0
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Physiological and genetic convergence supports hypoxia resistance in high-altitude songbirds

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Skeletal muscle plays a central role in regulating glucose uptake and body metabolism; however, highland hypoxia is a severe challenge to aerobic metabolism in small endotherms. Therefore, understanding the physiological and genetic convergence of muscle hypoxia tolerance has a potential broad range of medical implications. Here we report and experimentally validate a common physiological mechanism across multiple high-altitude songbirds that improvement in insulin sensitivity contributes to glucose homeostasis, low oxygen consumption, and relative activity, and thus increases body weight. By contrast, low-altitude songbirds exhibit muscle loss, glucose intolerance, and increase energy expenditures under hypoxia. This adaptive mechanism is attributable to convergent missense mutations in the BNIP3L gene, and METTL8 gene that activates MEF2C expression in highlanders, which in turn increases hypoxia tolerance. Together, our findings from wild high-altitude songbirds suggest convergent physiological and genetic mechanisms of skeletal muscle in hypoxia resistance, which highlights the potentially medical implications of hypoxia-related metabolic diseases.

          Author summary

          We integrate physiological, genomic and functional experimental methods to illustrate the convergent molecular and genetic mechanisms of hypoxia resistance in wild songbirds. We find that highland native songbirds have greater body and muscle mass with an increase in insulin sensitivity and aerobic metabolism comparing to lowland songbirds. Comparative transcriptomes and functional experiments show that MEF2C is a shared overexpression gene in highland songbirds and maintains muscle mass and insulin sensitivity in hypoxia. Genetically, four genes with high genetic divergence between altitudinal tree sparrows have convergent nonsynonymous substitutions in snow finches and three of these are related with hypoxia including HBB, BNIP3L and METTL8. METTL8 may regulate the expression of MEF2C and thus increase muscle hypoxia resistance. These results uncover the physiological and genetic convergence on muscle hypoxia resistance in highland songbirds, and support novel and valuable insights into highland adaptation.

          Related collections

          Most cited references56

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              STAR: ultrafast universal RNA-seq aligner.

              Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
                Bookmark

                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: MethodologyRole: SoftwareRole: Writing – review & editing
                Role: Formal analysisRole: MethodologyRole: Writing – review & editing
                Role: Formal analysisRole: MethodologyRole: Writing – review & editing
                Role: Formal analysisRole: Writing – review & editing
                Role: Writing – review & editing
                Role: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, CA USA )
                1553-7390
                1553-7404
                28 December 2020
                December 2020
                : 16
                : 12
                : e1009270
                Affiliations
                [1 ] Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
                [2 ] University of Chinese Academy of Sciences, Beijing, China
                [3 ] National Forest Ecosystem Observation & Research Station of Nyingchi Tibet, Institute of Plateau Ecology, Tibet Agriculture & Animal Husbandry University, Linzhi City, China
                [4 ] Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agriculture & Animal Husbandry University), Ministry of Education, Linzhi City, China
                [5 ] Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
                University of Wisconsin–Madison, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0002-1415-7610
                https://orcid.org/0000-0003-1161-5716
                Article
                PGENETICS-D-20-00747
                10.1371/journal.pgen.1009270
                7793309
                33370292
                19b89172-022e-4cb0-a7cd-dd2ed67975d2
                © 2020 Xiong et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 12 May 2020
                : 2 November 2020
                Page count
                Figures: 4, Tables: 1, Pages: 22
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 31630069
                Award Recipient :
                Funded by: Strategic Priority Research Program of the Chinese Academy of Sciences
                Award ID: XDA19050202
                Award Recipient :
                Funded by: Strategic Priority Research Program of the Chinese Academy of Sciences
                Award ID: XDB13020300
                Award Recipient :
                Funded by: Second Tibetan Plateau Scientific Expedition and Research (STEP) program
                Award ID: 2019QZKK0501
                Award Recipient :
                This work was funded by National Natural Science Foundation of China (No. 31630069 to F.L.), the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant Nos. XDA19050202 and XDB13020300 to F.L.) and the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (Grant No. 2019QZKK0304 to F.L.).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Cell Biology
                Hypoxia
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Birds
                Biology and Life Sciences
                Zoology
                Animals
                Vertebrates
                Amniotes
                Birds
                Medicine and Health Sciences
                Endocrinology
                Diabetic Endocrinology
                Insulin
                Biology and Life Sciences
                Biochemistry
                Hormones
                Insulin
                Biology and Life Sciences
                Genetics
                Animal Genetics
                Bird Genetics
                Biology and Life Sciences
                Zoology
                Animal Physiology
                Vertebrate Physiology
                Bird Physiology
                Biology and Life Sciences
                Zoology
                Ornithology
                Bird Physiology
                Biology and Life Sciences
                Biochemistry
                Bioenergetics
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Anatomy
                Musculoskeletal System
                Muscles
                Skeletal Muscles
                Medicine and Health Sciences
                Anatomy
                Musculoskeletal System
                Muscles
                Skeletal Muscles
                Physical Sciences
                Chemistry
                Chemical Compounds
                Organic Compounds
                Carbohydrates
                Monosaccharides
                Glucose
                Physical Sciences
                Chemistry
                Organic Chemistry
                Organic Compounds
                Carbohydrates
                Monosaccharides
                Glucose
                Custom metadata
                vor-update-to-uncorrected-proof
                2021-01-08
                All relevant data are within the manuscript and its Supporting Information files.

                Genetics
                Genetics

                Comments

                Comment on this article