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Gao K, He Z, Xiong J, Chen Q, Lai B, Liu F, Chen P, Chen M, Luo W, Huang J, Ding W, Wang H, Pu Y, Zheng L, Jiao Y, Zhang M, Tang Z, Yue Q, Yang D, Yan T. Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing. BMC Genomics 2024; 25:145. [PMID: 38321406 PMCID: PMC10845765 DOI: 10.1186/s12864-024-09975-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Schizothorax o'connori is an endemic fish distributed in the upper and lower reaches of the Yarlung Zangbo River in China. It has experienced a fourth round of whole gene replication events and is a good model for exploring the genetic differentiation and environmental adaptability of fish in the Qinghai-Tibet Plateau. The uplift of the Qinghai-Tibet Plateau has led to changes in the river system, thereby affecting gene exchange and population differentiation between fish populations. With the release of fish whole genome data, whole genome resequencing has been widely used in genetic evolutionary analysis and screening of selected genes in fish, which can better elucidate the genetic basis and molecular environmental adaptation mechanisms of fish. Therefore, our purpose of this study was to understand the population structure and adaptive characteristics of S. o'connori using the whole-genome resequencing method. RESULTS The results showed that 23,602,746 SNPs were identified from seven populations, mostly distributed on chromosomes 2 and 23. There was no significant genetic differentiation between the populations, and the genetic diversity was relatively low. However, the Zangga population could be separated from the Bomi, Linzhi, and Milin populations in the cluster analysis. Based on historical dynamics analysis of the population, the size of the ancestral population of S. o'connori was affected by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Glacial Age. The selected sites were mostly enriched in pathways related to DNA repair and energy metabolism. CONCLUSION Overall, the whole-genome resequencing analysis provides valuable insights into the population structure and adaptive characteristics of S. o'connori. There was no obvious genetic differentiation at the genome level between the S. o'connori populations upstream and downstream of the Yarlung Zangbo River. The current distribution pattern and genetic diversity are influenced by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Ice Age. The selected sites of S. o'connori are enriched in the energy metabolism and DNA repair pathways to adapt to the low temperature and strong ultraviolet radiation environment at high altitude.
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Affiliation(s)
- Kuo Gao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinxin Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bolin Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Fei Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ping Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingqiang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenjie Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junjie Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenxiang Ding
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Haochen Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yong Pu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yuanyuan Jiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ziting Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingsong Yue
- Huadian Tibet Hydropower Development Co.,Ltd, Dagu Hydropower Station, Sangri, 856200, Shannan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
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Tian F, Zhou B, Li X, Zhang Y, Qi D, Qi H, Jiang H, Zhao K, Liu S. Population genomics analysis to identify ion and water transporter genes involved in the adaptation of Tibetan naked carps to brackish water. Int J Biol Macromol 2023; 247:125605. [PMID: 37392922 DOI: 10.1016/j.ijbiomac.2023.125605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/31/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023]
Abstract
Understanding how evolutionary processes shape the genetic variations and influence the response of species to environmental alterations is critical for biodiversity conservation and molecular breeding. Gymnocypris przewalskii przewalskii is the only known cyprinid fish that dwells in the brackish water of Lake Qinghai on the Qinghai-Tibetan Plateau. To reveal the genetic basis of its adaptation to high salinity and alkalinity, whole-genome sequencing was performed in G. p. przewalskii and its freshwater relatives Gymnocypris eckloni and Gymnocypris przewalskii ganzihonensis. Compared with freshwater species, lower genetic diversity and higher linkage disequilibrium were observed in G. p. przewalskii. Selective sweep analysis identified 424 core-selective genes enriched in transport activities. Transfection analysis showed that genetic changes in the positively selected gene aquaporin 3 (AQP3) improved cell viability after salt treatment, suggesting its involvement in brackish water adaptation. Our analysis indicates that ion and water transporter genes experienced intensive selection, which might have contributed to the maintenance of high osmolality and ion content in G. p. przewalskii. The current study identified key molecules involved in the adaptation of fish to brackish water, providing valuable genomic resources for the molecular breeding of salt-tolerant fish.
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Affiliation(s)
- Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Bingzheng Zhou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohuan Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Hongfang Qi
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris przewalskii, The rescue center of Qinghai Lake Naked Carp, Xining, Qinghai, China
| | - Huamin Jiang
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris przewalskii, The rescue center of Qinghai Lake Naked Carp, Xining, Qinghai, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.
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Yan T, He J, Yang D, Ma Z, Chen H, Zhang Q, Deng F, Ye L, Pu Y, Zhang M, Yang S, Yang S, Tang Z, He Z. Fish Community Structure and Biomass Particle-Size Spectrum in the Upper Reaches of the Jinsha River (China). Animals (Basel) 2022; 12:ani12233412. [PMID: 36496933 PMCID: PMC9739501 DOI: 10.3390/ani12233412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
To understand the characteristics of the fish community structure and biomass particle-size spectrum in the upper reaches of the Jinsha River, fish and environmental surveys were conducted in 21 segments of the upper reaches of the Jinsha River in September 2019 and June 2020. A total of 4062 fish belonging to 2 orders, 5 families, 18 genera, and 28 species were collected. Among them, Cyprinidae fish were the most abundant (14 species), accounting for 50.00%. The Shannon index and Pielou evenness index values varied from 0.402-1.770 and 0.254-0.680, respectively. The dominant species of fish were Triplophysa stenura, Schizothorax wangchiachii, and Schizopygopsis malacanthus. Redundancy analysis (RDA) was used to analyse the relationship between the fish community and environmental factors. Velocity, altitude, and dissolved oxygen were the main influencing factors of fish community structure differences in the upper reaches of the Jinsha River. The abundance/biomass curves showed that the fish communities in the upper reaches of the Jinsha River were moderately or severely disturbed. The standardized biomass particle-size spectrum of fish showed that the degree of disturbance of fish in tributaries was much lower than that in the main stream. Compared with the historical data, the fish community structure in the Jinsha River has changed significantly, with the number of exotic species increasing, and the individual fish showing miniaturization and younger ages. It is suggested that habitat conservation strategies be adopted in the upper tributaries of the Jinsha River to provide a reference for the restoration of fishery resources and the conservation of fish diversity in the Yangtze River.
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Affiliation(s)
- Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiayang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhijun Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongjun Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qian Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lijuan Ye
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Pu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shiyong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziting Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence:
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Li X, Liu S, Qi D, Qi H, Wang Y, Zhao K, Tian F. Genome-wide identification and expression of the peroxisome proliferator-activated receptor gene family in the Tibetan highland fish Gymnocypris przewalskii. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:1685-1699. [PMID: 36469183 DOI: 10.1007/s10695-022-01152-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Peroxisome proliferator-activated receptor (PPAR) plays an important role in the regulation of lipid metabolism and has been widely identified in diverse species. Gymnocypris przewalskii is a native fish of the Qinghai Tibetan Plateau that survives in a chronically cold environment. In the current study, we conducted genome-wide identification of PPAR genes, revealing the existence of seven PPARs in the G. przewalskii genome. Collinearity was observed between two copies of PPARαb and PPARγ in G. przewalskii, suggesting that the additional copy might be gained through whole genome duplication. Both phylogenetic and multiple sequence alignment analyses indicated that PPARs in G. przewalskii were conserved with teleosts. The cold treatment (10 °C and 4 °C) led to the developmental delay of G. przewalskii embryos. Continuous expression of PPARs was observed during the embryonic development of G. przewalskii under normal and cold conditions, with significantly different transcriptional patterns. These results indicated that PPARs participated in the embryonic development of G. przewalskii, and were involved in the cold response during development. The current study proposed a potential role of PPARs in the cold response in the embryonic development of G. przewalskii, which shed light on understanding cold adaptation in Tibetan highland fish.
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Affiliation(s)
- Xiaohuan Li
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810001, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijia Liu
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810001, Qinghai, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Hongfang Qi
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris Przewalskii, Xining, Qinghai, China
| | - Yang Wang
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris Przewalskii, Xining, Qinghai, China
| | - Kai Zhao
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810001, Qinghai, China.
| | - Fei Tian
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810001, Qinghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Nie M, Ni W, Wang L, Gao Q, Liu D, Tian F, Wang Z, Zhang C, Qi D. Insights Into miRNA-mRNA Regulatory Mechanisms of Cold Adaptation in Gymnocypris eckloni: Ubiquitin-Mediated Proteolysis Is Pivotal for Adaptive Energy Metabolism. Front Genet 2022; 13:903995. [PMID: 35937996 PMCID: PMC9354851 DOI: 10.3389/fgene.2022.903995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
This study aimed to understand cold stress adaptations mechanism in fish. Thus, the transcriptional response to cold conditions in Gymnocypris eckloni was evaluated using RNA-seq and microRNA (miRNA)-seq analyses. Low-temperature (LT) group G. eckloni was cultivated outdoors in waters cooled to 2–4°C for 3 weeks, while individuals in the control temperature (CT) group were exposed to 14–16°C. Significantly different responses were observed in both mRNA and miRNA expression profiles, with more mRNAs (1,833 and 1,869 mRNAs were up- and downregulated, respectively) and fewer miRNAs (15 and 6 were up- and downregulated, respectively) observed in the LT group individuals relative to the CT group individuals. A miRNA-mRNA network involved in the regulation of G. eckloni responses to cold stress was constructed; this network included ubiquitin-mediated proteolysis, protein processing, and oxidative phosphorylation. These results provided new insights into mechanisms of cold tolerance by fish, including decreased metabolic activity in addition to proteolysis.
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Affiliation(s)
- Miaomiao Nie
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Weilin Ni
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Lihan Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Dan Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhenji Wang
- Fishery Environmental Monitoring Station of Qinghai Province, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- *Correspondence: Delin Qi,
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6
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Zhou B, Qi D, Liu S, Qi H, Wang Y, Zhao K, Tian F. Physiological, morphological and transcriptomic responses of Tibetan naked carps (Gymnocypris przewalskii) to salinity variations. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100982. [PMID: 35279439 DOI: 10.1016/j.cbd.2022.100982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022]
Abstract
Gymnocypris przewalskii is a native cyprinid fish that dwells in the Lake Qinghai with salinity of 12-13‰. It migrates annually to the freshwater rivers for spawning, experiencing the significant changes in salinity. In the present study, we performed the physiological, morphological and transcriptomic analyses to understand the osmoregulation in G. przewalskii. The physiological assay showed that the osmotic pressure of G. przewalskii was almost isosmotic to the brackish lake water. The low salinity reduced its ionic concentrations and osmotic pressure. The plasticity of gill microstructure was linked to the salinity variations, including the presence of mucus and intact tight junctions in brackish water and the development of the mitochondria-rich cells and the loosened tight junctions in freshwater. RNA-seq analysis identified 1926 differentially expressed genes, including 710 and 1216 down- and up-regulated genes in freshwater, which were enriched in ion transport, cell-cell adhesion, and mucus secretion. Genes in ion uptake were activated in low salinity, and mucus pathways and tight junction showed the higher transcription in brackish water. The isosmoticity between the body fluid and the environment suggested G. przewalskii was in the metabolic-saving condition in the brackish water. The decreased salinity disrupted this balance, which activated the ion uptake in freshwater to maintain osmotic homeostasis. The gill remodeling was involved in this process through the development of the mitochondria-rich cells to enhance ion uptake. The current finding provided insights into the potential mechanisms of G. przewalskii to cope with salinity alteration.
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Affiliation(s)
- Bingzheng Zhou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Hongfang Qi
- Qinghai Provincial Key Laboratory of Gymnocypris przewalskii breeding and reproduction, Xining 810008, China
| | - Yang Wang
- Qinghai Provincial Key Laboratory of Gymnocypris przewalskii breeding and reproduction, Xining 810008, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
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7
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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: 0] [Impact Index Per Article: 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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Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol 2021; 38:3864-3883. [PMID: 34426843 PMCID: PMC8382914 DOI: 10.1093/molbev/msab028] [Citation(s) in RCA: 9] [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] [Indexed: 12/11/2022] Open
Abstract
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.
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Affiliation(s)
- Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Department of Earth and Planetary Science, Yale University, 210 Whitney Ave, New Haven, CT, USA
| | - Miluska K R Sanchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Escola Superior de Agricultura ‘Luiz de Queiroz,’ Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kim Warren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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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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Yuan D, Chen X, Gu H, Zou M, Zou Y, Fang J, Tao W, Dai X, Xiao S, Wang Z. Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation. Gigascience 2020; 9:giaa132. [PMID: 33231676 PMCID: PMC7684707 DOI: 10.1093/gigascience/giaa132] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Intense stresses caused by high-altitude environments may result in noticeable genetic adaptions in native species. Studies of genetic adaptations to high elevations have been largely limited to terrestrial animals. How fish adapt to high-elevation environments is largely unknown. Triplophysa bleekeri, an endemic fish inhabiting high-altitude regions, is an excellent model to investigate the genetic mechanisms of adaptation to the local environment. Here, we assembled a chromosomal genome sequence of T. bleekeri, with a size of ∼628 Mb (contig and scaffold N50 of 3.1 and 22.9 Mb, respectively). We investigated the origin and environmental adaptation of T. bleekeri based on 21,198 protein-coding genes in the genome. RESULTS Compared with fish species living at low altitudes, gene families associated with lipid metabolism and immune response were significantly expanded in the T. bleekeri genome. Genes involved in DNA repair exhibit positive selection for T. bleekeri, Triplophysa siluroides, and Triplophysa tibetana, indicating that adaptive convergence in Triplophysa species occurred at the positively selected genes. We also analyzed whole-genome variants among samples from 3 populations. The results showed that populations separated by geological and artificial barriers exhibited obvious differences in genetic structures, indicating that gene flow is restricted between populations. CONCLUSIONS These results will help us expand our understanding of environmental adaptation and genetic diversity of T. bleekeri and provide valuable genetic resources for future studies on the evolution and conservation of high-altitude fish species such as T. bleekeri.
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Affiliation(s)
- Dengyue Yuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xuehui Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ming Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Yu Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Jian Fang
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiangyan Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
- College of Plant Protection, Jilin Agriculture University, Changchun, Jilin 130118, China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
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Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish. Int J Biol Macromol 2020; 149:341-347. [DOI: 10.1016/j.ijbiomac.2020.01.207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/21/2019] [Accepted: 01/15/2020] [Indexed: 12/18/2022]
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12
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Tong C, Najm GM, Pinter-Wollman N, Pruitt JN, Linksvayer TA. Comparative Genomics Identifies Putative Signatures of Sociality in Spiders. Genome Biol Evol 2020; 12:122-133. [PMID: 31960912 PMCID: PMC7108510 DOI: 10.1093/gbe/evaa007] [Citation(s) in RCA: 12] [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] [Accepted: 01/15/2020] [Indexed: 12/15/2022] Open
Abstract
Comparative genomics has begun to elucidate the genomic basis of social life in insects, but insight into the genomic basis of spider sociality has lagged behind. To begin, to characterize genomic signatures associated with the evolution of social life in spiders, we performed one of the first spider comparative genomics studies including five solitary species and two social species, representing two independent origins of sociality in the genus Stegodyphus. We found that the two social spider species had a large expansion of gene families associated with transport and metabolic processes and an elevated genome-wide rate of molecular evolution compared with the five solitary spider species. Genes that were rapidly evolving in the two social species relative to the five solitary species were enriched for transport, behavior, and immune functions, whereas genes that were rapidly evolving in the solitary species were enriched for energy metabolism processes. Most rapidly evolving genes in the social species Stegodyphus dumicola were broadly expressed across four tissues and enriched for transport functions, but 12 rapidly evolving genes showed brain-specific expression and were enriched for social behavioral processes. Altogether, our study identifies putative genomic signatures and potential candidate genes associated with spider sociality. These results indicate that future spider comparative genomic studies, including broader sampling and additional independent origins of sociality, can further clarify the genomic causes and consequences of social life.
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Affiliation(s)
- Chao Tong
- Department of Biology, University of Pennsylvania
| | - Gabriella M Najm
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Noa Pinter-Wollman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Jonathan N Pruitt
- Department of Psychology, Neurobiology & Behaviour, McMaster University, Hamilton, Ontario, Canada
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13
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Tong C, Li M. Transcriptomic signature of rapidly evolving immune genes in a highland fish. FISH & SHELLFISH IMMUNOLOGY 2020; 97:587-592. [PMID: 31891809 DOI: 10.1016/j.fsi.2019.12.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/21/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Recent genome-wide studies have begun to elucidate the genomic basis of hypoxia, long-term cold and high saline and alkaline adaptation in highland fish, and a number of key genes contributed to its highland adaptation were identified. An increasing number of studies indicated that immune genes of Tibetan endemic fish species underwent positive selection towards functional shift, while the insight into immune gene repertoire of Tibetan highland fishes from genome-wide studies has largely lagged behind. In this study, we performed one of the first comparative genomics study in particular focusing on the signatures of immune genes in a highland fish, Gymnocypris przewalskii based on immune-relevant tissue transcriptome assemblies. We identified seven putative rapidly evolving immune genes with elevated molecular evolutionary rate (dN/dS) relative to lowland fish species. Using tissue-transcriptome data, we found most of rapidly evolving immune genes were broadly expressed in head-kidney, spleen, gills and skin tissues, which significantly enriched for complement activation and inflammatory response processes. In addition, we found a set of complement activation related genes underwent accelerated evolution and showed consistently repressed expression patterns in response to parasite Ichthyophthirius multifiliis infection. Moreover, we detected a number of immune genes involved in adaptive immune system exhibited distinct signature of upregulated expression patterns after parasite infection. Taken together, this study provided putative transcriptomic signatures of rapidly evolving immune genes, and will gain the insight into Schizothoracine fish adaptation to high-altitude extreme aquatic environments including diversified pathogen challenge.
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Affiliation(s)
- Chao Tong
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Miao Li
- Center for Advanced Retinal and Ocular Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Zhou C, Xiao S, Liu Y, Mou Z, Zhou J, Pan Y, Zhang C, Wang J, Deng X, Zou M, Liu H. Comprehensive transcriptome data for endemic Schizothoracinae fish in the Tibetan Plateau. Sci Data 2020; 7:28. [PMID: 31964888 PMCID: PMC6972879 DOI: 10.1038/s41597-020-0361-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/18/2019] [Indexed: 01/05/2023] Open
Abstract
The Schizothoracinae fishes, endemic species in the Tibetan Plateau, are considered as ideal models for highland adaptation and speciation investigation. Despite several transcriptome studies for highland fishes have been reported before, the transcriptome information of Schizothoracinae is still lacking. To obtain comprehensive transcriptome data for Schizothoracinae, the transcriptome of a total of 183 samples from 14 representative Schizothoracinae species, were sequenced and de novo assembled. As a result, about 1,363 Gb transcriptome clean data was obtained. After the assembly, we obtain 76,602-154,860 unigenes for each species with sequence N50 length of 1,564-2,143 bp. More than half of the unigenes were functionally annotated by public databases. The Schizothoracinae fishes in this work exhibited diversified ecological distributions, phenotype characters and feeding habits; therefore, the comprehensive transcriptome data of those species provided valuable information for the environmental adaptation and speciation of Schizothoracinae in the Tibetan Plateau.
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Affiliation(s)
- Chaowei Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
- Departments of Aquaculture, College of Animal Science, Southwest University, Chongqing, 402460, China
| | - Shijun Xiao
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430000, China
| | - Yanchao Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Zhenbo Mou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Yingzi Pan
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Jiu Wang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Xingxing Deng
- Departments of Aquaculture, College of Animal Science, Southwest University, Chongqing, 402460, China
| | - Ming Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430000, China
| | - Haiping Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China.
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Walsh J, Clucas GV, MacManes MD, Thomas WK, Kovach AI. Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone. Ecol Evol 2019; 9:13477-13494. [PMID: 31871659 PMCID: PMC6912898 DOI: 10.1002/ece3.5804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
The role of species divergence due to ecologically based divergent selection-or ecological speciation-in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms' adaptations to selective pressures that underlie ecological divergence. Sharp environmental gradients across the saline-freshwater ecotone within tidal marshes present extreme adaptive challenges to terrestrial vertebrates. Here, we sequence 20 whole genomes of two avian sister species endemic to tidal marshes-the saltmarsh sparrow (Ammospiza caudacutus) and Nelson's sparrow (A. nelsoni)-to evaluate the influence of selective and demographic processes in shaping genome-wide patterns of divergence. Genome-wide divergence between these two recently diverged sister species was notably high (genome-wide F ST = 0.32). Against a background of high genome-wide divergence, regions of elevated divergence were widespread throughout the genome, as opposed to focused within islands of differentiation. These patterns may be the result of genetic drift resulting from past tidal march colonization events in conjunction with divergent selection to different environments. We identified several candidate genes that exhibited elevated divergence between saltmarsh and Nelson's sparrows, including genes linked to osmotic regulation, circadian rhythm, and plumage melanism-all putative candidates linked to adaptation to tidal marsh environments. These findings provide new insights into the roles of divergent selection and genetic drift in generating and maintaining biodiversity.
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Affiliation(s)
- Jennifer Walsh
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyCornell UniversityIthacaNYUSA
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Gemma V. Clucas
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
- Present address:
Cornell Lab of OrnithologyIthacaNYUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Hubbard Center for Genome StudiesDurhamNHUSA
| | - W. Kelley Thomas
- Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Hubbard Center for Genome StudiesDurhamNHUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
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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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Sudhagar A, Kumar G, El-Matbouli M. Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review. Int J Mol Sci 2018; 19:ijms19010245. [PMID: 29342931 PMCID: PMC5796193 DOI: 10.3390/ijms19010245] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/12/2022] Open
Abstract
In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.
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Affiliation(s)
- Arun Sudhagar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
- Central Institute of Fisheries Education, Rohtak Centre, Haryana 124411, India.
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
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