaqi Liu
- Department of Computer Science, Wuhan University of Technology, Wuhan, China
| | - Shilin Zhu
- Department of Computer Science, Wuhan University of Technology, Wuhan, China
| | - Yajuan Li
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Yanchao Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Fei Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Wanliang Wang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Benhe Zeng
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Di Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Haiping Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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12
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Khalik MZ, Bozkurt E, Schilthuizen M. Morphological parallelism of sympatric cave‐dwelling microsnails of the genus Georissaat Mount Silabur, Borneo (Gastropoda, Neritimorpha, Hydrocenidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohd Zacaery Khalik
- Naturalis Biodiversity Center Leiden The Netherlands
- Institute of Biology Leiden Faculty of Science Leiden University Leiden The Netherlands
- Faculty of Resource Science and Technology Universiti Malaysia Sarawak Sarawak Malaysia
| | - Esra Bozkurt
- Naturalis Biodiversity Center Leiden The Netherlands
| | - Menno Schilthuizen
- Naturalis Biodiversity Center Leiden The Netherlands
- Institute of Biology Leiden Faculty of Science Leiden University Leiden The Netherlands
- Institute for Tropical Biology and Conservation Universiti Malaysia Sabah, Jalan UMS Sabah Malaysia
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13
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Chen J, Shen Y, Wang J, Ouyang G, Kang J, Lv W, Yang L, He S. Analysis of Multiplicity of Hypoxia-Inducible Factors in the Evolution of Triplophysa Fish (Osteichthyes: Nemacheilinae) Reveals Hypoxic Environments Adaptation to Tibetan Plateau. Front Genet 2020; 11:433. [PMID: 32477402 PMCID: PMC7235411 DOI: 10.3389/fgene.2020.00433] [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] [Received: 12/25/2019] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
HIF (Hypoxia-inducible factor) gene family members function as master regulators of cellular and systemic oxygen homeostasis during changes in oxygen availability. Qinghai-Tibet Plateau is a natural laboratory for for long-term hypoxia and cold adaptation. In this context, T. scleroptera that is restricted to >3500 m high-altitude freshwater rivers was selected as the model to compare with a representative species from the plain, P. dabryanus. We cloned different HIF-α and carried out a phylogenetic analysis from invertebrates to vertebrates for identifying HIF-α genes and analyzing their evolutionary history. Intriguingly, the HIF-α has undergone gene duplications might be due to whole-genome duplication (WGD) events during evolution. PAML analysis indicated that HIF-1αA was subjected to positive selection acted on specific sites in Triplophysa lineages. To investigate the relationship between hypoxia adaptation and the regulation of HIF-α stability by pVHL in plateau and plain fish, a series of experiments were carried out. Comparison the luciferase transcriptional activity and protein levels of HIF-αs and the differing interactions of HIF-αs with pVHL, show clear differences between plateau and plain fish. T. scleroptera pVHL could enhance HIF-α transcriptional activity under hypoxia, and functional validation through pVHL protein mutagenesis showed that these mutations increased the stability of HIF-α and its hetero dimerization affinity to ARNT. Our research shows that missense mutations of pVHL induced evolutionary molecular adaptation in Triplophysa fishes living in high altitude hypoxic environments.
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Affiliation(s)
- Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Gang Ouyang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jingliang Kang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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14
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Rehman A, Khan MF, Bibi S, Nouroz F. Comparative phylogeny of ( Schizothorax esocinus) with reference to 12s and 16 sribosomal RNA from River Swat, Pakistan. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:81-85. [PMID: 32192393 DOI: 10.1080/24701394.2020.1741561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Schizothorax esocinus is one of the important cold water delicious fish belonging to family Cyprinidae and found in River Swat which is one of the main river flowing in Khyber Pakhtunkhwa, Pakistan.The complete mitochondrial genomes of the S. esocinus species was found to be 16,591bp. Phylogenetic analysis of S. esocinus based on 12 s ribosomal RNA and 16S rRNA confirmed that, the phylogenetic position of S. esocinus was slightly different, but clustered closed to S. plagiostomus, S. labiatus, S. richardsonii, S. nepalensis, and S. progastus predicting a close homology in genome and hence a monophyletic line of evolution also this specie showed close relationship and homologs to the Aspiorhynchus laticeps, Spinibarbus sinensis, Aspiorhynchus laticeps, and Percocypris respectively. This study provided phylogenetic relationship between Schizothoracinae fishes and with the other fishes of family cyprinidae even at the subfamily level.
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Affiliation(s)
- Aqsa Rehman
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | | | - Saira Bibi
- Department of Zoology, Hazara University, Mansehra, Pakistan.,Department of Zoology Women, University of Swabi, Pakistan
| | - Faisal Nouroz
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
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15
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Wang C, Wu X, Hu X, Jiang H, Chen L, Xu Q. Hypoxia-inducible factor 1α from a high-altitude fish enhances cytoprotection and elevates nitric oxide production in hypoxic environment. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:39-49. [PMID: 31595407 DOI: 10.1007/s10695-019-00694-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Hypoxia-inducible factors (HIFs) are master transcription factor regulating hypoxic responses in vertebrates. Species of Schizothoracine, a sub-family of cyprinidae, are highly endemic to the hypoxic Qinghai-Tibetan Plateau (QTP). What roles the HIFs play in hypoxic adaptation in the Schizothoracine fish is little known. In this study, the HIF-1α/B gene from Gymnocypris dobula (Gd) was characterized. The predicted protein for Gd-HIF-1α/B contains the main domains (bHLH, PAS, PAC, ODD, N-TAD, and C-TAD). Moreover, a specific mutation that the proline hydroxylation motif (LXXLAP) mutated into PxxLAP was observed in Gd-HIF-1α/B CODD domain, which may lead to changes in the function. To clarify whether HIF-1α/B of G. dobula possesses hypoxic adaptive features, Gd-HIF1α/B and Schizothorax prenanti-HIF1α/B (Sp-HIF1α/B) were cloned into an expression vector and transfected into 293T cells. Cell viability was found to be significantly higher in cells transfected with Gd-HIF-1α/B than those transfected with Sp-HIF-1α/B under hypoxic conditions. In addition, G. dobula HIF-1α/B showed stronger activity in transactivating the expression of nitric oxide (NO)-synthesizing enzyme, NOS2B under hypoxia stresses than the orthologous gene from S. prenanti, which were accompanied with upregulated expressions of NOS2B in heart of G. dobula, which may attribute to elevated NO levels detected in G. dobula than the lower land species. These results indicated that the HIF-1α plays an important role in mediating the iNOS signaling system in the process of evolutionary adaptation of the Schizothoracine to the highland environment.
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Affiliation(s)
- Congcong Wang
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
- Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Xiaohui Wu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Xingxing Hu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Huapeng Jiang
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Liangbiao Chen
- Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China.
| | - Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China.
- National Distant-water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
- Collaborative Innovation Center for Distant-water Fisheries, Shanghai, 201306, China.
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16
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Sun S, Wu Y, Ge X, Jakovlić I, Zhu J, Mahboob S, Al-Ghanim KA, Al-Misned F, Fu H. Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of Gammarus pisinnus and Gammarus lacustris. ROYAL SOCIETY OPEN SCIENCE 2020; 7:190669. [PMID: 32218929 PMCID: PMC7029888 DOI: 10.1098/rsos.190669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 11/29/2019] [Indexed: 05/16/2023]
Abstract
We hypothesized that the mitogenome of Gammarus lacustris (GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of Gammarus pisinnus (GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200-1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55% atp8 to 76.1% cox1). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but 'heterogeneous' CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, GP and Gammarus fossarum exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in atp8) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining Gammarus species populating the same geographical range as GP.
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Affiliation(s)
- Shengming Sun
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
| | - Ying Wu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
| | - Xianping Ge
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, People's Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan, People's Republic of China
| | - Jian Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, People's Republic of China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh-11451, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | - Khalid Abdullah Al-Ghanim
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh-11451, Riyadh, Saudi Arabia
| | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh-11451, Riyadh, Saudi Arabia
| | - Hongtuo Fu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
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17
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Chen M, An R, Li J, Li K, Li F. Identifying operation scenarios to optimize attraction flow near fishway entrances for endemic fishes on the Tibetan Plateau of China to match their swimming characteristics: A case study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133615. [PMID: 31376753 DOI: 10.1016/j.scitotenv.2019.133615] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/04/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Attracting fish at fishway entrances is vital for ensuring fish passage efficiency, which requires consideration of the swimming characteristics of fish. The objective of this case study was to propose optimized flow conditions downstream of a dam on the Tibetan Plateau to attract fish into fishways. Six local endemic species of Cyprinidae: Schizothoracinae were considered as protection targets. However, the swimming abilities of most endemic fishes on the plateau remain unclear, and no previous projects in this area could serve as a reference. Thus, the swimming performances of the target species were first tested based on three indexes, induction velocity, critical swimming speed and bursting swimming speed, and six behavior zones were classified by different flow velocity thresholds based on the test results. A verified 3D hydrodynamic model was then adopted to simulate the flow field downstream of the dam under four typical reservoir operation scenarios. By matching the simulated flow fields to the different behavior zones, all scenarios were assessed for the passability of the target fishes, and the results showed that there would be different potential migration routes under each scenario. For the most common scenario during the fish passage season, symmetrical use of turbines T1 and T6 was recommended so that the flow would be lower velocity and the turbulence would be less intense near the fishway entrances than the current regime. Moreover, the addition of a new entrance was suggested on the migration routes with high potential use to increase the chance that fish would enter. Beyond providing a solution for this specific case, this study enriches knowledge about the swimming features of endemic fishes on the Tibetan Plateau. Furthermore, this research provides a possible technical methodology that combines fish behavioral characteristics and hydraulic indexes when determining attraction flows in similar fish passage projects.
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Affiliation(s)
- Min Chen
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, Sichuan, China
| | - Ruidong An
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, Sichuan, China.
| | - Jia Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, Sichuan, China
| | - Kefeng Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, Sichuan, China
| | - Fang Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, Sichuan, China
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18
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Chao Y, Xia M, Wu R, Chen Q, Zheng Z, Qi D. Molecular characterization and expression changes of cytoglobin genes in response to hypoxia in a Tibetan schizothoracine fish, Schizopygopsis pylzovi. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:863-872. [PMID: 30406573 DOI: 10.1007/s10695-018-0582-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
Schizopygopsis pylzovi, an endemic fish of the subfamily Schizothoracinae, is comparatively well adapted to dissolved oxygen fluctuations in the aqueous environments of the Qinghai-Tibetan Plateau. Here, we cloned the complete cDNA of cytoglobin 1 and 2 (Cygb1 and Cygb2) from S. pylzovi and then investigated transcriptional changes of both genes in the selected tissues in response to hypoxia. Both the two genes had the standard exon-intron structure of vertebrate Mb genes but lacked an exon at downstream of the H helix (HC11.2) as seen in mammals. We applied severe hypoxia (4 h at PO2 = 3.6% saturation) and moderate hypoxia (72 h at PO2 = 36.0% saturation) to adult S. pylzovi. Under severe hypoxia, the Cygb1 mRNA levels decreased significantly in the liver, kidney, and brain, but increased significantly in the heart, while the Cygb2 mRNA levels downregulated significantly in the muscle and liver. But, the transcriptional activity of Cygb1 in muscle and that of Cygb2 in the kidney, brain, and heart remained almost unchanged. Under moderate hypoxia, the transcriptional activities of both genes in muscle and brain were turned down quickly after onset hypoxia, while in the liver, kidney, and heart, the transcriptional activities of both genes showed a short-term upregulation in different time periods of hypoxia exposure. Our data suggest that both the Cygb1 and Cygb2 in S. pylzovi are hypoxia-induced genes, and the responses of the transcription regulation of Cygb1 and Cygb2 genes to hypoxia are tissue specific and also depend on the hypoxia regime, which are different from that of other fish species.
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Affiliation(s)
- Yan Chao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Mingzhe Xia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Rongrong Wu
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Qichang Chen
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Zhiqin Zheng
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, No. 251 Ningda Road, Xining, 810016, China.
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19
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Wang T, Qi D, Sun S, Liu Z, Du Y, Guo S, Ma J. DNA barcodes and their characteristic diagnostic sites analysis of Schizothoracinae fishes in Qinghai province. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:592-601. [PMID: 30952197 DOI: 10.1080/24701394.2019.1580273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Qinghai-Tibetan Plateau (QTP), the source and upper reaches of many Asian rivers, are crisscrossed by rivers and dotted with lakes. Schizothoracinae fishes, species native to the QTP, are distributed widely through these rivers and lakes. Over the past decades, ecological protection has become increasingly intense. The rapid acquisition of the genetic information and accurate gene sequence database are assumed to play an important role in the conservation of species diversity and biodiversity. In this study, 153 COI sequences (648bp in length) covering 13 species in 8 genera of Schizothoracinae fishes in Qinghai Province were used to determine whether barcode could identify Schizothoracinae species accurately. The average Kimura two parameter (K2P) genetic distances within and among species were 0.35% and 8.83%, respectively. The maximum K2P distance within species was observed in Gymnocypris eckloni (1.36%) while minimum K2P distance among species was observed between Chuanchia labiosa and Schizopygopsis pylzovi (0.23%). Overlaps existed in K2P distance intra- and inter- species based on both the genes. Eleven groups with 9 single-species groups and 2 multi-species groups were identified through Automatic Barcode Gap Discovery System, which were consistent with the overlaps of K2P distance. 96.7% as the accurate ratio for COI barcode was calculated and high solution was observed in the phylogenetic trees based on COI gene and Cyt b gene. Except for the similar results based on two genes above, COI barcode was more economical than Cyt b gene. The SOM model successfully predicted characteristic-diagnostic sites at species level: 36 characteristic-diagnostic sites from eight species, in which 12 from Gmnodiptychus pachycgeilus, 2 from Platypharodon extremus, 7 from Ptychobarbus kaznakovi, 2 from Schizopygopsis anteroventris, 2 from Schizopygopsis malacanthus, 3 from Schizopygopsis malacanthus chengi, 3 from Schizothorax dolichonema and 5 from Schizothorax lantsangensis. Our results show that Schizothoracinae fishes can be identified validly by using COI DNA barcode. Thirty-six characteristic-diagnostic sites were proposed to be applied into works of species identification for the Schizothoracinae fishes in Qinghai Province.
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Affiliation(s)
- Ting Wang
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Desheng Qi
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Shihao Sun
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Zhonghao Liu
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Yurong Du
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Songchang Guo
- c College of Animal Science and Technology , Hunan Agricultural University , Changsha , China
| | - Jianbin Ma
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
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20
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Convergent evolution misled taxonomy in schizothoracine fishes (Cypriniformes: Cyprinidae). Mol Phylogenet Evol 2019; 134:323-337. [PMID: 30641272 DOI: 10.1016/j.ympev.2019.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 12/26/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022]
Abstract
Highly specialized grade (HSG; genera Gymnocypris, Oxygymnocypris, Schizopygopsis, Platypharodon and Chuanchia) of the Schizothoracinae (Cypriniformes: Cyprinidae) are endemic to the Qinghai-Tibet Plateau (QTP). Previously, two distinct ecomorphs were recognized according to trophic traits. One was a limnetic omnivore with normal lower jaw morphology, terminal mouth, and moderate or dense gill rakers, mostly inhabiting in open water of lakes, including Gymnocypris and Oxygymnocypris. Another was a benthic feeder with inferior mouth, sparse gill rakers and sharp horny sheath on the lower jaw for scraping of attached prey off hard substrates, including Schizopygopsis, Platypharodon and Chuanchia. However, traditional taxonomy of HSG based on these trophic traits presented extensive conflicts with the molecular studies in recent years. The possible cause could be convergent evolution in morphology, retention of ancestral polymorphisms or mitochondrial introgression, but these hypotheses could not be assessed due to incomplete taxon sampling and only mitochondrial data employed in previous works. Here, we conducted the most comprehensive molecular analysis on HSG fishes to date, using four mitochondrial loci and 152,464 genome-wide SNPs, and including 21 of 24 putative species and one undescribed Schizopygopsis species. Both SNP and mtDNA trees confirmed extensive paraphyly of genera Gymnocypris and Schizopygopsis, where species often were clustered together by watershed instead of by genus. Basal split into the north clade B and the south clade C (ca. 3.03 Ma) approximately by the Tanggula-Tanitawen Mountains in SLAF tree coincided with a violent uplift of the QTP during the phase A of 'Qingzang movement' (ca. 3.6 Ma). Ancestral state reconstruction of the trophic ecomorph showed that the limnetic omnivore ecomorph had evolved repeatedly in clade B and C. Furthermore, we presented a striking case of convergent evolution between two 'subspecies' Gymnocypris chui chui and G. chui longimandibularis, which had diverged as early as two million years ago (ca. 2.42 Ma). Ecological analyses revealed that similar food utilization, particularly in zooplankton, was the main underlying driving force. This work showed an example of taxonomy with the most extensive errors at the genus/species levels due to convergent evolution and suggested that trophic traits could be misleading in fish taxonomy. Therefore, we propose a major generic revision for HSG species.
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Adaptive Evolution of the Eda Gene and Scales Loss in Schizothoracine Fishes in Response to Uplift of the Tibetan Plateau. Int J Mol Sci 2018; 19:ijms19102953. [PMID: 30262767 PMCID: PMC6213870 DOI: 10.3390/ijms19102953] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 12/16/2022] Open
Abstract
Schizothoracine is the predominant wild fish subfamily of the Tibetan plateau (TP). Their scales, pharyngeal teeth and barbels have gradually regressed with increasing altitude. Schizothoracine have been divided into three groups: primitive, specialized and highly specialized. Ectodysplasin-A (Eda) has been considered as a major gene that contributes to the development of skin appendages. The present study cloned the Eda genes of 51 Schizothoracine fish species which represent the three groups and five Barbinae species. Phylogenetic analyses indicated that Eda may have acted as the genetic trigger for scale loss in the Schizothoracine. Furthermore, 14 single nucleotide polymorphisms (SNPs) and two deletions (18 bp and 6 bp in size), were also detected in the Eda coding sequence of the highly specialized group compared to the primitive group. The same SNPs and two indels result in four non-synonymous and two G-X-Y and 1 XY motif indels, which possibly contribute to significant structure changes in the Eda gene. The domain including (G-X-Y)n motif in the Eda gene is relatively conserved amongst teleosts. Based on the above results, we hypothesize that the evolution of Eda gene might be associated with the scale loss in Schizothoracine fishes in response to the phased uplift of the TP.
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Qi D, Chao Y, Wu R, Xia M, Chen Q, Zheng Z. Transcriptome Analysis Provides Insights Into the Adaptive Responses to Hypoxia of a Schizothoracine Fish ( Gymnocypris eckloni). Front Physiol 2018; 9:1326. [PMID: 30298021 PMCID: PMC6160557 DOI: 10.3389/fphys.2018.01326] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/03/2018] [Indexed: 01/12/2023] Open
Abstract
The schizothoracine fish endemic to the Qinghai-Tibetan Plateau are comparatively well adapted to aquatic environments with low oxygen partial pressures. However, few studies have used transcriptomic profiling to investigate the adaptive responses of schizothoracine fish tissues to hypoxic stress. This study compared the transcriptomes of Gymnocypris eckloni subjected to 72 h of hypoxia (Dissolved oxygen, DO = 3.0 ± 0.1 mg/L) to those of G. eckloni under normoxia (DO = 8.4 ± 0.1 mg/L). To identify the potential genes and pathways activated in response to hypoxic stress, we collected muscle, liver, brain, heart, and blood samples from normoxic and hypoxic fish for RNA-Seq analysis. We annotated 337,481 gene fragments. Of these, 462 were differentially expressed in the hypoxic fish as compared to the normoxic fish. Under hypoxia, the transcriptomic profiles of the tissues differed, with muscle the most strongly affected by hypoxia. Our data indicated that G. eckloni underwent adaptive changes in gene expression in response to hypoxia. Several strategies used by G. eckloni to cope with hypoxia were similar to those used by other fish, including a switch from aerobic oxidation to anaerobic glycolysis and the suppression of major energy-requiring processes. However, G. eckloni used an additional distinct strategy to survive hypoxic environments: a strengthening of the antioxidant system and minimization of ischemic injury. Here, we identified several pathways and related genes involved in the hypoxic response of the schizothoracine fish. This study provides insights into the mechanisms used by schizothoracine fish to adapt to hypoxic environments.
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Affiliation(s)
- Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Yan Chao
- Animal Science Department, Agriculture and Animal Husbandry College, Qinghai University, Xining, China
| | - Rongrong Wu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Mingzhe Xia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Qichang Chen
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Zhiqin Zheng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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Vreven EJWMN, Musschoot T, Decru E, Wamuini Lunkayilakio S, Obiero K, Cerwenka AF, Schliewen UK. The complex origins of mouth polymorphism in the Labeobarbus (Cypriniformes: Cyprinidae) of the Inkisi River basin (Lower Congo, DRC, Africa): insights from an integrative approach. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Emmanuel J W M N Vreven
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
- KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat, Leuven, Belgium
| | - Tobias Musschoot
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
| | - Eva Decru
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
- KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat, Leuven, Belgium
| | | | - Kevin Obiero
- Kenya Marine and Fisheries Research Institute, Lake Turkana Research Station, Lodwar, Kenya
| | - Alexander F Cerwenka
- SNSB Bavarian Natural History Collections, Bavarian State Collection of Zoology, Department of Ichthyology, Münchhausenstrasse, München, Germany
| | - Ulrich K Schliewen
- SNSB Bavarian Natural History Collections, Bavarian State Collection of Zoology, Department of Ichthyology, Münchhausenstrasse, München, Germany
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Ye H, Zhang Z, Zhou C, Zhu C, Yang Y, Xiang M, Zhou X, Zhou J, Luo H. De novo assembly of Schizothorax waltoni transcriptome to identify immune-related genes and microsatellite markers. RSC Adv 2018; 8:13945-13953. [PMID: 35539357 PMCID: PMC9079874 DOI: 10.1039/c8ra00619a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/09/2018] [Indexed: 11/30/2022] Open
Abstract
Schizothorax waltoni (S. waltoni) is one kind of the subfamily Schizothoracinae and an indigenous economic tetraploid fish to Tibet in China. It is rated as a vulnerable species in the Red List of China's Vertebrates, owing to overexploitation and biological invasion. S. waltoni plays an important role in ecology and local fishery economy, but little information is known about genetic diversity, local adaptation, immune system and so on. Functional gene identification and molecular marker development are the first and essential step for the following biological function and genetics studies. For this purpose, the transcriptome from pooled tissues of three adult S. waltoni was sequenced and analyzed. Using paired-end reads from the Illumina Hiseq4000 platform, 83 103 transcripts with an N50 length of 2337 bp were assembled, which could be further clustered into 66 975 unigenes with an N50 length of 2087 bp. The majority of the unigenes (58 934, 87.99%) were successfully annotated by 7 public databases, and 15 KEGG pathways of immune-related genes were identified for the following functional research. Furthermore, 19 497 putative simple sequence repeats (SSRs) of 1-6 bp unit length were detected from 14 690 unigenes (21.93%) with an average distribution density of 1 : 3.28 kb. We identified 3590 unigenes (5.36%) containing more than one SSR, providing abundant potential polymorphic markers in functional genes. This is the first reported high-throughput transcriptome analysis of S. waltoni, and it would provide valuable genetic resources for the functional genes involved in multiple biological processes, including the immune system, genetic conservation, and molecular marker-assisted breeding of S. waltoni.
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Affiliation(s)
- Hua Ye
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Zhengshi Zhang
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Chaowei Zhou
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Chengke Zhu
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Yuejing Yang
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Mengbin Xiang
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Xinghua Zhou
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Jian Zhou
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences Chengdu 611731 China
| | - Hui Luo
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
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Qi D, Chao Y, Zhao Y, Xia M, Wu R. Molecular evolution of myoglobin in the Tibetan Plateau endemic schizothoracine fish (Cyprinidae, Teleostei) and tissue-specific expression changes under hypoxia. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:557-571. [PMID: 29230594 DOI: 10.1007/s10695-017-0453-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 11/30/2017] [Indexed: 06/07/2023]
Abstract
Myoglobin (Mb) is an oxygen-binding hemoprotein that was once thought to be exclusively expressed in oxidative myocytes of skeletal and cardiac muscle where it serves in oxygen storage and facilitates intracellular oxygen diffusion. In this study, we cloned the coding sequence of the Mb gene from four species, representing three groups, of the schizothoracine fish endemic to the Qinghai-Tibetan Plateau (QTP), then conducted molecular evolution analyses. We also investigated tissue expression patterns of Mb and the expression response to moderate and severe hypoxia at the mRNA and protein levels in a representative of the highly specialized schizothoracine fish species, Schizopygopsis pylzovi. Molecular evolution analyses showed that Mb from the highly specialized schizothoracine fish have undergone positive selection and one positively selected residue (81L) was identified, which is located in the F helix, close to or in contact with the heme. We present tentative evidence that the Mb duplication event occurred in the ancestor of the schizothoracine and Cyprininae fish (common carp and goldfish), and that the Mb2 paralog was subsequently lost in the schizothoracine fish. In S. pylzovi, Mb mRNA is expressed in various tissues with the exception of the intestine and gill, but all such tissues, including the liver, muscle, kidney, brain, eye, and skin, expressed very low levels of Mb mRNA (< 8.0%) relative to that of the heart. The trace levels of Mb expression in non-muscle tissues are perhaps the major reason why non-muscle Mb remained undiscovered for so long. The expression response of the Mb gene to hypoxia at the mRNA and protein levels was strikingly different in S. pylzovi compared to that found in the common carp, medaka, zebrafish, and goldfish, suggesting that the hypoxia response of Mb in fish may be species and tissue-specific. Notably, severe hypoxia induced significant expression of Mb at the mRNA and protein levels in the S. pylzovi heart, which suggests Mb has a major role in the supply of oxygen to the heart of Tibetan Plateau fish.
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Affiliation(s)
- Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, No. 251 Ningda Road, Xining, 810016, China.
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, No. 251 Ningda Road, Xining, 810016, China.
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Yongli Zhao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Mingzhe Xia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Rongrong Wu
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
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Qi D, Chao Y, Liang J, Gao Q, Wu R, Mather I, Zhao Y, Chen Q. Adaptive evolution of interferon regulatory factors is not correlated with body scale reduction or loss in schizothoracine fish. FISH & SHELLFISH IMMUNOLOGY 2018; 73:145-151. [PMID: 29246809 DOI: 10.1016/j.fsi.2017.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/06/2017] [Accepted: 12/10/2017] [Indexed: 06/07/2023]
Abstract
Body scales in teleost fish are the first line of defense in protecting the fish from invading pathogens. However, the relationship between the adaptive evolution of immune-related genes and changes in the body scale-covering of fish has not been previously studied. Schizothoracine fish, characterized by progressive reduction of body scales from the primitive to the highly specialized species, are a good group to investigate this relationship. We obtained 11 IRF genes (IRF1-11) from 14 of schizothoracine fish representing primitive, specialized, and highly specialized species, of which seven IRF genes (IRF2, IRF3, IRF5, IRF6, IRF7, IRF8 and IRF9) contained the complete CDS. Sequence analysis demonstrated the deletion or insertion of 4-7 amino acids in IRF2, IRF3, IRF6 and IRF9, which seems to be a common phenomenon in the schizothoracine fish. Selection pressure analysis supported the hypothesis that positive selection has been driving the rapid evolution of IRFs in specific lineages of the schizothoracine fish. This, however, is not correlated with body scale reduction or loss in the evolution of these IRFs. Remarkably, the deletion or insertion found in IRF protein sequences presented a regular pattern corresponding to the scale-covering changes in schizothoracine fish. Our study provides evidence for positive selection in the IRF family, contributing to a better understanding of the adaptive evolution of immune-related genes in schizothoracine fish in response to environmental changes of the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China.
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Rongrong Wu
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China
| | - Ian Mather
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yongli Zhao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China
| | - Qichang Chen
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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Genetic Adaptation of Schizothoracine Fish to the Phased Uplifting of the Qinghai-Tibetan Plateau. G3-GENES GENOMES GENETICS 2017; 7:1267-1276. [PMID: 28209761 PMCID: PMC5386875 DOI: 10.1534/g3.116.038406] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Many species of Schizothoracine, a subfamily of Cyprinidae, are highly endemic to the Qinghai–Tibetan Plateau (QTP). To characterize the adaptive changes associated with the Schizothoracine expansion at high altitudes, we sequenced tissue transcriptomes of two highland and two subhighland Schizothoracines and analyzed gene evolution patterns by comparing with lowland cyprinids. Phylogenetic tree reconstruction and divergence time estimation indicated that the common ancestor of Schizothoracine fish lived ∼32.7 million years ago (MYA), coinciding with the timing of the first phase of QTP uplifting. Both high- and subhigh-Schizothoracines demonstrated elevated dN/dS ratios in the protein-coding genes compared to lowland cyprinids, from which some biological processes implicated in altitude adaptation were commonly identified. On the other hand, the highland and subhighland lineages presented drastically divergent landscapes of positively selected genes (PSGs), enriched with very different gene ontology (GO) profiles, including those in “sensory organ morphogenesis,” “regulation of protein ubiquitination,” “blood circulation,” and “blood vessel development.” These results indicated different selection pressures imposed on the highland and subhighland lineages of the Schizothoracine subfamily, with a higher number of genes in the high-altitude species involved in adaptations such as sensory perception, blood circulation, and protein metabolism. Our study indicated divergent genetic adaptations in the aquatic species facing the phased uplifting of QTP.
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Yu M, Zhang D, Hu P, Peng S, Li W, He S, Zhai W, Xu Q, Chen L. Divergent adaptation to Qinghai-Tibetan Plateau implicated from transciptome study of Gymnocypris dobula and Schizothorax nukiangensis. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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29
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Isolation and characterization of twenty-one polymorphic microsatellite loci from Schizothorax o’connori and cross-species amplification. J Genet 2016. [DOI: 10.1007/s12041-013-0236-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Li G, Tang Y, Zhang R, Zhao K. Phylogeography of Diptychus maculatus (Cyprinidae) endemic to the northern margin of the QTP and Tien Shan region. BMC Evol Biol 2016; 16:186. [PMID: 27613240 PMCID: PMC5017051 DOI: 10.1186/s12862-016-0756-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/26/2016] [Indexed: 11/11/2022] Open
Abstract
Background Phylogeography and historical demography of the cyprinid fish Diptychus maculatus (subfamily Schizothoracinae) are evaluated across three river systems in the Northern Qinghai-Tibetan Plateau (QTP) and Tien Shan range: the Indus River, Tarim River and Ili River. Results Results from both mtDNA (16S rRNA, Cyt b and D-loop) and nucDNA (RAG-2) resolved four reciprocally monophyletic clades, representing populations from Indus River, South Tarim River, North Tarim River and Ili River, respectively. The divergence times was estimated to be 1.5–2.5 Mya. It is consistent with the hypothesis that the split of four clades is the consequence of vicariance resulting from both the intensive uplift of QTP and Tien Shan as well as the resultant expansion of the Taklimakan Desert. Several lines of evidences indicate dynamic demographic histories for the populations, with late Pleistocene and Holocene population bottlenecks and expansions except the Indus River. Conclusions Our results clearly depicted the phylogenetic relationship of D. maculatus from Indus River, Tarim River and Ili River. The analyses implicated the relationship among the distribution of D. maculatus, paleo-drainages and geographic events, and implied the existence of the South Tarim River in history. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0756-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guogang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Renyi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China. .,Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.
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Aso T, Nishimura K, Kiyonaka T, Aoki T, Inagawa M, Matsuhashi M, Tobinaga Y, Fukuyama H. Dynamic interactions of the cortical networks during thought suppression. Brain Behav 2016; 6:e00503. [PMID: 27547504 PMCID: PMC4980473 DOI: 10.1002/brb3.503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/06/2016] [Accepted: 05/03/2016] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES Thought suppression has spurred extensive research in clinical and preclinical fields, particularly with regard to the paradoxical aspects of this behavior. However, the involvement of the brain's inhibitory system in the dynamics underlying the continuous effort to suppress thoughts has yet to be clarified. This study aims to provide a unified perspective for the volitional suppression of internal events incorporating the current understanding of the brain's inhibitory system. MATERIALS AND METHODS Twenty healthy volunteers underwent functional magnetic resonance imaging while they performed thought suppression blocks alternating with visual imagery blocks. The whole dataset was decomposed by group-independent component analysis into 30 components. After discarding noise components, the 20 valid components were subjected to further analysis of their temporal properties including task-relatedness and between-component residual correlation. RESULTS Combining a long task period and a data-driven approach, we observed a right-side-dominant, lateral frontoparietal network to be strongly suppression related. This network exhibited increased fluctuation during suppression, which is compatible with the well-known difficulty of suppression maintenance. CONCLUSIONS Between-network correlation provided further insight into the coordinated engagement of the executive control and dorsal attention networks, as well as the reciprocal activation of imagery-related components, thus revealing neural substrates associated with the rivalry between intrusive thoughts and the suppression process.
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Affiliation(s)
- Toshihiko Aso
- Human Brain Research CenterKyoto University Graduate School of MedicineKyotoJapan
| | | | - Takashi Kiyonaka
- Human Brain Research CenterKyoto University Graduate School of MedicineKyotoJapan
| | - Takaaki Aoki
- Institute of Economic ResearchKyoto UniversityKyotoJapan
| | | | - Masao Matsuhashi
- Human Brain Research CenterKyoto University Graduate School of MedicineKyotoJapan
| | | | - Hidenao Fukuyama
- Human Brain Research CenterKyoto University Graduate School of MedicineKyotoJapan
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Chen W, Shen Y, Gan X, Wang X, He S. Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong). Ecol Evol 2016; 6:6023-36. [PMID: 27648223 PMCID: PMC5016629 DOI: 10.1002/ece3.2319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 11/28/2022] Open
Abstract
The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China; Graduate School of Chinese Academy of Sciences Beijing 10001 China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China; Graduate School of Chinese Academy of Sciences Beijing 10001 China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
| | - Xuzhen Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
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Xia M, Chao Y, Jia J, Li C, Kong Q, Zhao Y, Guo S, Qi D. Changes of hemoglobin expression in response to hypoxia in a Tibetan schizothoracine fish, Schizopygopsis pylzovi. J Comp Physiol B 2016; 186:1033-1043. [PMID: 27424163 DOI: 10.1007/s00360-016-1013-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 06/10/2016] [Accepted: 07/09/2016] [Indexed: 11/26/2022]
Abstract
Fishes endemic to the Qinghai-Tibetan Plateau are comparatively well adapted to aquatic environments with low oxygen partial pressures (hypoxia). Here, we cloned the complete cDNA of hemoglobin (Hb) α and β from the Tibetan schizothoracine fish Schizopygopsis pylzovi, and then investigated changes in Hb mRNA and protein levels in spleen, liver and kidney in response to hypoxia. We applied severe hypoxia (4 h at PO2 = 0.6 kPa) and moderate hypoxia (72 h at PO2 = 6.0 kPa) to adult S. pylzovi. Changes of Hb expression under hypoxia, together with the investigations of spleen somatic index, kidney somatic index and Hb concentration in circulation, suggest that the kidney may not only serve as the erythropoietic organ, but also act as the major blood reservoir in S. pylzovi. From this perspective, the transcriptional activity of Hb in S. pylzovi, as reflected in the kidney, was turned down quickly after the onset of severe hypoxia, while under moderate hypoxia the transcriptional activity of Hb showed upregulation for a short time, but then the transcriptional machinery was turned down slowly on prolonged exposure. Notably, the changes in Hb protein levels in spleen, liver and kidney in response to severe and moderate hypoxia were not in line with the changes in mRNA levels, which are related with the blood reservoir in the kidney. Tibetan schizothoracine fish, at least S. pylzovi, show a particular response of the transcription regulation of Hb to moderate hypoxia, which is different from that of other fish species.
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Affiliation(s)
- Mingzhe Xia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Yan Chao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Jianlei Jia
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Changzhong Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Qinghui Kong
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Yongli Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Songchang Guo
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, The Chinese Academy of Sciences, Xining, 810001, China.
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China.
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Zhang J, Chen Z, Zhou C, Kong X. Molecular phylogeny of the subfamily Schizothoracinae (Teleostei: Cypriniformes: Cyprinidae) inferred from complete mitochondrial genomes. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2015.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Vreven EJWMN, Musschoot T, Snoeks J, Schliewen UK. The African hexaploid Torini (Cypriniformes: Cyprinidae): review of a tumultuous history. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12366] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emmanuel J. W. M. N. Vreven
- Vertebrate section, Ichthyology; Royal Museum for Central Africa, RMCA; Leuvensesteenweg 13 Tervuren B-3080 Belgium
- KU Leuven; Laboratory of Biodiversity and Evolutionary Genomics; Charles Deberiotstraat 32 B-3000 Leuven Belgium
| | - Tobias Musschoot
- Vertebrate section, Ichthyology; Royal Museum for Central Africa, RMCA; Leuvensesteenweg 13 Tervuren B-3080 Belgium
| | - Jos Snoeks
- Vertebrate section, Ichthyology; Royal Museum for Central Africa, RMCA; Leuvensesteenweg 13 Tervuren B-3080 Belgium
- KU Leuven; Laboratory of Biodiversity and Evolutionary Genomics; Charles Deberiotstraat 32 B-3000 Leuven Belgium
| | - Ulrich K. Schliewen
- SNSB Bavarian Natural History Collections, Bavarian State Collection of Zoology; Department of Ichthyology; Münchhausenstrasse 21 81247 München Germany
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Guo X, Xie L, Zhang X, Ji Y, Chen J, Pang B, Xu Y, Qi D, Guo S. Signatures of functional constraint at Fgfr1a Genes in schizothoracine fishes (Pisces: Cypriniformes): The dermal skeleton variation adapted to high-altitude environments. Integr Zool 2016; 11:86-97. [PMID: 26767459 DOI: 10.1111/1749-4877.12178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fishes harbor a huge resource of phenotypic diversity and are useful for understanding the genetic basis of morphological variation. However, it is difficult to transfer classical genetic mapping to most non-model species. In this study, we performed a comparative sequence analysis of Fgfr1a to first interpret the evolution of this candidate scale-loss gene in 15 schizothoracine fishes with various scale phenotypes. While considerable amino acid (AA) substitutions were observed, molecular evolution analysis indicates that the overall coding regions were subject to functional constraint. We also identified extra copies of Fgfr1a in 4 scale-loss fishes and detected accelerated evolution in one AA substitution specific to these duplicates. We speculate that Fgfr1a had accumulated mutations in the ancestral lineage of scale-loss schizothoracine fishes before experiencing duplication events, which was further followed by the diversification of species. In silico mutation analysis predicted deleterious effects of the mutations while no disruptive molecular mechanism was detected. Collectively, our results highlight the important role of Fgfr1a gene in the adaptive evolution of schizothoracine fishes during their radiation in the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Xinyi Guo
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ling Xie
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuze Zhang
- Qinghai University for Nationalities, Xining, China
| | - Yinfa Ji
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China
| | - Juan Chen
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bo Pang
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongtao Xu
- Qinghai Normal University, Xining, China
| | - Delin Qi
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, China
| | - Songchang Guo
- Key laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, CAS, Xining, China
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Xu Q, Zhang C, Zhang D, Jiang H, Peng S, Liu Y, Zhao K, Wang C, Chen L. Analysis of the erythropoietin of a Tibetan Plateau schizothoracine fish (Gymnocypris dobula) reveals enhanced cytoprotection function in hypoxic environments. BMC Evol Biol 2016; 16:11. [PMID: 26768152 PMCID: PMC4714423 DOI: 10.1186/s12862-015-0581-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/30/2015] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Erythropoietin (EPO) is a glycoprotein hormone that plays a principal regulatory role in erythropoiesis and initiates cell homeostatic responses to environmental challenges. The Qinghai-Tibet Plateau is a natural laboratory for hypoxia adaptation. Gymnocypris dobula is a highly specialized plateau schizothoracine fish that is restricted to > 4500 m high-altitude freshwater rivers and ponds in the Qinghai-Tibet Plateau. The role of EPO in the adaptation of schizothoracine fish to hypoxia is unknown. RESULTS The EPO and EPO receptor genes from G. dobula and four other schizothoracine fish from various altitudinal habitats were characterized. Schizothoracine EPOs are predicted to possess 2-3 N-glycosylation (NGS) sites, 4-5 casein kinase II phosphorylation (CK2) sites, 1-2 protein kinase C (PKC) phosphorylation sites, and four conserved cysteine residues within four helical domains, with variations in the numbers of NGS and CK2 sites in G. dobula. PAML analysis indicated a d N/d S value (ω) = 1.112 in the G. dobula lineage, and a few amino acids potentially under lineage-specific positive selection were detected within the G. dobula EPO. Similarly, EPO receptors of the two high-altitude schizothoracines (G. dobula and Ptychobarbus kaznakovi), were found to be statistically on the border of positive selection using the branch-site model (P-value = 0.096), and some amino acids located in the ligand-binding domain and the fibronectin type III domain were identified as potentially positive selection sites. Tissue EPO expression profiling based on transcriptome sequencing of three schizothoracines (G. dobula, Schizothorax nukiangensis Tsao, and Schizothorax prenanti) showed significant upregulation of EPO expression in the brain and less significantly in the gill of G. dobula. The elevated expression together with the rapid evolution of the EPO gene in G. dobula suggested a possible role for EPO in adaptation to hypoxia. To test this hypothesis, Gd-EPO and Sp-EPO were cloned into an expression vector and transfected into the cultured cell line 293 T. Significantly higher cell viability was observed in cells transfected with Gd-EPO than cells harboring Sp-EPO when challenged by hypoxia. CONCLUSION The deduced EPO proteins of the schizothoracine fish contain characteristic structures and important domains similar to EPOs from other taxa. The presence of potentially positive selection sites in both EPO and EPOR in G. dobula suggest possible adaptive evolution in the ligand-receptor binding activity of the EPO signaling cascade in G. dobula. Functional study indicated that the EPO from high-altitude schizothoracine species demonstrated features of hypoxic adaptation by reducing toxic effects or improving cell survival when expressed in cultured cells, providing evidence of molecular adaptation to hypoxic conditions in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
- Collaborative Innovation Center for Distant-water Fisheries, Shanghai, China.
| | - Chi Zhang
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
| | - Dongsheng Zhang
- Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China.
| | - Huapeng Jiang
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
| | - Sihua Peng
- Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China.
| | - Yang Liu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.
| | - Congcong Wang
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
| | - Liangbiao Chen
- Key Laboratory of Aquaculture Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China.
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He D, Chen Y, Liu C, Tao J, Ding C, Chen Y. Comparative phylogeography and evolutionary history of schizothoracine fishes in the Changtang Plateau and their implications for the lake level and Pleistocene climate fluctuations. Ecol Evol 2016; 6:656-74. [PMID: 26865956 PMCID: PMC4739559 DOI: 10.1002/ece3.1890] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 11/17/2015] [Accepted: 11/23/2015] [Indexed: 11/13/2022] Open
Abstract
The water level oscillation of endorheic lakes and extent change of glaciers associated with the Asian monsoon are known as prominent representatives of climatic and environmental events in the Tibetan Plateau during the Quaternary. However, details process in spatial and temporal changes are still debated. We use the schizothoracines as a palaeoclimatic proxy to test two hypotheses concerning the evolution of Quaternary glaciations and lakes of the Changtang Plateau: (1) the Tibetan glaciations generally tended to decrease since the middle Pleistocene; (2) the lakes expansion was driven by summer monsoon rainfall. Based on a wide range‐wide sampling throughout in the Changtang Plateau and its adjacent drainages, we constructed phylogeny and demographic histories of schizothoracines in the Changtang Plateau. Our results showed that the populations of the exorheic rivers and lakes in southern Tibet possessed higher genetic variability, earlier coalescent and expansion times than those of the endorheic lakes in the Changtang Plateau. Population expansions are highly consistent with phases of strong summer monsoon and high lake level during interglacial stages. The maximum growth rate intervals showed three pulses from 64.7 to 54.8, 39.6 to 31.0, and 14.9 to 2.4 kya respectively. The significant positive correlations were found between regional precipitation and genetic diversity, as well as coalescence time of populations in the endorheic lakes. We suggested that the demographic history of the schizothoracines reflects the spatial and temporal changes in climate and lake level, in particular, in regional precipitation gradients associated with changes of the South Asian monsoon, and supports the climatic hypothesis of a general diminishing tend in Tibetan glaciations in the Tibetan Plateau since the middle Pleistocene.
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Affiliation(s)
- Dekui He
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Yifeng Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Chunlong Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Juan Tao
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Chengzhi Ding
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Yiyu Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
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Li G, Peng Z, Zhang R, Tang Y, Tong C, Feng C, Zhang C, Zhao K. Mito-nuclear phylogeography of the cyprinid fishGymnodiptychus dybowskiiin the arid Tien Shan region of Central Asia. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12724] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Guogang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish; Reproduction and Development (Ministry of Education); Southwest University School of Life Sciences; Chongqing China
| | - Renyi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Chenguang Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining Qinghai China
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Ma X, Kang J, Chen W, Zhou C, He S. Biogeographic history and high-elevation adaptations inferred from the mitochondrial genome of Glyptosternoid fishes (Sisoridae, Siluriformes) from the southeastern Tibetan Plateau. BMC Evol Biol 2015; 15:233. [PMID: 26511921 PMCID: PMC4625616 DOI: 10.1186/s12862-015-0516-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/20/2015] [Indexed: 01/19/2023] Open
Abstract
Background The distribution of the Chinese Glyptosternoid catfish is limited to the rivers of the Tibetan Plateau and peripheral regions, especially the drainage areas of southeastern Tibet. Therefore, Glyptosternoid fishes are ideal for reconstructing the geological history of the southeastern Tibet drainage patterns and mitochondrial genetic adaptions to high elevations. Results Our phylogenetic results support the monophyly of the Sisoridae and the Glyptosternoid fishes. The reconstructed ancestral geographical distribution suggests that the ancestral Glyptosternoids was widely distributed throughout the Brahmaputra drainage in the eastern Himalayas and Tibetan area during the Late Miocene (c. 5.5 Ma). We found that the Glyptosternoid fishes lineage had a higher ratio of nonsynonymous to synonymous substitutions than those found in non-Glyptosternoids. In addition, ωpss was estimated to be 10.73, which is significantly higher than 1 (p-value 0.0002), in COX1, which indicates positive selection in the common ancestral branch of Glyptosternoid fishes in China. We also found other signatures of positive selection in the branch of specialized species. These results imply mitochondrial genetic adaptation to high elevations in the Glyptosternoids. Conclusions We reconstructed a possible scenario for the southeastern Tibetan drainage patterns based on the adaptive geographical distribution of the Chinese Glyptosternoids in this drainage. The Glyptosternoids may have experienced accelerated evolutionary rates in mitochondrial genes that were driven by positive selection to better adapt to the high-elevation environment of the Tibetan Plateau. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0516-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiuhui Ma
- School of Life Science, Southwest University, Beibei, Chongqing, 400715, China. .,The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
| | - Jingliang Kang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 10001, China.
| | - Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 10001, China.
| | - Chuanjiang Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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Yonezawa T, Hasegawa M, Zhong Y. Polyphyletic origins of schizothoracine fish (Cyprinidae, Osteichthyes) and adaptive evolution in their mitochondrial genomes. Genes Genet Syst 2015; 89:187-91. [PMID: 25747043 DOI: 10.1266/ggs.89.187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The schizothoracine fish, also called snow trout, are members of the Cyprinidae, and are the most diversified teleost fish in the Qinghai-Tibetan Plateau (QTP). Clarifying the evolutionary history of the schizothoracine fish is therefore important for better understanding the biodiversity of the QTP. Although morphological and molecular phylogenetic studies have supported the monophyly of the Schizothoracinae, a recent molecular phylogenetic study based on the mitochondrial genome questioned the monophyly of this taxon. However, the phylogenetic analysis of that study was on the basis of only three schizothoracine species, and the support values were low. In this report, we inferred the phylogenetic tree on the basis of mitochondrial genome data including 21 schizothoracine species and five closely related species, and the polyphyletic origins of the Schizothoracinae were strongly supported. The tree further suggests that the Schizothoracinae consists of two clades, namely the "morphologically specialized clade" and the "morphologically primitive clade", and that these two clades migrated independently of each other to the QTP and adapted to high altitude. We also detected in their mitochondrial genomes strong signals of positive selection, which probably represent evidence of high-altitude adaptation. In the case of the morphologically specialized clade, positive selection mainly occurred during the Late Paleocene to the Early Oligocene. Its migration also seems to have occurred in the Early Eocene, and this timing is consistent with the drastic uplifting of the QTP. On the other hand, positive selection in the morphologically primitive clade has mainly occurred since the Late Miocene. Because its members are thought to have migrated to the QTP recently, it is possible that they are now undergoing high-altitude adaptation.
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Affiliation(s)
- Takahiro Yonezawa
- School of Life Sciences, Fudan University, SongHu Rd. 2005, Shanghai 200438, China; Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa Tokyo 190-8562, Japan
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Qi D, Guo S, Chao Y, Kong Q, Li C, Xia M, Xie B, Zhao K. The biogeography and phylogeny of schizothoracine fishes (Schizopygopsis) in the Qinghai-Tibetan Plateau. ZOOL SCR 2015. [DOI: 10.1111/zsc.12116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Delin Qi
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Songchang Guo
- Key laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810001 China
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Qinghui Kong
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Changzhong Li
- College of Eco-Environmental Engineering; Qinghai University; Xining 810016 China
| | - Mingzhe Xia
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Baosheng Xie
- College of Eco-Environmental Engineering; Qinghai University; Xining 810016 China
| | - Kai Zhao
- Key laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810001 China
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Ahnelt H, Herdina AN, Metscher BD. Unusual pharyngeal dentition in the African Chedrin fishes (Teleostei: Cyprinindae): Significance for phylogeny and character evolution. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lai J, Liu Y, Chen Y, Li H, Du J, Li L. The complete mitochondrial genome of Schizopygopsis pylzovi (Teleostei, Cyprinidae, Schizopygopsis). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3235-7. [PMID: 25690050 DOI: 10.3109/19401736.2015.1007362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Schizopygopsis pylzovi, an endemic species in the Qinghai-Tibetan Plateau, has a unique ability to adapt to the extreme ecological condition of the plateau. In this study, we successfully sequenced the first mitochondrial genome of S. pylzovi. The mitogenome is 16,814 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region (D-loop). The overall base composition of the heavy strand (H-strand) is 28.3% A, 26.1% C, 18.6% G, and 27.0% T, with a slight AT bias of 55.3%. Most of the genes are encoded on H-strand, except for eight tRNAs (tRNA(Gln), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), tRNA(Ser), tRNA(Glu) and tRNA(Pro)) and ND6 genes.
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Affiliation(s)
- Jiansheng Lai
- a The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , China
| | - Ya Liu
- a The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , China
| | - Yeyu Chen
- a The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , China
| | - Hua Li
- a The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , China
| | - Jun Du
- a The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , China
| | - Lianman Li
- a The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , China
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Meng W, Yang TY, Guo Y, Hai S, Ma YW, Ma XF, Cai LG. Remarkable genetic divergence of Gymnodiptychus dybowskii between south and north of Tianshan Mountain in northwest China. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Guan L, Chi W, Xiao W, Chen L, He S. Analysis of hypoxia-inducible factor alpha polyploidization reveals adaptation to Tibetan Plateau in the evolution of schizothoracine fish. BMC Evol Biol 2014; 14:192. [PMID: 25205386 PMCID: PMC4162920 DOI: 10.1186/s12862-014-0192-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/15/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Hypoxia-inducible factor (HIF) is a master regulator that mediates major changes in gene expression under hypoxic conditions. Though HIF family has been identified in many organisms, little is known about this family in schizothoracine fish. RESULTS Duplicated hif-α (hif-1αA, hif-1αB, hif-2αA, and hif-2αB) genes were identified in schizothoracine fish. All the deduced HIF-α proteins contain the main domains (bHLH-PAS, ODDD, and TAD), also found in humans. Evidence suggests a Cyprinidae-specific deletion, specifically, a conserved proline hydroxylation motif LxxLAP, in the NODD domain of schizothoracine fish HIF-1αA. In addition, a schizothoracine-specific mutation was observed in the CODD domain of the specialized and highly specialized schizothoracine fish HIF-1αB, which is the proline hydroxylation motif mutated into PxxLAP. Standard and stochastic branch-site codon model analysis indicated that only HIF-1αB has undergone positive selection, which may have led to changes in function. To confirm this hypothesis, HIF-αs tagged with Myc were transfected into HEK 293 T cells. Each HIF-1αB was found to significantly upregulate luciferase activity under normoxic and hypoxic conditions, which indicated that the HIF-1αB protein was more stable than other HIF-αs. CONCLUSIONS All deduced HIF-α proteins of schizothoracine fish contain important domains, like their mammalian counterparts, and each HIF-α is shorter than that of human. Our experiments reveal that teleost-specific duplicated hif-α genes played different roles under hypoxic conditions, and HIF-1αB may be the most important regulator in the adaptation of schizothoracine fish to the environment of the Tibetan Plateau.
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Affiliation(s)
- Lihong Guan
- />Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei P. R. China
- />University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Wei Chi
- />College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei P. R. China
| | - Wuhan Xiao
- />Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei P. R. China
| | - Liangbiao Chen
- />College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
| | - Shunping He
- />Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei P. R. China
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Guo SS, Zhang GR, Guo XZ, Wei KJ, Ji W, Wei QW. Isolation and characterization of eighteen polymorphic microsatellite loci in Schizopygopsis younghusbandi Regan and cross-amplification in three other schizothoracinae species. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414010062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Guo SS, Zhang GR, Guo XZ, Wei KJ, Qin JH, Wei QW. Isolation and characterization of twenty-four polymorphic microsatellite loci in Oxygymnocypris stewartii. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9959-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Guo XZ, Zhang GR, Wei KJ, Guo SS, Gardner JP, Xie CX. Development of twenty-one polymorphic tetranucleotide microsatellite loci for Schizothorax o'connori and their conservation application. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Ongoing speciation in the Tibetan plateau Gymnocypris species complex. PLoS One 2013; 8:e71331. [PMID: 23977018 PMCID: PMC3744573 DOI: 10.1371/journal.pone.0071331] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/28/2013] [Indexed: 11/30/2022] Open
Abstract
Local adaptation towards divergent ecological conditions often results in genetic differentiation and adaptive phenotypic divergence. To illuminate the ecological distinctiveness of the schizothoracine fish, we studied a Gymnocypris species complex consisting of three morphs distributed across four bodies of water (the Yellow River, Lake Qinghai, the Ganzi River and Lake Keluke) in the Northeast Tibetan Plateau. We used a combination of mitochondrial (16S rRNA and Cyt b) and nuclear (RAG-2) genetic sequences to investigate the phylogeography of these morphs based on a sample of 277 specimens. Analysis of gill rakers allowed for mapping of phenotypic trajectories along the phylogeny. The phylogenetic and morphological analyses showed that the three sparsely rakered morphs were present at two extremes of the phylogenetic tree: the Yellow River morphs were located at the basal phylogenetic split, and the Lake Keluke and Ganzi River morphs at the peak, with the densely rakered Lake Qinghai morphs located between these two extremes. Age estimation further indicated that the sparsely rakered morphs constituted the oldest and youngest lineages, whereas the densely rakered morph was assigned to an intermediate-age lineage. These results are most compatible with the process of evolutionary convergence or reversal. Disruptive natural selection due to divergent habitats and dietary preferences is likely the driving force behind the formation of new morphs, and the similarities between their phenotypes may be attributable to the similarities between their forms of niche tracking associated with food acquisition. This study provides the first genetic evidence for the occurrence of convergence or reversal in the schizothoracine fish of the Tibetan Plateau at small temporal scales.
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