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Zhang XZ, Ma XD, Wang WT, Peng F, Hou YM, Shen YX, Sun YQ, Chen JF, Yin YJ, Zeng YY, Yu Y, Zhou P, Zhang FH, He YF, Shen YF. Comparative skin histological and transcriptomic analysis of Rana kukunoris with two different skin colors. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101217. [PMID: 38412702 DOI: 10.1016/j.cbd.2024.101217] [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: 09/02/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/29/2024]
Abstract
This study compares the skin structures of Rana kukunoris with two different skin colors living in the same area of Haibei in the Northeastern Qinghai-Tibet Plateau. The skin thickness of the khaki R. kukunoris was significantly greater than that of the brown R. kukunoris (P < 0.01), and significantly more mucous and granular glands were present on the dorsal skin of the khaki frog (P < 0.05). Meanwhile, the melanocytes on the dorsal skin of the brown frog were significantly larger than those on the khaki one (P < 0.05). Morphological changes in the expansion and aggregation of melanocytes seemed to deepen the skin color of R. kukunoris. Moreover, transcriptome sequencing identified tyrosine metabolism, melanogenesis, and riboflavin metabolism as the main pathways involved in melanin formation and metabolism in brown R. kukunoris. TYR, MC1R was upregulated as the skin color of R. kukunoris was deepened and contributed to melanin production and metabolism. In contrast, the khaki frog had significantly more upregulated genes and metabolic pathways related to autoimmunity. The khaki frog appeared to defend against ultraviolet (UV) radiation-induced damage by secreting mucus and small molecular peptides, whereas the brown frog protected itself by distributing a large amount of melanin. Hence, the different skin colors of R. kukunoris might represent different adaptation strategies for survival in the intense UV radiation environment of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xu-Ze Zhang
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810001, China; Key Laboratory of Resource Chemistry and Eco-environmental Protection in Tibetan Plateau of State Ethnic Affairs Commission, Qinghai Minzu University, Xining 810007, China.
| | - Xiao-Dong Ma
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China; Key Laboratory of Resource Chemistry and Eco-environmental Protection in Tibetan Plateau of State Ethnic Affairs Commission, Qinghai Minzu University, Xining 810007, China
| | - Wan-Ting Wang
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Fei Peng
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Ye-Mao Hou
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Yue-Xia Shen
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Yu-Qi Sun
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Jin-Fang Chen
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Yi-Jin Yin
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Yu-Ye Zeng
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Yi Yu
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China
| | - Peng Zhou
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810001, China
| | - Fu-Hao Zhang
- Key Laboratory of Resource Chemistry and Eco-environmental Protection in Tibetan Plateau of State Ethnic Affairs Commission, Qinghai Minzu University, Xining 810007, China; College of Pharmaceutical, Qinghai Minzu University, Xining 810007, China
| | - Yan-Feng He
- Key Laboratory of Resource Chemistry and Eco-environmental Protection in Tibetan Plateau of State Ethnic Affairs Commission, Qinghai Minzu University, Xining 810007, China; College of Pharmaceutical, Qinghai Minzu University, Xining 810007, China.
| | - Ying-Fang Shen
- College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China; Key Laboratory of Resource Chemistry and Eco-environmental Protection in Tibetan Plateau of State Ethnic Affairs Commission, Qinghai Minzu University, Xining 810007, China.
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Chen W, Chen H, Liao J, Tang M, Qin H, Zhao Z, Liu X, Wu Y, Jiang L, Zhang L, Fang B, Feng X, Zhang B, Reid K, Merilä J. Chromosome-level genome assembly of a high-altitude-adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation. Front Zool 2023; 20:1. [PMID: 36604706 PMCID: PMC9817415 DOI: 10.1186/s12983-022-00482-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The high-altitude-adapted frog Rana kukunoris, occurring on the Tibetan plateau, is an excellent model to study life history evolution and adaptation to harsh high-altitude environments. However, genomic resources for this species are still underdeveloped constraining attempts to investigate the underpinnings of adaptation. RESULTS The R. kukunoris genome was assembled to a size of 4.83 Gb and the contig N50 was 1.80 Mb. The 6555 contigs were clustered and ordered into 12 pseudo-chromosomes covering ~ 93.07% of the assembled genome. In total, 32,304 genes were functionally annotated. Synteny analysis between the genomes of R. kukunoris and a low latitude species Rana temporaria showed a high degree of chromosome level synteny with one fusion event between chr11 and chr13 forming pseudo-chromosome 11 in R. kukunoris. Characterization of features of the R. kukunoris genome identified that 61.5% consisted of transposable elements and expansions of gene families related to cell nucleus structure and taste sense were identified. Ninety-five single-copy orthologous genes were identified as being under positive selection and had functions associated with the positive regulation of proteins in the catabolic process and negative regulation of developmental growth. These gene family expansions and positively selected genes indicate regions for further interrogation to understand adaptation to high altitude. CONCLUSIONS Here, we reported a high-quality chromosome-level genome assembly of a high-altitude amphibian species using a combination of Illumina, PacBio and Hi-C sequencing technologies. This genome assembly provides a valuable resource for subsequent research on R. kukunoris genomics and amphibian genome evolution in general.
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Affiliation(s)
- Wei Chen
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China ,Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi, 247230 China ,grid.252245.60000 0001 0085 4987Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, 230601 China
| | - Hongzhou Chen
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Jiahong Liao
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Min Tang
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Haifen Qin
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Zhenkun Zhao
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Xueyan Liu
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Yanfang Wu
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Lichun Jiang
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Lixia Zhang
- grid.462338.80000 0004 0605 6769Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Bohao Fang
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA USA
| | - Xueyun Feng
- grid.7737.40000 0004 0410 2071Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Baowei Zhang
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China
| | - Kerry Reid
- grid.194645.b0000000121742757Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Juha Merilä
- grid.7737.40000 0004 0410 2071Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland ,grid.194645.b0000000121742757Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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Chen Y, Tan S, Fu J. Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans). J Mol Evol 2022; 90:389-399. [PMID: 36029325 DOI: 10.1007/s00239-022-10070-4] [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: 04/02/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
High-elevation adaptation provides an excellent system for examining adaptive evolution, and adaptive variations may manifest at gene expression or any other phenotypic levels. We examined gene expression profiles of Asiatic toads (Bufo gargarizans) along an elevational gradient from both wild and common-garden acclimated populations. Asiatic toads originated from high altitudes have distinctive gene expression patterns. We identified 18 fixed differentially expressed genes (DEGs), which are different in both wild and acclimated samples, and 1217 plastic DEGs, which are different among wild samples. The expression levels of most genes were linearly correlated with altitude gradient and down-regulated in high-altitude populations. Expression variations of several genes associated with metabolic process are fixed, and we also identified a co-expression module that is significantly different between acclimated populations and has functions related to DNA repair. The differential expression of the vast majority genes, however, are due to phenotypic plasticity, revealing the highly plastic nature of gene expression variations. Expression modification of some specific genes related to metabolism and response to UV radiation play crucial role in adaptation to high altitude for Asiatic toads. Common-garden experiments are essential for evaluating adaptive evolution of natural populations.
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Affiliation(s)
- Ying Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
- The University of Chinese Academy of Science, Beijing, China.
| | - Song Tan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The University of Chinese Academy of Science, Beijing, China
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
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Liu XW, Wang YH, Shen SK. Transcriptomic and metabolomic analyses reveal the altitude adaptability and evolution of different-colored flowers in alpine Rhododendron species. TREE PHYSIOLOGY 2022; 42:1100-1113. [PMID: 34850945 DOI: 10.1093/treephys/tpab160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/25/2021] [Indexed: 05/28/2023]
Abstract
Understanding the molecular mechanisms and evolutionary process of plant adaptation to the heterogeneous environment caused by altitude gradients in plateau mountain ecosystems can provide novel insight into species' responses to global changes. Flower color is the most conspicuous and highly diverse trait in nature. Herein, the gene expression patterns, evolutionary adaptation and metabolites changes of different-colored flowers of alpine Rhododendron L. species along altitude gradients were investigated based on a combined analysis of transcriptomics and metabolomics. Differentially expressed genes were found to be related to the biosynthesis of carbohydrates, fatty acids, amino acids and flavonoids, suggesting their important roles in the altitude adaptability of Rhododendron species. The evolution rate of high-altitude species was faster than that of low-altitude species. Genes related to DNA repair, mitogen-activated protein kinase and ABA signal transduction, and lipoic acid and propanoate metabolism were positively selected in the flowers of high-altitude Rhododendron species and those associated with carotenoid biosynthesis pathway, ABA signal transduction and ethylene signal transduction were positively selected in low-altitude species. These results indicated that the genes with differentiated expressions or functions exhibit varying evolution during the adaptive divergence of heterogeneous environment caused by altitude gradients. Flower-color variation might be attributed to the significant differences in gene expression or metabolites related to sucrose, flavonoids and carotenoids at the transcription or metabolism levels of Rhododendron species. This work suggests that Rhododendron species have multiple molecular mechanisms in their adaptation to changing environments caused by altitude gradients.
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Affiliation(s)
- Xing-Wen Liu
- School of Ecology and Environmental Science, Yunnan University, No.2 Green lake North road Kunming, Kunming, Yunnan 650091, China
| | - Yue-Hua Wang
- School of Ecology and Environmental Science, Yunnan University, No.2 Green lake North road Kunming, Kunming, Yunnan 650091, China
| | - Shi-Kang Shen
- School of Ecology and Environmental Science, Yunnan University, No.2 Green lake North road Kunming, Kunming, Yunnan 650091, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, No.2 Green lake North road Kunming, Kunming, Yunnan 650091, China
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, No.2 Green lake North road Kunming, Kunming, Yunnan 650091, China
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Smirnov DN, Shekhovtsov SV, Shipova AA, Gazizova GR, Shagimardanova EI, Bulakhova NA, Meshcheryakova EN, Poluboyarova TV, Khrameeva EE, Peltek SE, Berman DI. De novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensis. Vavilovskii Zhurnal Genet Selektsii 2022; 26:109-116. [PMID: 35342853 PMCID: PMC8894097 DOI: 10.18699/vjgb-22-07] [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] [Received: 08/10/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
The Siberian wood frog Rana amurensis Boulenger, 1886 is the most hypoxia-tolerant amphibian. It can survive for several months in an almost complete absence of oxygen. Little is known about the mechanisms of this remarkable resilience, in part because studies of amphibian genomes are impeded by their large size. To make the Siberian wood frog more amenable for genetic analysis, we performed transcriptome sequencing and de novo assembly for the R. amurensis brain under hypoxia and normoxia, as well as for the normoxic heart. In order to build a de novo transcriptome assembly of R. amurensis, we utilized 125-bp paired-end reads obtained from the brain under normoxia and hypoxia conditions, and from the heart under normoxia. In the transcriptome assembled from about 100,000,000 reads, 81.5 % of transcripts were annotated as complete, 5.3 % as fragmented, and 13.2 % as missing. We detected 59,078 known transcripts that clustered into 22,251 genes; 11,482 of them were assigned to specific GO categories. Among them, we found 6696 genes involved in protein binding, 3531 genes involved in catalytic activity, and 576 genes associated with transporter activity. A search for genes encoding receptors of the most important neurotransmitters, which may participate in the response to hypoxia, resulted in a set of expressed receptors of dopamine, serotonin, GABA, glutamate, acetylcholine, and norepinephrine. Unexpectedly, no transcripts for histamine receptors were found. The data obtained in this study create a valuable resource for studying the mechanisms of hypoxia tolerance in the Siberian wood frog, as well as for amphibian studies in general.
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Affiliation(s)
- D. N. Smirnov
- Center of Life Sciences, Skolkovo Institute of Science and Technology; Ben-Gurion University of the Negev, Department of Life Sciences
| | - S. V. Shekhovtsov
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. A. Shipova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - G. R. Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University
| | | | - N. A. Bulakhova
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
| | - E. N. Meshcheryakova
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
| | - T. V. Poluboyarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. E. Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology
| | - S. E. Peltek
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - D. I. Berman
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
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De novo Assembly, Annotation, and Analysis of Transcriptome Data of the Ladakh Ground Skink Provide Genetic Information on High-Altitude Adaptation. Genes (Basel) 2021; 12:genes12091423. [PMID: 34573405 PMCID: PMC8466045 DOI: 10.3390/genes12091423] [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: 08/10/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
The Himalayan Arc is recognized as a global biodiversity hotspot. Among its numerous cryptic and undiscovered organisms, this composite high-mountain ecosystem harbors many taxa with adaptations to life in high elevations. However, evolutionary patterns and genomic features have been relatively rarely studied in Himalayan vertebrates. Here, we provide the first well-annotated transcriptome of a Greater Himalayan reptile species, the Ladakh Ground skink Asymblepharus ladacensis (Squamata: Scincidae). Based on tissues from the brain, an embryonic disc, and pooled organ material, using pair-end Illumina NextSeq 500 RNAseq, we assembled ~77,000 transcripts, which were annotated using seven functional databases. We tested ~1600 genes, known to be under positive selection in anurans and reptiles adapted to high elevations, and potentially detected positive selection for 114 of these genes in Asymblepharus. Even though the strength of these results is limited due to the single-animal approach, our transcriptome resource may be valuable data for further studies on squamate reptile evolution in the Himalayas as a hotspot of biodiversity.
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Yang L, Wang Y, Sun N, Chen J, He S. Genomic and functional evidence reveals convergent evolution in fishes on the Tibetan Plateau. Mol Ecol 2021; 30:5752-5764. [PMID: 34516715 DOI: 10.1111/mec.16171] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022]
Abstract
High-altitude environments are strong drivers of adaptive evolution in endemic organisms. However, little is known about the genetic mechanisms of convergent adaptation among different lineages, especially in fishes. There are three independent fish groups on the Tibetan Plateau: Tibetan Loaches, Schizothoracine fishes and Glyptosternoid fishes; all are well adapted to the harsh environmental conditions. They represent an excellent example of convergent evolution but with an unclear genetic basis. We used comparative genomic analyses between Tibetan fishes and fishes from low altitudes and detected genomic signatures of convergent evolution in fishes on the Tibetan Plateau. The Tibetan fishes exhibited genome-wide accelerated evolution in comparison with a control set of fishes from low altitudes. A total of 368 positively selected genes were identified in Tibetan fishes, which were enriched in functional categories related to energy metabolism and hypoxia response. Widespread parallel amino acid substitutions were detected among the Tibetan fishes and a subset of these substitutions occurred in positively selected genes associated with high-altitude adaptation. Functional assays suggested that von Hippel-Lindau (VHL) tumour suppressor genes from Tibetan fishes enhance hypoxia-inducible factor (HIF) activity convergently under hypoxia compared to low-altitude fishes. The results provide genomic and functional evidence supporting convergent genetic mechanisms for high-altitude adaptation in fishes on the Tibetan Plateau.
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Affiliation(s)
- Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China.,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ying Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Juan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Krishnan A. Lessons Across Scales: Molecular Ecology and Wildlife Conservation. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00232-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Abstract
Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.
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Affiliation(s)
- Yan-Bo Sun
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, Yunnan 650091, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Yi Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, Oklahoma 73072, USA
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10
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Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing. BMC Genomics 2020; 21:840. [PMID: 33246410 PMCID: PMC7694352 DOI: 10.1186/s12864-020-07267-6] [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: 06/30/2020] [Accepted: 11/23/2020] [Indexed: 11/27/2022] Open
Abstract
Background Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus) using Illumina short-read sequencing data, by comparing our lab data for 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) to public data for 26 individuals from three other breeds (two Moroccan and one Chinese) and 21samples from Bezoar ibexes. Results We obtained a total of 2394 CNV regions (CNVRs) by merging 208,649 high-confidence CNVs, which spanned ~ 267 Mb of total length and accounted for 10.80% of the goat autosomal genome. Functional analyses showed that 2322 genes overlapping with the CNVRs were significantly enriched in 57 functional GO terms and KEGG pathways, most related to the nervous system, metabolic process, and reproduction system. Clustering patterns of all 85 samples generated separately from duplications and deletions were generally consistent with the results from SNPs, agreeing with the geographical origins of these goats. Based on genome-wide FST at each CNV locus, some genes overlapping with the highly divergent CNVs between domestic and wild goats were mainly enriched for several immunity-related pathways, whereas the genes overlapping with the highly differentiated CNVs between highland and lowland goats were mainly related to vitamin and lipid metabolism. Remarkably, a 507-bp deletion at ~ 14 kb downstream of FGF5 on chromosome 6 showed highly divergent (FST = 0.973) between the highland and lowland goats. Together with an enhancer activity of this sequence shown previously, the function of this duplication in regulating fiber growth deserved to be further investigated in detail. Conclusion We generated a comprehensive map of CNVs in goats. Many genetically differentiated CNVs among various goat populations might be associated with the population characteristics of domestic goat breeds. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07267-6.
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Zhang QL, Li HW, Dong ZX, Yang XJ, Lin LB, Chen JY, Yuan ML. Comparative transcriptomic analysis of fireflies (Coleoptera: Lampyridae) to explore the molecular adaptations to fresh water. Mol Ecol 2020; 29:2676-2691. [PMID: 32512643 DOI: 10.1111/mec.15504] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
Aquatic insects are well adapted to freshwater environments, but the molecular basis of these adaptations remains largely unknown. Most firefly species (Coleoptera: Lampyridae) are terrestrial, but the larvae of several species are aquatic. Here, larval and adult transcriptomes from Aquatica leii (freshwater) and Lychnuris praetexta (terrestrial) were generated to test whether the genes associated with metabolic efficiency and morphology have undergone adaptive evolution to fresh water. The aquatic fireflies had a significantly lower ratio of nonsynonymous to synonymous substitutions than the terrestrial insects, indicating a genomewide evolutionary constraint in the aquatic fireflies. We identified 341 fast-evolving genes and 116 positively selected genes in the aquatic fireflies. Of these, 76 genes exhibiting both fast evolution and positive selection were primarily involved in ATP production, energy metabolism and the hypoxia response. We identified 7,271 differentially expressed genes (DEGs) in A. leii (adults versus larvae) and 8,309 DEGs in L. praetexta (adults versus larvae). DEGs specific to the aquatic firefly (n = 1,445) were screened via interspecific comparisons (A. leii versus L. praetexta) and were significantly enriched for genes involved in metabolic efficiency (e.g., ATP production, hypoxia, and immune responses) and certain aspects of morphology (e.g., cuticle chitin, tracheal and compound eye morphology). These results indicate that sequence and expression-level changes in genes associated with both metabolic efficiency and morphological attributes related to the freshwater lifestyle contributed to freshwater adaptation in fireflies. This study provides new insights into the molecular mechanisms of aquatic adaptation in insects.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiao-Jie Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
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12
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Multi-Tissue Transcriptomes Yield Information on High-Altitude Adaptation and Sex-Determination in Scutiger cf. sikimmensis. Genes (Basel) 2019; 10:genes10110873. [PMID: 31683620 PMCID: PMC6895926 DOI: 10.3390/genes10110873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/20/2022] Open
Abstract
The Himalayas are one of earth’s hotspots of biodiversity. Among its many cryptic and undiscovered organisms, including vertebrates, this complex high-mountain ecosystem is expected to harbour many species with adaptations to life in high altitudes. However, modern evolutionary genomic studies in Himalayan vertebrates are still at the beginning. Moreover, in organisms, like most amphibians with relatively high DNA content, whole genome sequencing remains bioinformatically challenging and no complete nuclear genomes are available for Himalayan amphibians. Here, we present the first well-annotated multi-tissue transcriptome of a Greater Himalayan species, the lazy toad Scutiger cf. sikimmensis (Anura: Megophryidae). Applying Illumina NextSeq 500 RNAseq to six tissues, we obtained 41.32 Gb of sequences, assembled to ~111,000 unigenes, translating into 54362 known genes as annotated in seven functional databases. We tested 19 genes, known to play roles in anuran and reptile adaptation to high elevations, and potentially detected diversifying selection for two (TGS1, SENP5) in Scutiger. Of a list of 37 genes, we also identify 27 candidate genes for sex determination or sexual development, all of which providing the first such data for this non-model megophryid species. These transcriptomes will serve as a valuable resource for further studies on amphibian evolution in the Greater Himalaya as a biodiversity hotspot.
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13
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Meyer‐Lucht Y, Luquet E, Jóhannesdóttir F, Rödin‐Mörch P, Quintela M, Richter‐Boix A, Höglund J, Laurila A. Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor
C/EBP‐1. Mol Ecol 2019; 28:2786-2801. [DOI: 10.1111/mec.15123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Emilien Luquet
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 Villeurbanne France
| | - Fríða Jóhannesdóttir
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Patrik Rödin‐Mörch
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - María Quintela
- Department of Population Genetics Institute of Marine Research Bergen Norway
| | - Alex Richter‐Boix
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
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14
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Salvador-Martínez I, Coronado-Zamora M, Castellano D, Barbadilla A, Salazar-Ciudad I. Mapping Selection within Drosophila melanogaster Embryo's Anatomy. Mol Biol Evol 2019; 35:66-79. [PMID: 29040697 DOI: 10.1093/molbev/msx266] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns, and development with the aim of mapping adaptation over the entire embryo's anatomy. Our adaptation map is based on analyzing spatial gene expression information for 5,969 genes (from text-based annotations of in situ hybridization data directly from the BDGP database, Tomancak et al. 2007) and the polymorphism and divergence in these genes (from the project DGRP, Mackay et al. 2012).The proportion of nonsynonymous substitutions that are adaptive, neutral, or slightly deleterious are estimated for the set of genes expressed in each embryonic anatomical structure using the distribution of fitness effects-alpha method (Eyre-Walker and Keightley 2009). This method is a robust derivative of the McDonald and Kreitman test (McDonald and Kreitman 1991). We also explore whether different anatomical structures differ in the phylogenetic age, codon usage, or expression bias of the genes they express and whether genes expressed in many anatomical structures show more adaptive substitutions than other genes.We found that: 1) most of the digestive system and ectoderm-derived structures are under selective constraint, 2) the germ line and some specific mesoderm-derived structures show high rates of adaptive substitution, and 3) the genes that are expressed in a small number of anatomical structures show higher expression bias, lower phylogenetic ages, and less constraint.
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Affiliation(s)
- Irepan Salvador-Martínez
- Evo-devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Marta Coronado-Zamora
- Departament de Genètica i de Microbiologia, Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David Castellano
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Antonio Barbadilla
- Departament de Genètica i de Microbiologia, Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Isaac Salazar-Ciudad
- Evo-devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Departament de Genètica i de Microbiologia, Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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15
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Palomar G, Vasemägi A, Ahmad F, Nicieza AG, Cano JM. Mapping of quantitative trait loci for life history traits segregating within common frog populations. Heredity (Edinb) 2019; 122:800-808. [PMID: 30631147 DOI: 10.1038/s41437-018-0175-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/08/2018] [Accepted: 12/12/2018] [Indexed: 02/01/2023] Open
Abstract
The evolution of complex traits is often shaped by adaptive divergence. However, very little is known about the number, effect size, and location of the genomic regions influencing the variation of these traits in natural populations. Based on a dense linkage map of the common frog, Rana temporaria, we have localized, for the first time in amphibians, three significant and nine suggestive quantitative trait loci (QTLs) for metabolic rate, growth rate, development time, and weight at metamorphosis, explaining 5.6-18.9% of the overall phenotypic variation in each trait. We also found a potential pleiotropic QTL between development time and size at metamorphosis that, if confirmed, might underlie the previously reported genetic correlation between these traits. Furthermore, we demonstrate that the genetic variation linked to fitness-related larval traits segregates within Rana temporaria populations. This study provides the first insight into the genomic regions that affect larval life history traits in anurans, providing a valuable resource to delve further into the genomic basis of evolutionary change in amphibians.
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Affiliation(s)
- Gemma Palomar
- Research Unit of Biodiversity (UO-CSIC-PA), 33600, Mieres, Asturias, Spain. .,Department of Biology of Organisms and Systems, University of Oviedo, 33006, Oviedo, Asturias, Spain. .,Molecular and Behavioral Ecology Group, Institute of Environmental Sciences, Jagiellonian University, 30-387, Krakow, Poland.
| | - Anti Vasemägi
- Department of Biology, University of Turku, 20014, Turku, Finland.,Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51006, Tartu, Estonia.,Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893, Drottningholm, Sweden
| | - Freed Ahmad
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Alfredo G Nicieza
- Research Unit of Biodiversity (UO-CSIC-PA), 33600, Mieres, Asturias, Spain.,Department of Biology of Organisms and Systems, University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - José Manuel Cano
- Research Unit of Biodiversity (UO-CSIC-PA), 33600, Mieres, Asturias, Spain.,Department of Biology of Organisms and Systems, University of Oviedo, 33006, Oviedo, Asturias, Spain
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16
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Identification of critical sex-biased genes in Andrias davidianus by de novo transcriptome. Mol Genet Genomics 2018; 294:287-299. [PMID: 30377773 DOI: 10.1007/s00438-018-1508-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
The Chinese giant salamander Andrias davidianus is a protected amphibian with high nutritional and economic value. Understanding its sex determination mechanism is important for improving culture techniques and sex control in breeding. However, little information on the characterization of critical genes involved in sex is available. Herein, sequencing of ovary and test produced 40,783,222 and 46,128,902 raw reads, respectively, which were jointly assembled into 80,497 unigenes. Of these, 36,609 unigenes were annotated, of which 8907 were female-biased and 10,385 were male-biased. Several sex-related pathways were observed, including the Wnt signaling pathway. After elevated temperature and estrogen exposure, neomale and neofemale specimens were identified by a female-specific marker for the first time. RT-qPCR analysis showed the expression profile of ten selected sex-biased genes to be exhibited consistently in male and neomale and in female and neofemale, with the exception of the Amh and TfIIIa genes. Results suggested that these genes may play important roles in A. davidianus sex determination and gonad development. This provides a basis for further investigation of the molecular mechanisms of sex determination in amphibians.
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17
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Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations. Proc Natl Acad Sci U S A 2018; 115:E10634-E10641. [PMID: 30348757 DOI: 10.1073/pnas.1813593115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although many cases of genetic adaptations to high elevations have been reported, the processes driving these modifications and the pace of their evolution remain unclear. Many high-elevation adaptations (HEAs) are thought to have arisen in situ as populations rose with growing mountains. In contrast, most high-elevation lineages of the Qinghai-Tibetan Plateau appear to have colonized from low-elevation areas. These lineages provide an opportunity for studying recent HEAs and comparing them with ancestral low-elevation alternatives. Herein, we compare four frogs (three species of Nanorana and a close lowland relative) and four lizards (Phrynocephalus) that inhabit a range of elevations on or along the slopes of the Qinghai-Tibetan Plateau. The sequential cladogenesis of these species across an elevational gradient allows us to examine the gradual accumulation of HEA at increasing elevations. Many adaptations to high elevations appear to arise gradually and evolve continuously with increasing elevational distributions. Numerous related functions, especially DNA repair and energy metabolism pathways, exhibit rapid change and continuous positive selection with increasing elevations. Although the two studied genera are distantly related, they exhibit numerous convergent evolutionary changes, especially at the functional level. This functional convergence appears to be more extensive than convergence at the individual gene level, although we found 32 homologous genes undergoing positive selection for change in both high-elevation groups. We argue that species groups distributed along a broad elevational gradient provide a more powerful system for testing adaptations to high-elevation environments compared with studies that compare only pairs of high-elevation versus low-elevation species.
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18
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Zhang QL, Wang F, Guo J, Deng XY, Chen JY, Lin LB. Characterization of ladybird Henosepilachna vigintioctopunctata transcriptomes across various life stages. Sci Data 2018; 5:180093. [PMID: 29870033 PMCID: PMC5987669 DOI: 10.1038/sdata.2018.93] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/27/2018] [Indexed: 12/17/2022] Open
Abstract
Henosepilachna vigintioctopunctata is a vegetable pest that has spread worldwide. It belongs to the Coccinellidae family, whose members exhibit remarkable diversity, both in terms of their diets and the colored spots that appear on the elytra in the adult stage. Transcriptomic data from H. vigintioctopunctata at different life stages would be useful for further investigating the genetic basis of this dietary diversity and the formation of the colored spots in ladybird beetles, as well as revealing the population dynamics of H. vigintioctopunctata, which could be useful in pest control. Here, we generated a comprehensive RNA-seq data set (a total of ~24 Gb of clean data) for H. vigintioctopunctata by sequencing samples collected at different life stages. We characterized the transcriptomes of each of the four life stages (egg, larva, pupa, adult) and generated a high-coverage pool by combining all the RNA-seq reads. Furthermore, we identified a catalog of simple sequence repeat (SSR) markers. This represents the first study to collect transcriptome data from all life stages of a ladybird beetle.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun-Yuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
- LPS, Nanjing Institute of Geology and Paleontology, CAS, Nanjing 210008, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
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19
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Campbell LJ, Hammond SA, Price SJ, Sharma MD, Garner TWJ, Birol I, Helbing CC, Wilfert L, Griffiths AGF. A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations. Mol Ecol 2018; 27:1413-1427. [PMID: 29420865 DOI: 10.1111/mec.14528] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 01/01/2023]
Abstract
Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read-filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in nonlaboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception among others. A large proportion of potential noncoding RNA transcripts present in our differentially expressed set provide first evidence of a possible role for long noncoding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from positive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild.
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Affiliation(s)
- Lewis J Campbell
- Environment and Sustainability Institute, University of Exeter, Penryn, UK.,Institute of Zoology, Zoological Society of London, London, UK
| | - Stewart A Hammond
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Stephen J Price
- Institute of Zoology, Zoological Society of London, London, UK.,UCL Genetics Institute, University College London, London, UK
| | - Manmohan D Sharma
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Caren C Helbing
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Lena Wilfert
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
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20
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Zhang QL, Zhang L, Yang XZ, Wang XT, Li XP, Wang J, Chen JY, Yuan ML. Comparative transcriptomic analysis of Tibetan Gynaephora to explore the genetic basis of insect adaptation to divergent altitude environments. Sci Rep 2017; 7:16972. [PMID: 29208990 PMCID: PMC5717227 DOI: 10.1038/s41598-017-17051-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/21/2017] [Indexed: 01/01/2023] Open
Abstract
Adaptation of insects to different altitudes remain largely unknown, especially those endemic to the Tibetan Plateau (TP). Here, we generated the transcriptomes of Gynaephora menyuanensis and G. alpherakii, inhabiting different high altitudes on the TP, and used these and the previously available transcriptomic and genomic sequences from low-altitude insects to explore potential genetic basis for divergent high-altitude adaptation in Gynaephora. An analysis of 5,869 orthologous genes among Gynaephora and other three low-altitude insects uncovered that fast-evolving genes and positively selected genes (PSGs) in the two Gynaephora species were enriched in energy metabolism and hypoxia response categories (e.g. mitochondrion, oxidation-reduction process, and response to oxidative stress). Particularly, mTOR signaling pathway involving hypoxia was enriched by PSGs, indicating this well-known pathway in mammal hypoxia adaptation may be an important signaling system in Gynaephora. Furthermore, some PSGs were associated with response to hypoxia (e.g. cytochrome proteins), cold (e.g. dehydrogenase) and DNA repair (e.g. DNA repair proteins). Interestingly, several insect-specific genes that were associated with exoskeleton and cuticle development (e.g. chitinase and ecdysteroids) had experienced positive selection, suggesting the specific adaptive mechanisms in insects. This study is favourable for understanding the adaptive evolution of Gynaephora and even TP insects to divergent altitudes.
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Affiliation(s)
- Qi-Lin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China.,Evo-devo Institute, School of Life Science, Nanjing University, Nanjing 210023, China; Nanjing Institute of Geology and Paleontology, Nanjing, 210008, China
| | - Li Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of, Agriculture, China
| | - Xing-Zhuo Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of, Agriculture, China
| | - Xiao-Tong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xiao-Peng Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Juan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jun-Yuan Chen
- Evo-devo Institute, School of Life Science, Nanjing University, Nanjing 210023, China; Nanjing Institute of Geology and Paleontology, Nanjing, 210008, China.
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China. .,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of, Agriculture, China.
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22
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Kang J, Ma X, He S. Evidence of high-altitude adaptation in the glyptosternoid fish, Creteuchiloglanis macropterus from the Nujiang River obtained through transcriptome analysis. BMC Evol Biol 2017; 17:229. [PMID: 29169322 PMCID: PMC5701497 DOI: 10.1186/s12862-017-1074-0] [Citation(s) in RCA: 16] [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: 07/03/2017] [Accepted: 11/15/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Organisms living at high altitudes face low oxygen and temperature conditions; thus, the genetic mechanisms underlying the adaptations in these organisms merit investigation. The glyptosternoid fish, Creteuchiloglanis macropterus mainly inhabits regions with gradual increases in altitudes along the Nujiang River and might serve as an appropriate evolutionary model for detecting adaptation processes in environments with altitude changes. RESULTS We constructed eleven RNA-sequencing (RNA-seq) libraries of C. macropterus collected from five locations at different altitudes to identify the genetic signatures of high-altitude adaptation. The comparative genomic analysis indicated that C. macropterus has an accelerated evolutionary rate compared with that of fishes in the lowland, and fishes at higher altitudes might evolve faster. Functional enrichment analysis of the fast-evolving and positively selected genes, differentially expressed genes and highly expressed genes, showed that these genes were involved in many functions related to energy metabolism and hypoxia. CONCLUSIONS Our study provides evidence of high-altitude adaptation in C. macropterus, and the detected adaptive genes might be a resource for future investigations of adaptations to high-altitude environments in other fishes.
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Affiliation(s)
- Jingliang Kang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Science, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 China
- University of the Chinese Academy of Science, Beijing, China
| | - Xiuhui Ma
- College of Animal Science, Guizhou University, Guiyang, Guizhou 550025 China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Science, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 China
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23
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Huang Y, Xiong JL, Gao XC, Sun XH. Transcriptome analysis of the Chinese giant salamander ( Andrias davidianus) using RNA-sequencing. GENOMICS DATA 2017; 14:126-131. [PMID: 29159068 PMCID: PMC5675895 DOI: 10.1016/j.gdata.2017.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/21/2017] [Accepted: 10/21/2017] [Indexed: 12/21/2022]
Abstract
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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24
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Zhang L, Zhang QL, Wang XT, Yang XZ, Li XP, Yuan ML. Selection of reference genes for qRT-PCR and expression analysis of high-altitude-related genes in grassland caterpillars (Lepidoptera: Erebidae: Gynaephora) along an altitude gradient. Ecol Evol 2017; 7:9054-9065. [PMID: 29152197 PMCID: PMC5677504 DOI: 10.1002/ece3.3431] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 08/19/2017] [Accepted: 08/31/2017] [Indexed: 12/19/2022] Open
Abstract
Changes in gene expression patterns can reflect the adaptation of organisms to divergent environments. Quantitative real‐time PCR (qRT‐PCR) is an important tool for ecological adaptation studies at the gene expression level. The quality of the results of qRT‐PCR analysis largely depends on the availability of reliable reference genes (RGs). To date, reliable RGs have not been determined for adaptive evolution studies in insects using a standard approach. Here, we evaluated the reliability of 17 candidate RGs for five Gynaephora populations inhabiting various altitudes of the Tibetan Plateau (TP) using four independent (geNorm, NormFinder, BestKeeper, and the deltaCt method) and one comprehensive (RefFinder) algorithms. Our results showed that EF1‐α, RPS15, and RPS13 were the top three most suitable RGs, and a combination of these three RGs was the most optimal for normalization. Conversely, RPS2,ACT, and RPL27 were the most unstable RGs. The expression profiles of two target genes (HSP70 and HSP90) were used to confirm the reliability of the chosen RGs. Additionally, the expression patterns of four other genes (GPI,HIF1A,HSP20, and USP) associated with adaptation to extreme environments were assessed to explore the adaptive mechanisms of TP Gynaephora species to divergent environments. Each of these six target genes showed discrepant expression patterns among the five populations, suggesting that the observed expression differences may be associated with the local adaptation of Gynaephora to divergent altitudinal environments. This study is a useful resource for studying the adaptive evolution of TP Gynaephora to divergent environments using qRT‐PCR, and it also acts as a guide for selecting suitable RGs for ecological and evolutionary studies in insects.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Grassland Agro-Ecosystems College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Qi-Lin Zhang
- State Key Laboratory of Pharmaceutical Biotechnology School of Life Sciences Nanjing University Nanjing China
| | - Xiao-Tong Wang
- State Key Laboratory of Grassland Agro-Ecosystems College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Xing-Zhuo Yang
- State Key Laboratory of Grassland Agro-Ecosystems College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Xiao-Peng Li
- State Key Laboratory of Grassland Agro-Ecosystems College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
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25
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Pastenes L, Valdivieso C, Di Genova A, Travisany D, Hart A, Montecino M, Orellana A, Gonzalez M, Gutiérrez RA, Allende ML, Maass A, Méndez MA. Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa. Sci Rep 2017; 7:1966. [PMID: 28512324 PMCID: PMC5434060 DOI: 10.1038/s41598-017-01982-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 04/06/2017] [Indexed: 11/18/2022] Open
Abstract
The anuran Rhinella spinulosa is distributed along the Andes Range at altitudes that undergo wide daily and seasonal variation in temperature. One of the populations inhabits geothermal streams, a stable environment that influences life history traits such as the timing of metamorphosis. To investigate whether this population has undergone local adaptation to this unique habitat, we carried out transcriptome analyses in animals from two localities in two developmental stages (prometamorphic and metamorphic) and exposed them to two temperatures (20 and 25 °C). RNA-Seq, de novo assembly and annotation defined a transcriptome revealing 194,469 high quality SNPs, with 1,507 genes under positive selection. Comparisons among the experimental conditions yielded 1,593 differentially expressed genes. A bioinformatics search for candidates revealed a total of 70 genes that are highly likely to be implicated in the adaptive response of the population living in a stable environment, compared to those living in an environment with variable temperatures. Most importantly, the population inhabiting the geothermal environment showed decreased transcriptional plasticity and reduced genetic variation compared to its counterpart from the non-stable environment. This analysis will help to advance the understanding of the molecular mechanisms that account for the local adaptation to geothermal streams in anurans.
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Affiliation(s)
- Luis Pastenes
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.,Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Av. San Miguel 3605, Talca, Chile
| | - Camilo Valdivieso
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.,Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Alex Di Genova
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.,Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Dante Travisany
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.,Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Andrew Hart
- Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Martín Montecino
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.,Centro de Investigaciones Biomédicas, Universidad Andrés Bello, República 239, Santiago, Chile
| | - Ariel Orellana
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile
| | - Mauricio Gonzalez
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.,Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Líbano 5524, Santiago, Chile
| | | | - Miguel L Allende
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.,Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Alejandro Maass
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile.,Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, Santiago, Chile.,Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Marco A Méndez
- Center for Genome Regulation, Blanco Encalada 2085, Santiago, Chile. .,Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile. .,Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile.
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26
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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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27
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Zhang QL, Zhang L, Zhao TX, Wang J, Zhu QH, Chen JY, Yuan ML. Gene sequence variations and expression patterns of mitochondrial genes are associated with the adaptive evolution of two Gynaephora species (Lepidoptera: Lymantriinae) living in different high-elevation environments. Gene 2017; 610:148-155. [DOI: 10.1016/j.gene.2017.02.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 01/05/2017] [Accepted: 02/06/2017] [Indexed: 01/06/2023]
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28
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Ji R, Wang Y, Cheng Y, Zhang M, Zhang HB, Zhu L, Fang J, Zhu-Salzman K. Transcriptome Analysis of Green Peach Aphid ( Myzus persicae): Insight into Developmental Regulation and Inter-Species Divergence. FRONTIERS IN PLANT SCIENCE 2016; 7:1562. [PMID: 27812361 PMCID: PMC5072348 DOI: 10.3389/fpls.2016.01562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Green peach aphid (Myzus persicae) and pea aphid (Acyrthosiphon pisum) are two phylogenetically closely related agricultural pests. While pea aphid is restricted to Fabaceae, green peach aphid feeds on hundreds of plant species from more than 40 families. Transcriptome comparison could shed light on the genetic factors underlying the difference in host range between the two species. Furthermore, a large scale study contrasting gene expression between immature nymphs and fully developed adult aphids would fill a previous knowledge gap. Here, we obtained transcriptomic sequences of green peach aphid nymphs and adults, respectively, using Illumina sequencing technology. A total of 2244 genes were found to be differentially expressed between the two developmental stages, many of which were associated with detoxification, hormone production, cuticle formation, metabolism, food digestion, and absorption. When searched against publically available pea aphid mRNA sequences, 13,752 unigenes were found to have no homologous counterparts. Interestingly, many of these unigenes that could be annotated in other databases were involved in the "xenobiotics biodegradation and metabolism" pathway, suggesting the two aphids differ in their adaptation to secondary metabolites of host plants. Conversely, 3989 orthologous gene pairs between the two species were subjected to calculations of synonymous and nonsynonymous substitutions, and 148 of the genes potentially evolved in response to positive selection. Some of these genes were predicted to be associated with insect-plant interactions. Our study has revealed certain molecular events related to aphid development, and provided some insight into biological variations in two aphid species, possibly as a result of host plant adaptation.
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Affiliation(s)
- Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural SciencesNanjing, China
- Department of Entomology, Texas A&M UniversityCollege Station, TX, USA
| | - Yujun Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
| | - Yanbin Cheng
- Department of Plant Pathology and Microbiology, Texas A&M UniversityCollege Station, TX, USA
| | - Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jichao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Keyan Zhu-Salzman
- Department of Entomology, Texas A&M UniversityCollege Station, TX, USA
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29
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Yang W, Qi Y, Fu J. Genetic signals of high-altitude adaptation in amphibians: a comparative transcriptome analysis. BMC Genet 2016; 17:134. [PMID: 27716028 PMCID: PMC5048413 DOI: 10.1186/s12863-016-0440-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High-altitude adaptation provides an excellent system for studying how organisms cope with multiple environmental stressors and interacting genetic modifications. To explore the genetic basis of high-altitude adaptation in poikilothermic animals, we acquired transcriptome sequences from a high-altitude population and a low-altitude population of the Asiatic toad (Bufo gargarizans). Transcriptome data from another high-altitude amphibian, Rana kukunoris and its low-altitude relative R. chensiensis, which are from a previous study, were also incorporated into our comparative analysis. RESULTS More than 40,000 transcripts were obtained from each transcriptome, and 5107 one-to-one orthologs were identified among the four taxa for comparative analysis. A total of 29 (Bufo) and 33 (Rana) putative positively selected genes were identified for the two high-altitude species, which were mainly concentrated in nutrient metabolism related functions. Using SNP-tagging and FST outlier analysis, we further tested 89 other nutrient metabolism related genes for signatures of natural selection, and found that two genes, CAPN2 and ITPR1, were likely under balancing selection. We did not detect any positively selected genes associated with response to hypoxia. CONCLUSIONS Amphibians clearly employ different genetic mechanisms for high-altitude adaptation compared to endotherms. Modifications of genes associated with nutrient metabolism feature prominently while genes related to hypoxia tolerance appear to be insignificant. Poikilotherms represent the majority of animal diversity, and we hope that our results will provide useful directions for future studies of amphibians as well as other poikilotherms.
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Affiliation(s)
- Weizhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Present address: Department of Biology, Lund University, 223 62, Lund, Sweden
| | - Yin Qi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Department of Integrative Biology, University of Guelph, Guelph, N1G 2 W1, ON, Canada.
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30
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Guo B, Lu D, Liao WB, Merilä J. Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toadBufo andrewsi. Mol Ecol 2016; 25:3884-900. [PMID: 27289071 DOI: 10.1111/mec.13722] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 06/02/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Baocheng Guo
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Di Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Juha Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
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31
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Zhao J, He K, Peng Y, Wu X, Sun S. Net neutral effects of a generalist vertebrate predator on seed production result from simultaneous suppression of plant antagonists and mutualists. Basic Appl Ecol 2016. [DOI: 10.1016/j.baae.2015.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Characterizing the transcriptome and molecular markers information for roach, Rutilus rutilus. J Genet 2016; 95:45-51. [PMID: 27019431 DOI: 10.1007/s12041-015-0597-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Rutilus rutilus (roach) is native to most of Europe and western Asia, and the Irtysh River basin in Sinkiang, northwest China is the marginal area of their natural distribution. The wide distribution and unique characteristic of this species makes it an ideal model for analysing ecological and comparative genomics. However, the limited genome sequences available for this species have hindered these investigations. Transcriptomes from the brains and livers of five individuals collected from the Irtysh River basin were sequenced using Illumina paired-end sequencing technology. A collection of 132,289 unigenes for this species were obtained using a de novo assembly method based on nearly 120 million clean reads encompassing more than 14 Gb data. Approximately 37.5% (49,656), 27.1% (35,867) and 21.2% (27,987) of the transcriptome had homologues deposited in Nt, Nr and Swiss-Prot, respectively; 12.3% (16,328) were assigned to eukaryotic orthologous groups of proteins classifications, and 21.5% (28,429) harboured Interpro domains. On the basis of the assembled transcriptome, we detected 177,493 single-nuc leotide variation resident in 39.3% (52,029) of the sequences and 20.8% (27,497) of the sequences harbouring 36,639 simple sequence repeats. The identified molecular markers are a basis for further ecological analysis, and the transcriptome reported here allows for more extensive evolutionary analyses of the Cyprinidae, the most species-rich family of freshwater fishes.
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33
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Yang X, Wang Y, Zhang Y, Lee WH, Zhang Y. Rich diversity and potency of skin antioxidant peptides revealed a novel molecular basis for high-altitude adaptation of amphibians. Sci Rep 2016; 6:19866. [PMID: 26813022 PMCID: PMC4728494 DOI: 10.1038/srep19866] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/18/2015] [Indexed: 12/20/2022] Open
Abstract
Elucidating the mechanisms of high-altitude adaptation is an important research area in modern biology. To date, however, knowledge has been limited to the genetic mechanisms of adaptation to the lower oxygen and temperature levels prevalent at high altitudes, with adaptation to UV radiation largely neglected. Furthermore, few proteomic or peptidomic analyses of these factors have been performed. In this study, the molecular adaptation of high-altitude Odorrana andersonii and cavernicolous O. wuchuanensis to elevated UV radiation was investigated. Compared with O. wuchuanensis, O. andersonii exhibited greater diversity and free radical scavenging potentiality of skin antioxidant peptides to cope with UV radiation. This implied that O. andersonii evolved a much more complicated and powerful skin antioxidant peptide system to survive high-altitude UV levels. Our results provided valuable peptidomic clues for understanding the novel molecular basis for adaptation to high elevation habitats.
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Affiliation(s)
- Xinwang Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Chinese Academy of Sciences &Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.,Department of Anatomy and Histology &Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, China
| | - Ying Wang
- Key Laboratory of Chemistry in Ethnic Medicine Resource, State Ethnic Affairs Commission &Ministry of Education, School of Ethnic Medicine, Yunnan Minzu University, Kunming 650500, China
| | - Yue Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Chinese Academy of Sciences &Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Wen-Hui Lee
- Key Laboratory of Animal Models and Human Disease Mechanisms, Chinese Academy of Sciences &Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Yun Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Chinese Academy of Sciences &Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
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34
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Transcriptomes reveal the genetic mechanisms underlying ionic regulatory adaptations to salt in the crab-eating frog. Sci Rep 2015; 5:17551. [PMID: 26619819 PMCID: PMC4664912 DOI: 10.1038/srep17551] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/30/2015] [Indexed: 12/12/2022] Open
Abstract
The crab-eating frog, Fejervarya cancrivora, is the only frog that lives near seas. It tolerates increased environmental concentrations of sodium, chloride and potassium partly by raising ion and urea levels in its blood plasma. The molecular mechanism of the adaptation remains rarely documented. Herein, we analyze transcriptomes of the crab-eating frog and its closely related saline-intolerant species, F. limnocharis, to explore the molecular basis of adaptations to such extreme environmental conditions. Analyses reveal the potential genetic mechanism underlying the adaptation to salinity for the crab-eating frog. Genes in categories associated with ion transport appear to have evolved rapidly in F. cancrivora. Both positively selected and differentially expressed genes exhibit enrichment in the GO category regulation of renal sodium excretion. In this category, the positively selected sites of ANPEP and AVPR2 encode CD13 and V2 receptors, respectively; they fall precisely on conserved domains. More differentially expressed rapidly evolved genes occur in the kidney of F. cancrivora than in F. limnocharis. Four genes involved in the regulation of body fluid levels show signs of positive selection and increased expression. Significant up-regulation occurs in several genes of F. cancrivora associated with renin-angiotensin system and aldosterone-regulated sodium reabsorption pathways, which relate to osmotic regulation.
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35
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Shao Y, Li JX, Ge RL, Zhong L, Irwin DM, Murphy RW, Zhang YP. Genetic adaptations of the plateau zokor in high-elevation burrows. Sci Rep 2015; 5:17262. [PMID: 26602147 PMCID: PMC4658562 DOI: 10.1038/srep17262] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022] Open
Abstract
The plateau zokor (Myospalax baileyi) spends its entire life underground in sealed burrows. Confronting limited oxygen and high carbon dioxide concentrations, and complete darkness, they epitomize a successful physiological adaptation. Here, we employ transcriptome sequencing to explore the genetic underpinnings of their adaptations to this unique habitat. Compared to Rattus norvegicus, genes belonging to GO categories related to energy metabolism (e.g. mitochondrion and fatty acid beta-oxidation) underwent accelerated evolution in the plateau zokor. Furthermore, the numbers of positively selected genes were significantly enriched in the gene categories involved in ATPase activity, blood vessel development and respiratory gaseous exchange, functional categories that are relevant to adaptation to high altitudes. Among the 787 genes with evidence of parallel evolution, and thus identified as candidate genes, several GO categories (e.g. response to hypoxia, oxygen homeostasis and erythrocyte homeostasis) are significantly enriched, are two genes, EPAS1 and AJUBA, involved in the response to hypoxia, where the parallel evolved sites are at positions that are highly conserved in sequence alignments from multiple species. Thus, accelerated evolution of GO categories, positive selection and parallel evolution at the molecular level provide evidences to parse the genetic adaptations of the plateau zokor for living in high-elevation burrows.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
| | - Jin-Xiu Li
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
| | - Ri-Li Ge
- Key Laboratory for High Altitude Medicine of Ministry of Chinese Education and Research Center for High Altitude Medicine, Qinghai University, Xining 810001, China
| | - Li Zhong
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, M5S 1A8, Canada.,Banting and Best Diabetes Centre, University of Toronto, Ontario, M5S 1A8, Canada
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ont., M5S 2C6, Canada
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.,Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
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36
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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37
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Wang Y, Yang L, Zhou K, Zhang Y, Song Z, He S. Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes. Genome Biol Evol 2015; 7:2970-82. [PMID: 26454018 PMCID: PMC5635588 DOI: 10.1093/gbe/evv192] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, and Triplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.
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Affiliation(s)
- Ying Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China University of the 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 University of the Chinese Academy of Sciences, Beijing, China
| | - Kun Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan, China
| | - Yanping Zhang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics Breeding, Gansu Fishers Research Institute, Lanzhou, China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 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
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38
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Wang Y, Yang L, Wu B, Song Z, He S. Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes. Gene 2015; 565:211-20. [DOI: 10.1016/j.gene.2015.04.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 12/28/2022]
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39
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Yang Y, Wang L, Han J, Tang X, Ma M, Wang K, Zhang X, Ren Q, Chen Q, Qiu Q. Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude Lizard living in the Qinghai-Tibet Plateau. BMC Evol Biol 2015; 15:101. [PMID: 26031664 PMCID: PMC4450828 DOI: 10.1186/s12862-015-0371-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Organisms living at high altitudes must overcome three major environmental challenges: hypoxia, cold, and intense UV radiation. The molecular mechanisms that enable these challenges to be overcome have mainly been studied in endothermic organisms; relatively little attention has been paid to poikilothermic species. Here, we present deep transcriptome sequencing in two closely related lizards, the high altitude-dwelling Phrynocephalus erythrurus and the lowland-dwelling P. putjatia, to identify candidate genes under positive selection and to explore the convergent evolutionary adaptation of poikilothermic animals to high altitude life. RESULTS More than 70 million sequence reads were generated for each species via Illumina sequencing. De novo assembly produced 56,845 and 63,140 transcripts for P. erythrurus and P. putjatia, respectively. P. erythrurus had higher Ka/Ks ratios than P. putjatia, implying an accelerated evolutionary rate in the high altitude lizard lineage. 206 gene ontology (GO) categories with accelerated evolutionary rates and 43 candidate positively selected genes were detected along the P. erythrurus lineage. Some of these GO categories have functions associated with responses to hypoxia, energy metabolism and responses to UV damage. We also found that the high-altitude ranid frog R. kukunoris had higher Ka/Ks ratios than the closely related low-altitude frog R. chensinensis, and that the functional categories with accelerated evolutionary rates in R. kukunoris overlapped extensively with those detected along the P. erythrurus lineage. CONCLUSIONS The mechanisms of high altitude adaptation in P. erythrurus were tentatively inferred. By comparing two pairs of low- and high-altitude poikilothermic species, we found that similar functional categories had undergone positive selection in high altitude-dwelling Phrynocephalus and Rana lineages, indicating that similar mechanisms of adaptation to high altitude might have evolved in both genera. Our findings provide important guidance for future functional studies on high altitude adaptation in poikilothermic animals.
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Affiliation(s)
- Yongzhi Yang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Lizhong Wang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Jin Han
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Xiaolong Tang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Ming Ma
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Kun Wang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Xiao Zhang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Qian Ren
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Qiang Chen
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Qiang Qiu
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
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Pardo-Diaz C, Salazar C, Jiggins CD. Towards the identification of the loci of adaptive evolution. Methods Ecol Evol 2015; 6:445-464. [PMID: 25937885 PMCID: PMC4409029 DOI: 10.1111/2041-210x.12324] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022]
Abstract
1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature.
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Affiliation(s)
- Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Chris D Jiggins
- Department of Zoology, University of CambridgeDowning Street, Cambridge, CB2 3EJ, UK
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Addis BR, Lowe WH, Hossack BR, Allendorf FW. Population genetic structure and disease in montane boreal toads: more heterozygous individuals are more likely to be infected with amphibian chytrid. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0704-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Shaffer HB, Gidiş M, McCartney-Melstad E, Neal KM, Oyamaguchi HM, Tellez M, Toffelmier EM. Conservation genetics and genomics of amphibians and reptiles. Annu Rev Anim Biosci 2015; 3:113-38. [PMID: 25580719 DOI: 10.1146/annurev-animal-022114-110920] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.
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Yang W, Qi Y, Fu J. Exploring the genetic basis of adaptation to high elevations in reptiles: a comparative transcriptome analysis of two toad-headed agamas (genus Phrynocephalus). PLoS One 2014; 9:e112218. [PMID: 25386640 PMCID: PMC4227734 DOI: 10.1371/journal.pone.0112218] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 10/10/2014] [Indexed: 12/05/2022] Open
Abstract
High elevation adaptation offers an excellent study system to understand the genetic basis of adaptive evolution. We acquired transcriptome sequences of two closely related lizards, Phrynocephalus przewalskii from low elevations and P. vlangalii from high elevations. Within a phylogenetic framework, we compared their genomic data along with green anole, chicken and Chinese softshell turtle, and identified candidate genes and functional categories that are potentially linked to adaptation to high elevation environments. More than 100 million sequence reads were generated for each species via Illumina sequencing. A de novo assembly produced 70,919 and 62,118 transcripts for P. przewalskii and P. vlangalii, respectively. Based on a well-established reptile phylogeny, we detected 143 positively selected genes (PSGs) along the P. vlangalii lineage from the 7,012 putative orthologs using a branch-site model. Furthermore, ten GO categories and one KEGG pathway that are over-represented by PSGs were recognized. In addition, 58 GO categories were revealed to have elevated evolutionary rates along the P. vlangalii lineage relative to P. przewalskii. These functional analyses further filter out PSGs that are most likely involved in the adaptation process to high elevations. Among them, ADAM17, MD, and HSP90B1 likely contributed to response to hypoxia, and POLK likely contributed to DNA repair. Many other candidate genes involved in gene expression and metabolism were also identified. Genome-wide scan for candidate genes may serve as the first step to explore the genetic basis of high elevation adaptation. Detailed comparative study and functional verification are needed to solidify any conclusions. High elevation adaptation requires coordinated changes in multiple genes that involve various physiological and biochemical pathways; we hope that our genetic studies will provide useful directions for future physiological or molecular studies in reptiles as well as other poikilothermic species.
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Affiliation(s)
- Weizhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yin Qi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Qi Y, Lu B, Gao H, Hu P, Fu J. Hybridization and mitochondrial genome introgression between Rana chensinensis and R. kukunoris. Mol Ecol 2014; 23:5575-88. [PMID: 25308955 DOI: 10.1111/mec.12960] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 02/01/2023]
Abstract
Mitochondrial genome (mito-genome) introgression among metazoans is commonplace, and several biological processes may promote such introgression. We examined two proposed processes for the mito-genome introgression between Rana chensinensis and R. kukunoris: natural hybridization and sex-biased dispersal. We sampled 477 individuals from 28 sites in the potential hybrid zone in the western Tsinling Mountains. Mitochondrial gene (cyt-b) trees were used to examine the introgression events. Microsatellite DNA loci, cyt-b and morphological data were used to identify hybrids and to examine the extent of natural hybridization. We detected rampant bidirectional introgressions, both ancient and recent, between the two species. Furthermore, we found a wide hybrid zone, and frequent and asymmetric hybridization. The hybrid zone cline analysis revealed a clear mitochondrial-nuclear discordance; while most nuclear markers displayed similar and steep clines, cyt-b had a displaced cline centre and a more gradual and wider cline. We also detected strong and asymmetric historical maternal gene flow across the hybrid zone. This widespread hybridization and detected low mito-nuclear conflicts may, at least partially, explain the high frequency of introgression. Lastly, microsatellite data and population genetic methods were used to assess sex-biased dispersal. A weak pattern of female-biased dispersal was detected in both species, suggesting it may not play an important role in the observed introgression. Our data are consistent with the hybridization hypothesis, but support for the sex-biased dispersal hypothesis is weak. We further suggest that selective advantages of the R. kukunoris-type mito-genome in thermal adaptation may also contribute to the introgression between the two species.
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Affiliation(s)
- Yin Qi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
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Regnault C, Worms IAM, Oger-Desfeux C, MelodeLima C, Veyrenc S, Bayle ML, Combourieu B, Bonin A, Renaud J, Raveton M, Reynaud S. Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: transcriptomic and metabolic evidence. BMC Genomics 2014; 15:666. [PMID: 25103525 PMCID: PMC4141109 DOI: 10.1186/1471-2164-15-666] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/30/2014] [Indexed: 12/20/2022] Open
Abstract
Background Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. Amongst the most common aquatic contaminants, polycyclic aromatic hydrocarbons (PAHs) have been shown to induce several adverse effects on amphibian species in the larval stages. Conversely, adults exposed to high concentrations of the ubiquitous PAH, benzo[a]pyrene (BaP), tolerate the compound thanks to their highly efficient hepatic detoxification mechanisms. Due to this apparent lack of toxic effect on adults, no studies have examined in depth the potential toxicological impact of PAH on the physiology of adult amphibian livers. This study sheds light on the hepatic responses of Xenopus tropicalis when exposed to high environmentally relevant concentrations of BaP, by combining a high throughput transcriptomic approach (mRNA deep sequencing) and a characterization of cellular and physiological modifications to the amphibian liver. Results Transcriptomic changes observed in BaP-exposed Xenopus were further characterized using a time-dependent enrichment analysis, which revealed the pollutant-dependent gene regulation of important biochemical pathways, such as cholesterol biosynthesis, insulin signaling, adipocytokines signaling, glycolysis/gluconeogenesis and MAPK signaling. These results were substantiated at the physiological level with the detection of a pronounced metabolic disorder resulting in a possible insulin resistance-like syndrome phenotype. Hepatotoxicity induced by lipid and cholesterol metabolism impairments was clearly identified in BaP-exposed individuals. Conclusions Our data suggested that BaP may disrupt overall liver physiology, and carbohydrate and cholesterol metabolism in particular, even after short-term exposure. These results are further discussed in terms of how this deregulation of liver physiology can lead to general metabolic impairment in amphibians chronically exposed to contaminants, thereby illustrating the role xenobiotics might play in the global decline in amphibian populations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-666) contains supplementary material, which is available to authorized users.
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Savage AE, Kiemnec-Tyburczy KM, Ellison AR, Fleischer RC, Zamudio KR. Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes. Gene 2014; 542:98-108. [PMID: 24680726 DOI: 10.1016/j.gene.2014.03.051] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/06/2014] [Accepted: 03/26/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Frogs are a diverse group of vertebrates for which limited genomic resources are available. Natural frog populations face a multitude of threats, including habitat degradation, infectious disease, and environmental change. Characterizing the functional genomics of anuran tissues in general - and the immune system in particular - will enhance our knowledge of genetic and epigenetic responses to environmental threats and inform conservation and recovery efforts. RESULTS To increase the number of species with genomic datasets and characterize gene expression in immune-related tissues, we sequenced the transcriptomes of three tissues from two frogs (Espadarana prosoblepon and Lithobates yavapaiensis) on the Roche 454 GS FLX platform. Our sequencing produced 8881 E. prosoblepon and 5428 L. yavapaiensis annotated gene products after de novo assembly and Gene Ontology classification. Transcripts of the innate and acquired immune system were expressed in all three tissues. Inflammatory response and acquired immunity transcripts were significantly more diverged between E. prosoblepon and L. yavapaiensis compared to innate immunity and immune system development transcripts. Immune-related transcripts did not show an overall elevated rate of functional evolution, with the exception of glycosyl proteases, which include lysozymes, central bacterial and fungal-killing enzymes of the innate immune system. CONCLUSIONS The three frog transcriptomes provide more than 600 Mbp of new genomic data, and will serve as a valuable framework for future comparative studies of non-model anurans. Additionally, we show that immune gene divergence varies by functional group and that transcriptome studies can be useful in comparing rates of evolutionary change across gene families.
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Affiliation(s)
- Anna E Savage
- Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013, United States; Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Karen M Kiemnec-Tyburczy
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Amy R Ellison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Robert C Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013, United States.
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
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Che R, Sun Y, Wang R, Xu T. Transcriptomic analysis of endangered Chinese salamander: identification of immune, sex and reproduction-related genes and genetic markers. PLoS One 2014; 9:e87940. [PMID: 24498226 PMCID: PMC3909259 DOI: 10.1371/journal.pone.0087940] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/01/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The Chinese salamander (Hynobius chinensis), an endangered amphibian species of salamander endemic to China, has attracted much attention because of its value of studying paleontology evolutionary history and decreasing population size. Despite increasing interest in the Hynobius chinensis genome, genomic resources for the species are still very limited. A comprehensive transcriptome of Hynobius chinensis, which will provide a resource for genome annotation, candidate genes identification and molecular marker development should be generated to supplement it. PRINCIPAL FINDINGS We performed a de novo assembly of Hynobius chinensis transcriptome by Illumina sequencing. A total of 148,510 nonredundant unigenes with an average length of approximately 580 bp were obtained. In all, 60,388 (40.66%) unigenes showed homologous matches in at least one database and 33,537 (22.58%) unigenes were annotated by all four databases. In total, 41,553 unigenes were categorized into 62 sub-categories by BLAST2GO search, and 19,468 transcripts were assigned to 140 KEGG pathways. A large number of unigenes involved in immune system, local adaptation, reproduction and sex determination were identified, as well as 31,982 simple sequence repeats (SSRs) and 460,923 putative single nucleotide polymorphisms (SNPs). CONCLUSION This dataset represents the first transcriptome analysis of the Chinese salamander (Hynobius chinensis), an endangered species, to be also the first time of hynobiidae. The transcriptome will provide valuable resource for further research in discovery of new genes, protection of population, adaptive evolution and survey of various pathways, as well as development of molecule markers in Chinese salamander; and reference information for closely related species.
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Affiliation(s)
- Rongbo Che
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Yuena Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Rixin Wang
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
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Wu X, Zhang C, Griffin JN, Sun S. The brown-world role of insectivores: Frogs reduce plant growth by suppressing detritivores in an alpine meadow. Basic Appl Ecol 2014. [DOI: 10.1016/j.baae.2013.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hendrickson SL. A genome wide study of genetic adaptation to high altitude in feral Andean Horses of the páramo. BMC Evol Biol 2013; 13:273. [PMID: 24344830 PMCID: PMC3878729 DOI: 10.1186/1471-2148-13-273] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 12/03/2013] [Indexed: 12/25/2022] Open
Abstract
Background Life at high altitude results in physiological and metabolic challenges that put strong evolutionary pressure on performance due to oxidative stress, UV radiation and other factors dependent on the natural history of the species. To look for genes involved in altitude adaptation in a large herbivore, this study explored genome differentiation between a feral population of Andean horses introduced by the Spanish in the 1500s to the high Andes and their Iberian breed relatives. Results Using allelic genetic models and Fst analyses of ~50 K single nucleotide polymorphisms (SNPs) across the horse genome, 131 candidate genes for altitude adaptation were revealed (Bonferoni of p ≤ 2 × 10–7). Significant signals included the EPAS1 in the hypoxia-induction-pathway (HIF) that was previously discovered in human studies (p = 9.27 × 10-8); validating the approach and emphasizing the importance of this gene to hypoxia adaptation. Strong signals in the cytochrome P450 3A gene family (p = 1.5 ×10-8) indicate that other factors, such as highly endemic vegetation in altitude environments are also important in adaptation. Signals in tenuerin 2 (TENM2, p = 7.9 × 10-14) along with several other genes in the nervous system (gene categories representation p = 5.1 × 10-5) indicate the nervous system is important in altitude adaptation. Conclusions In this study of a large introduced herbivore, it becomes apparent that some gene pathways, such as the HIF pathway are universally important for high altitude adaptation in mammals, but several others may be selected upon based on the natural history of a species and the unique ecology of the altitude environment.
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Affiliation(s)
- Sher L Hendrickson
- Department of Biology, Shepherd University, Shepherdstown WV 25443, USA.
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50
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Wray GA. Genomics and the Evolution of Phenotypic Traits. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135828] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary genetics has entered an unprecedented era of discovery, catalyzed in large part by the development of technologies that provide information about genome sequence and function. An important benefit is the ability to move beyond a handful of model organisms in lab settings to identify the genetic basis for evolutionarily interesting traits in many organisms in natural settings. Other benefits are the abilities to identify causal mutations and validate their phenotypic consequences more readily and in many more species. Genomic technologies have reinvigorated interest in some of the most fundamental and persistent questions in evolutionary genetics, revealed previously unsuspected evolutionary phenomena, and opened the door to a wide range of new questions.
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Affiliation(s)
- Gregory A. Wray
- Department of Biology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27701
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