1
|
Wang Z, Song B, Yao J, Li X, Zhang Y, Tang Z, Yi G. Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs. J Anim Sci Biotechnol 2024; 15:97. [PMID: 38982489 PMCID: PMC11234542 DOI: 10.1186/s40104-024-01053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/20/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear. RESULTS Here, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments. CONCLUSIONS In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.
Collapse
Affiliation(s)
- Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China
| | - Bangmin Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Jianyu Yao
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China
| | - Yan Zhang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.
| |
Collapse
|
2
|
Gutiérrez-Guerrero YT, Phifer-Rixey M, Nachman MW. Across two continents: The genomic basis of environmental adaptation in house mice (Mus musculus domesticus) from the Americas. PLoS Genet 2024; 20:e1011036. [PMID: 38968323 PMCID: PMC11253941 DOI: 10.1371/journal.pgen.1011036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 07/17/2024] [Accepted: 06/10/2024] [Indexed: 07/07/2024] Open
Abstract
Replicated clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in putatively regulatory regions. Genes that contained the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, eye function, and the cardiovascular system. We then compared these results with the results of analyses of published data from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects. These genes are diverse, with functions relating to metabolism, immunity, cardiac function, and circadian rhythm, among others. We also found parallel shifts in allele frequency in candidate genes across latitudinal gradients. Finally, combining data from all three transects, we identified several genes associated with variation in body weight. Overall, our results provide strong evidence of shared responses to selection and identify genes that likely underlie recent environmental adaptation in house mice across North and South America.
Collapse
Affiliation(s)
- Yocelyn T. Gutiérrez-Guerrero
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Megan Phifer-Rixey
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| |
Collapse
|
3
|
Adams R, Cain Z, Assis R, DeGiorgio M. Robust Phylogenetic Regression. Syst Biol 2024; 73:140-157. [PMID: 38035624 PMCID: PMC11129599 DOI: 10.1093/sysbio/syad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023] Open
Abstract
Modern comparative biology owes much to phylogenetic regression. At its conception, this technique sparked a revolution that armed biologists with phylogenetic comparative methods (PCMs) for disentangling evolutionary correlations from those arising from hierarchical phylogenetic relationships. Over the past few decades, the phylogenetic regression framework has become a paradigm of modern comparative biology that has been widely embraced as a remedy for shared ancestry. However, recent evidence has shown doubt over the efficacy of phylogenetic regression, and PCMs more generally, with the suggestion that many of these methods fail to provide an adequate defense against unreplicated evolution-the primary justification for using them in the first place. Importantly, some of the most compelling examples of biological innovation in nature result from abrupt lineage-specific evolutionary shifts, which current regression models are largely ill equipped to deal with. Here we explore a solution to this problem by applying robust linear regression to comparative trait data. We formally introduce robust phylogenetic regression to the PCM toolkit with linear estimators that are less sensitive to model violations than the standard least-squares estimator, while still retaining high power to detect true trait associations. Our analyses also highlight an ingenuity of the original algorithm for phylogenetic regression based on independent contrasts, whereby robust estimators are particularly effective. Collectively, we find that robust estimators hold promise for improving tests of trait associations and offer a path forward in scenarios where classical approaches may fail. Our study joins recent arguments for increased vigilance against unreplicated evolution and a better understanding of evolutionary model performance in challenging-yet biologically important-settings.
Collapse
Affiliation(s)
- Richard Adams
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, USA
- Agricultural Statistics Laboratory, University of Arkansas, Fayetteville, AR, USA
| | - Zoe Cain
- Department of Biological and Environmental Sciences, Georgia College, Milledgeville, GA, USA
| | - Raquel Assis
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
| |
Collapse
|
4
|
Names GR, Grindstaff JL, Westneat DF, Heidinger BJ. Climate change and its effects on body size and shape: the role of endocrine mechanisms. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220509. [PMID: 38310941 PMCID: PMC10838645 DOI: 10.1098/rstb.2022.0509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/21/2023] [Indexed: 02/06/2024] Open
Abstract
In many organisms, rapidly changing environmental conditions are inducing dramatic shifts in diverse phenotypic traits with consequences for fitness and population viability. However, the mechanisms that underlie these responses remain poorly understood. Endocrine signalling systems often influence suites of traits and are sensitive to changes in environmental conditions; they are thus ideal candidates for uncovering both plastic and evolved consequences of climate change. Here, we use body size and shape, a set of integrated traits predicted to shift in response to rising temperatures with effects on fitness, and insulin-like growth factor-1 as a case study to explore these ideas. We review what is known about changes in body size and shape in response to rising temperatures and then illustrate why endocrine signalling systems are likely to be critical in mediating these effects. Lastly, we discuss research approaches that will advance understanding of the processes that underlie rapid responses to climate change and the role endocrine systems will have. Knowledge of the mechanisms involved in phenotypic responses to climate change will be essential for predicting both the ecological and the long-term evolutionary consequences of a warming climate. This article is part of the theme issue 'Endocrine responses to environmental variation: conceptual approaches and recent developments'.
Collapse
Affiliation(s)
- Gabrielle R. Names
- Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, Fargo, ND 58102, USA
- Biology Department, California Lutheran University, 60 West Olsen Road, Thousand Oaks, CA 91360, USA
| | | | - David F. Westneat
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, KY 40506, USA
| | - Britt J. Heidinger
- Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, Fargo, ND 58102, USA
| |
Collapse
|
5
|
Manahan DN, Nachman MW. Alternative splicing and environmental adaptation in wild house mice. Heredity (Edinb) 2024; 132:133-141. [PMID: 38012302 PMCID: PMC10923775 DOI: 10.1038/s41437-023-00663-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
A major goal of evolutionary genetics is to understand the genetic and molecular mechanisms underlying adaptation. Previous work has established that changes in gene regulation may contribute to adaptive evolution, but most studies have focused on mRNA abundance and only a few studies have investigated the role of post-transcriptional processing. Here, we use a combination of exome sequences and short-read RNA-Seq data from wild house mice (Mus musculus domesticus) collected along a latitudinal transect in eastern North America to identify candidate genes for local adaptation through alternative splicing. First, we identified alternatively spliced transcripts that differ in frequency between mice from the northern-most and southern-most populations in this transect. We then identified the subset of these transcripts that exhibit clinal patterns of variation among all populations in the transect. Finally, we conducted association studies to identify cis-acting splicing quantitative trait loci (cis-sQTL), and we identified cis-sQTL that overlapped with previously ascertained targets of selection from genome scans. Together, these analyses identified a small set of alternatively spliced transcripts that may underlie environmental adaptation in house mice. Many of these genes have known phenotypes associated with body size, a trait that varies clinally in these populations. We observed no overlap between these genes and genes previously identified by changes in mRNA abundance, indicating that alternative splicing and changes in mRNA abundance may provide separate molecular mechanisms of adaptation.
Collapse
Affiliation(s)
- David N Manahan
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA.
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA
| |
Collapse
|
6
|
Durkin SM, Ballinger MA, Nachman MW. Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice. PLoS Genet 2024; 20:e1010892. [PMID: 38306396 PMCID: PMC10866503 DOI: 10.1371/journal.pgen.1010892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/14/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Changes in gene regulation have long been appreciated as a driving force of adaptive evolution, however the relative contributions of cis- and trans-acting changes to gene regulation over short evolutionary timescales remain unclear. Instances of recent, parallel phenotypic evolution provide an opportunity to assess whether parallel patterns are seen at the level of gene expression, and to assess the relative contribution of cis- and trans- changes to gene regulation in the early stages of divergence. Here, we studied gene expression in liver and brown adipose tissue in two wild-derived strains of house mice that independently adapted to cold, northern environments, and we compared them to a strain of house mice from a warm, tropical environment. To investigate gene regulatory evolution, we studied expression in parents and allele-specific expression in F1 hybrids of crosses between warm-adapted and cold-adapted strains. First, we found that the different cold-adapted mice showed both unique and shared changes in expression, but that the proportion of shared changes (i.e. parallelism) was greater than expected by chance. Second, we discovered that expression evolution occurred largely at tissue-specific and cis-regulated genes, and that these genes were over-represented in parallel cases of evolution. Finally, we integrated the expression data with scans for selection in natural populations and found substantial parallelism in the two northern populations for genes under selection. Furthermore, selection outliers were associated with cis-regulated genes more than expected by chance; cis-regulated genes under selection influenced phenotypes such as body size, immune functioning, and activity level. These results demonstrate that parallel patterns of gene expression in mice that have independently adapted to cold environments are driven largely by tissue-specific and cis-regulatory changes, providing insight into the mechanisms of adaptive gene regulatory evolution at the earliest stages of divergence.
Collapse
Affiliation(s)
- Sylvia M. Durkin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mallory A. Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael W. Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| |
Collapse
|
7
|
Gutiérrez-Guerrero YT, Phifer-Rixey M, Nachman MW. Across two continents: the genomic basis of environmental adaptation in house mice ( Mus musculus domesticus) from the Americas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564674. [PMID: 37961195 PMCID: PMC10634997 DOI: 10.1101/2023.10.30.564674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Parallel clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in regulatory regions. Genes containing the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, and development or function of the eye as well as traits associated with the cardiovascular and renal systems. We then combined these results with published results from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects, providing strong evidence of parallel adaptation and identifying genes that likely underlie recent environmental adaptation in house mice across North and South America.
Collapse
Affiliation(s)
- Yocelyn T. Gutiérrez-Guerrero
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, United States of America
| | - Megan Phifer-Rixey
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, United States of America
| |
Collapse
|
8
|
Petak C, Frati L, Brennan RS, Pespeni MH. Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins. Am Nat 2023; 202:571-586. [PMID: 37792925 DOI: 10.1086/726013] [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] [Indexed: 10/06/2023]
Abstract
AbstractOrganisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).
Collapse
|
9
|
Shepherd MJ, Pierce AP, Taylor TB. Evolutionary innovation through transcription factor rewiring in microbes is shaped by levels of transcription factor activity, expression, and existing connectivity. PLoS Biol 2023; 21:e3002348. [PMID: 37871011 PMCID: PMC10621929 DOI: 10.1371/journal.pbio.3002348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/02/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
The survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way to achieve this is via change to gene regulatory network (GRN) connections-known as rewiring-that facilitate novel interactions and innovation of transcription factors. To understand the success of rapidly adapting organisms, we therefore need to determine the rules that create and constrain opportunities for GRN rewiring. Here, using an experimental microbial model system with the soil bacterium Pseudomonas fluorescens, we reveal a hierarchy among transcription factors that are rewired to rescue lost function, with alternative rewiring pathways only unmasked after the preferred pathway is eliminated. We identify 3 key properties-high activation, high expression, and preexisting low-level affinity for novel target genes-that facilitate transcription factor innovation. Ease of acquiring these properties is constrained by preexisting GRN architecture, which was overcome in our experimental system by both targeted and global network alterations. This work reveals the key properties that determine transcription factor evolvability, and as such, the evolution of GRNs.
Collapse
Affiliation(s)
- Matthew J. Shepherd
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Aidan P. Pierce
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Tiffany B. Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| |
Collapse
|
10
|
Ballinger MA, Mack KL, Durkin SM, Riddell EA, Nachman MW. Environmentally robust cis-regulatory changes underlie rapid climatic adaptation. Proc Natl Acad Sci U S A 2023; 120:e2214614120. [PMID: 37725649 PMCID: PMC10523592 DOI: 10.1073/pnas.2214614120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 07/26/2023] [Indexed: 09/21/2023] Open
Abstract
Changes in gene expression are thought to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene expression differences in natural populations. Here, we utilize allele-specific expression to characterize cis and trans gene regulatory divergence in temperate and tropical house mice in two metabolic tissues under two thermal conditions. First, we show that gene expression divergence is pervasive between populations and across thermal conditions, with roughly 5 to 10% of genes exhibiting genotype-by-environment interactions. Second, we found that most expression divergence was due to cis-regulatory changes that were stable across temperatures. In contrast, patterns of expression plasticity were largely attributable to trans-effects, which showed greater sensitivity to temperature. Nonetheless, we found a small subset of temperature-dependent cis-regulatory changes, thereby identifying loci underlying expression plasticity. Finally, we performed scans for selection in wild house mice to identify genomic signatures of rapid adaptation. Genomic outliers were enriched in genes with evidence for cis-regulatory divergence. Notably, these genes were associated with phenotypes that affected body weight and metabolism, suggesting that cis-regulatory changes are a possible mechanism for adaptive body size evolution between populations. Our results show that gene expression plasticity, largely controlled in trans, may facilitate the colonization of new environments, but that evolved changes in gene expression are largely controlled in cis, illustrating the genetic and nongenetic mechanisms underlying the establishment of populations in new environments.
Collapse
Affiliation(s)
- Mallory A. Ballinger
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
- Department of Biology, Utah State University, Logan, UT84322
| | - Katya L. Mack
- Department of Biology, Stanford University, Stanford, CA94305
| | - Sylvia M. Durkin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - Eric A. Riddell
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA50011
| | - Michael W. Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
| |
Collapse
|
11
|
Snyman M, Xu S. The effects of mutations on gene expression and alternative splicing. Proc Biol Sci 2023; 290:20230565. [PMID: 37403507 PMCID: PMC10320348 DOI: 10.1098/rspb.2023.0565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Understanding the relationship between mutations and their genomic and phenotypic consequences has been a longstanding goal of evolutionary biology. However, few studies have investigated the impact of mutations on gene expression and alternative splicing on the genome-wide scale. In this study, we aim to bridge this knowledge gap by utilizing whole-genome sequencing data and RNA sequencing data from 16 obligately parthenogenetic Daphnia mutant lines to investigate the effects of ethyl methanesulfonate-induced mutations on gene expression and alternative splicing. Using rigorous analyses of mutations, expression changes and alternative splicing, we show that trans-effects are the major contributor to the variance in gene expression and alternative splicing between the wild-type and mutant lines, whereas cis mutations only affected a limited number of genes and do not always alter gene expression. Moreover, we show that there is a significant association between differentially expressed genes and exonic mutations, indicating that exonic mutations are an important driver of altered gene expression.
Collapse
Affiliation(s)
- Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| |
Collapse
|
12
|
Cridland JM, Contino CE, Begun DJ. Selection and geography shape male reproductive tract transcriptomes in Drosophila melanogaster. Genetics 2023; 224:iyad034. [PMID: 36869688 PMCID: PMC10474930 DOI: 10.1093/genetics/iyad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Transcriptome analysis of several animal clades suggests that male reproductive tract gene expression evolves quickly. However, the factors influencing the abundance and distribution of within-species variation, the ultimate source of interspecific divergence, are poorly known. Drosophila melanogaster, an ancestrally African species that has recently spread throughout the world and colonized the Americas in the last roughly 100 years, exhibits phenotypic and genetic latitudinal clines on multiple continents, consistent with a role for spatially varying selection in shaping its biology. Nevertheless, geographic expression variation in the Americas is poorly described, as is its relationship to African expression variation. Here, we investigate these issues through the analysis of two male reproductive tissue transcriptomes [testis and accessory gland (AG)] in samples from Maine (USA), Panama, and Zambia. We find dramatic differences between these tissues in differential expression between Maine and Panama, with the accessory glands exhibiting abundant expression differentiation and the testis exhibiting very little. Latitudinal expression differentiation appears to be influenced by the selection of Panama expression phenotypes. While the testis shows little latitudinal expression differentiation, it exhibits much greater differentiation than the accessory gland in Zambia vs American population comparisons. Expression differentiation for both tissues is non-randomly distributed across the genome on a chromosome arm scale. Interspecific expression divergence between D. melanogaster and D. simulans is discordant with rates of differentiation between D. melanogaster populations. Strongly heterogeneous expression differentiation across tissues and timescales suggests a complex evolutionary process involving major temporal changes in the way selection influences expression evolution in these organs.
Collapse
Affiliation(s)
- Julie M Cridland
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Colin E Contino
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| |
Collapse
|
13
|
Ye F, Bitner MA, Shi GR. Variation of shell ornamentation with latitude and water depth-A case study using living brachiopods. Ecol Evol 2023; 13:e10006. [PMID: 37091558 PMCID: PMC10121232 DOI: 10.1002/ece3.10006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
As a potential anti-predatory defensive structure, the shell ornamentation of marine calcifiers is usually used to understand the macro coevolution of the interactions between predators and preys. Marine calcifiers' shell ornamentation complexity is generally believed to vary negatively with latitude and water depth. In this paper, we explored the association between shell ornamentation and latitude/bathymetry using the latest global database of living brachiopods. We found that (1) ~59% of living brachiopods species are characterized by smooth shells and that (2) there is no statistically significant linear trend, either positive or negative, between the ornamentation index and latitudes nor with water depths. Both findings are puzzling for living brachiopods as they are sharply contrasted to the patterns of fossil brachiopods whereby the latter, especially Paleozoic brachiopods, are known to exhibit (1) a much greater ornamentation diversity and (2) (at least for the geological periods that have been studied) a linear latitudinal gradient of ornamentation complexity existed. The reasons why living brachiopods have such a high proportion of smooth or weakly ornamented shells and fail to demonstrate an unequivocal linear latitudinal ornamentation gradient were explored and are linked to a multitude of potential factors rather than uniquely only to the predation pressure. Among these, the most plausible factor seems to be the cryptic (refuge-type) habitats (e.g., deep waters, cold polar regions, and submarine rock caves) that living brachiopods have been adapted to due to their low metabolism, where predation pressure is low, allowing brachiopods to enact the predator avoidance strategy rather than having to manufacture robust shell ornamentation to survive in an otherwise highly engaged predator-prey global marine ecosystem.
Collapse
Affiliation(s)
- Facheng Ye
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and HealthUniversity of WollongongWollongongNew South WalesAustralia
| | | | - Guang Rong Shi
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and HealthUniversity of WollongongWollongongNew South WalesAustralia
| |
Collapse
|
14
|
Yu Y, Bergland AO. Distinct signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster. Evolution 2022; 76:2758-2768. [PMID: 36097359 PMCID: PMC9710195 DOI: 10.1111/evo.14617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/31/2022] [Accepted: 08/17/2022] [Indexed: 01/22/2023]
Abstract
Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. Local adaptation can be reflected on both phenotypic and genetic levels, and it has been documented in many organisms. Although complex fitness-related phenotypes have been shown to vary across latitudinal clines and seasons in similar ways in Drosophila melanogaster populations, the comparative signals of local adaptation across space and time remain poorly understood. Here, we examined patterns of allele frequency change across a latitudinal cline and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by using differential expression profiles of fly populations collected across latitudinal clines or exposed to different environmental conditions. In general, we find that eQTLs are enriched for clinally varying polymorphisms, and that these eQTLs change in frequency in concordant ways across the cline and in response to starvation and chill-coma. The enrichment of eQTLs among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTLs appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is at least partially distinct from seasonal adaptation.
Collapse
Affiliation(s)
- Yang Yu
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
| | - Alan O. Bergland
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
| |
Collapse
|
15
|
Fujiwara K, Kawai Y, Takada T, Shiroishi T, Saitou N, Suzuki H, Osada N. Insights into Mus musculus Population Structure across Eurasia Revealed by Whole-Genome Analysis. Genome Biol Evol 2022; 14:evac068. [PMID: 35524942 PMCID: PMC9122283 DOI: 10.1093/gbe/evac068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (∼10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000-226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.
Collapse
Affiliation(s)
- Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, Sapporo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Toyoyuki Takada
- Integrated BioResource Information Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | | | | | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, Sapporo, Japan
| |
Collapse
|
16
|
Hersch M, Biasini A, Marques AC, Bergmann S. Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment. BMC Bioinformatics 2022; 23:147. [PMID: 35459101 PMCID: PMC9034570 DOI: 10.1186/s12859-022-04672-4] [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: 07/16/2021] [Accepted: 04/04/2022] [Indexed: 11/05/2022] Open
Abstract
Background Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted and are now turning to single cell measurements. Several computational methods to estimate RNA synthesis, processing and degradation rates from such experiments have been suggested, but they all require several RNA sequencing samples. Here we present a method that can estimate those three rates from a single sample. Methods Our method relies on the analytical solution to the Zeisel model of RNA dynamics. It was validated on metabolic labeling experiments performed on mouse embryonic stem cells. Resulting degradation rates were compared both to previously published rates on the same system and to a state-of-the-art method applied to the same data. Results Our method is computationally efficient and outputs rates that correlate well with previously published data sets. Using it on a single sample, we were able to reproduce the observation that dynamic biological processes tend to involve genes with higher metabolic rates, while stable processes involve genes with lower rates. This supports the hypothesis that cells control not only the mRNA steady-state abundance, but also its responsiveness, i.e., how fast steady state is reached. Moreover, degradation rates obtained with our method compare favourably with the other tested method. Conclusions In addition to saving experimental work and computational time, estimating rates for a single sample has several advantages. It does not require an error-prone normalization across samples and enables the use of replicates to estimate uncertainty and assess sample quality. Finally the method and theoretical results described here are general enough to be useful in other contexts such as nucleotide conversion methods and single cell metabolic labeling experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04672-4.
Collapse
Affiliation(s)
- Micha Hersch
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, 1015, Lausanne, CH, Switzerland.
| | - Adriano Biasini
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ana C Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015, Lausanne, CH, Switzerland
| |
Collapse
|
17
|
Brown KE, Kelly JK. Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations. Genetics 2022; 220:iyab189. [PMID: 34791192 PMCID: PMC8733635 DOI: 10.1093/genetics/iyab189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
We measured the floral bud transcriptome of 151 fully sequenced lines of Mimulus guttatus from one natural population. Thousands of single nucleotide polymorphisms (SNPs) are implicated as transcription regulators, but there is a striking difference in the allele frequency spectrum of cis-acting and trans-acting mutations. Cis-SNPs have intermediate frequencies (consistent with balancing selection) while trans-SNPs exhibit a rare-alleles model (consistent with purifying selection). This pattern only becomes clear when transcript variation is normalized on a gene-to-gene basis. If a global normalization is applied, as is typically in RNAseq experiments, asymmetric transcript distributions combined with "rarity disequilibrium" produce a superabundance of false positives for trans-acting SNPs. To explore the cause of purifying selection on trans-acting mutations, we identified gene expression modules as sets of coexpressed genes. The extent to which trans-acting mutations influence modules is a strong predictor of allele frequency. Mutations altering expression of genes with high "connectedness" (those that are highly predictive of the representative module expression value) have the lowest allele frequency. The expression modules can also predict whole-plant traits such as flower size. We find that a substantial portion of the genetic (co)variance among traits can be described as an emergent property of genetic effects on expression modules.
Collapse
Affiliation(s)
- Keely E Brown
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| |
Collapse
|
18
|
Triant DA, Nowick K, Shelest E. Editorial: Gene Regulation as a Driver of Adaptation and Speciation. Front Genet 2021; 12:793933. [PMID: 34868278 PMCID: PMC8633301 DOI: 10.3389/fgene.2021.793933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Deborah A Triant
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Katja Nowick
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ekaterina Shelest
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, United Kingdom
| |
Collapse
|
19
|
Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
Collapse
Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
20
|
Lawal RA, Arora UP, Dumont BL. Selection shapes the landscape of functional variation in wild house mice. BMC Biol 2021; 19:239. [PMID: 34794440 PMCID: PMC8603481 DOI: 10.1186/s12915-021-01165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/14/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Through human-aided dispersal over the last ~ 10,000 years, house mice (Mus musculus) have recently colonized diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantages in distinct environments. Despite their status as the premier mammalian model system, the impact of this demographic and selective history on the global patterning of disease-relevant trait variation in wild mouse populations is poorly understood. RESULTS Here, we leveraged 154 whole-genome sequences from diverse wild house mouse populations to survey the geographic organization of functional variation and systematically identify signals of positive selection. We show that a significant proportion of wild mouse variation is private to single populations, including numerous predicted functional alleles. In addition, we report strong signals of positive selection at many genes associated with both complex and Mendelian diseases in humans. Notably, we detect a significant excess of selection signals at disease-associated genes relative to null expectations, pointing to the important role of adaptation in shaping the landscape of functional variation in wild mouse populations. We also uncover strong signals of selection at multiple genes involved in starch digestion, including Mgam and Amy1. We speculate that the successful emergence of the human-mouse commensalism may have been facilitated, in part, by dietary adaptations at these loci. Finally, our work uncovers multiple cryptic structural variants that manifest as putative signals of positive selection, highlighting an important and under-appreciated source of false-positive signals in genome-wide selection scans. CONCLUSIONS Overall, our findings highlight the role of adaptation in shaping wild mouse genetic variation at human disease-associated genes. Our work also highlights the biomedical relevance of wild mouse genetic diversity and underscores the potential for targeted sampling of mice from specific populations as a strategy for developing effective new mouse models of both rare and common human diseases.
Collapse
Affiliation(s)
| | - Uma P Arora
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA.
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA.
| |
Collapse
|
21
|
Jacobs A, Elmer KR. Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish. Mol Ecol 2021; 30:4955-4969. [PMID: 33502030 PMCID: PMC8653899 DOI: 10.1111/mec.15817] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/06/2021] [Accepted: 01/18/2021] [Indexed: 12/25/2022]
Abstract
Understanding the contribution of different molecular processes to evolution and development is crucial for identifying the mechanisms of adaptation. Here, we used RNA-sequencing data to test the importance of alternative splicing and differential gene expression in a case of parallel adaptive evolution, the replicated postglacial divergence of the salmonid fish Arctic charr (Salvelinus alpinus) into sympatric benthic and pelagic ecotypes across multiple independent lakes. We found that genes differentially spliced between ecotypes were mostly not differentially expressed (<6% overlap) and were involved in different biological processes. Differentially spliced genes were primarily enriched for muscle development and functioning, while differentially expressed genes were involved in metabolism, immunity and growth. Furthermore, alternative splicing and gene expression were mostly controlled by independent cis-regulatory quantitative trait loci (<3.4% overlap). Cis-regulatory regions were associated with the parallel divergence in splicing (16.5% of intron clusters) and expression (6.7%-10.1% of differentially expressed genes), indicating shared regulatory variation across ecotype pairs. Contrary to theoretical expectation, we found that differentially spliced genes tended to be highly central in regulatory networks ("hub genes") and were annotated to significantly more gene ontology terms compared to nondifferentially spliced genes, consistent with a higher level of pleiotropy. Together, our results suggest that the concerted regulation of alternative splicing and differential gene expression through different regulatory regions leads to the divergence of complementary processes important for local adaptation. This provides novel insights into the importance of contrasting but putatively complementary molecular processes in rapid parallel adaptive evolution.
Collapse
Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| |
Collapse
|
22
|
Peng Y, Dong S, Song Y, Hou D, Wang L, Li B, Wang H. Key sunitinib-related biomarkers for renal cell carcinoma. Cancer Med 2021; 10:6917-6930. [PMID: 34402193 PMCID: PMC8495283 DOI: 10.1002/cam4.4206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022] Open
Abstract
Background Renal cell carcinoma (RCC) contributed to 403,262 new cases worldwide in 2018, which constitutes 2.2% of global cancer, nevertheless, sunitinib, one of the major targeted therapeutic agent for RCC, often developed invalid due to resistance. Emerging evidences suggested sunitinib can impact tumor environment which has been proven to be a vital factor for tumor progression. Methods In the present study, we used ssGSEA to extract the immune infiltrating abundance of clear cell RCC (ccRCC) and normal control samples from GSE65615, TCGA, and GTEx; key immune cells were determined by Student's t‐test and univariable Cox analysis. Co‐expression network combined with differentially expressed analysis was then applied to derive key immune‐related genes for ccRCC, followed by the identification of hub genes using differential expression analysis. Subsequently, explorations and validations of the biological function and the immune‐related and sunitinib‐related characteristics were conducted in KEGG, TISIDB, Oncomine, ICGC, and GEO databases. Results We refined immature dendritic cells and central memory CD4 T cells which showed associations with sunitinib and ccRCC. Following, five hub genes (CRYBB1, RIMBP3C, CEACAM4, HAMP, and LYL1) were identified for their strong relationships with sunitinib and immune infiltration in ccRCC. Further validations in external data refined CRYBB1, CEACAM4, and HAMP which play a vital role in sunitinib resistance, immune infiltrations in ccRCC, and the development and progression of ccRCC. In conclusion, our findings could shed light on the resistance of sunitinib in ccRCC and provide novel biomarkers or drug targets for ccRCC.
Collapse
Affiliation(s)
- Yun Peng
- Tianjin Institute of Urology, The 2nd Hospital of Tianjin Medical University, Tianjin, China
| | - Shiqiang Dong
- Tianjin Institute of Urology, The 2nd Hospital of Tianjin Medical University, Tianjin, China
| | - Yuxuan Song
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Dingkun Hou
- Tianjin Institute of Urology, The 2nd Hospital of Tianjin Medical University, Tianjin, China
| | - Lili Wang
- Department of Oncology, The 2nd Hospital of Tianjin Medical University, Tianjin, China
| | - Bowen Li
- Tianjin Institute of Urology, The 2nd Hospital of Tianjin Medical University, Tianjin, China
| | - Haitao Wang
- Department of Oncology, The 2nd Hospital of Tianjin Medical University, Tianjin, China
| |
Collapse
|
23
|
Mapping of quantitative trait loci underlying a magic trait in ongoing ecological speciation. BMC Genomics 2021; 22:615. [PMID: 34384356 PMCID: PMC8361645 DOI: 10.1186/s12864-021-07908-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/22/2021] [Indexed: 01/09/2023] Open
Abstract
Background Telmatochromis temporalis is a cichlid fish endemic to Lake Tanganyika. The normal and dwarf morphs of this fish are a clear example of ongoing ecological speciation, and body size plays an important role in this speciation event as a magic trait. However, the genetic basis underlying this trait has not been studied. Results Based on double-digested restriction-site associated DNA (ddRAD) sequencing of a hybrid cross between the morphs that includes F0 male, F0 female, and 206 F2 individuals, we obtained a linkage map consisting of 708 ddRAD markers in 22 linkage groups, which corresponded to the previously reported Oreochromis niloticus chromosomes, and identified one significant and five suggestive quantitative trait loci (QTL) for body size. From the body-size distribution pattern, the significant and three of the five suggestive QTL are possibly associated with genes responsible for the difference in body size between the morphs. Conclusions The QTL analysis presented here suggests that multiple genes, rather than a single gene, control morph-specific body size. The present results provide further insights about the genes underlying the morph specific body size and evolution of the magic trait during ecological speciation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07908-4.
Collapse
|
24
|
Petit‐Marty N, Nagelkerken I, Connell SD, Schunter C. Natural CO 2 seeps reveal adaptive potential to ocean acidification in fish. Evol Appl 2021; 14:1794-1806. [PMID: 34295364 PMCID: PMC8288007 DOI: 10.1111/eva.13239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 01/01/2023] Open
Abstract
Volcanic CO2 seeps are natural laboratories that can provide insights into the adaptation of species to ocean acidification. While many species are challenged by reduced-pH levels, some species benefit from the altered environment and thrive. Here, we explore the molecular mechanisms of adaptation to ocean acidification in a population of a temperate fish species that experiences increased population sizes under elevated CO2. Fish from CO2 seeps exhibited an overall increased gene expression in gonad tissue compared with those from ambient CO2 sites. Up-regulated genes at CO2 seeps are possible targets of adaptive selection as they can directly influence the physiological performance of fishes exposed to ocean acidification. Most of the up-regulated genes at seeps were functionally involved in the maintenance of pH homeostasis and increased metabolism, and presented a deviation from neutral evolution expectations in their patterns of DNA polymorphisms, providing evidence for adaptive selection to ocean acidification. The targets of this adaptive selection are likely regulatory sequences responsible for the increased expression of these genes, which would allow a fine-tuned physiological regulation to maintain homeostasis and thrive at CO2 seeps. Our findings reveal that standing genetic variation in DNA sequences regulating the expression of genes in response to a reduced-pH environment could provide for adaptive potential to near-future ocean acidification in fishes. Moreover, with this study we provide a forthright methodology combining transcriptomics and genomics, which can be applied to infer the adaptive potential to different environmental conditions in wild marine populations.
Collapse
Affiliation(s)
- Natalia Petit‐Marty
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong KongHong Kong SAR
| | - Ivan Nagelkerken
- Southern Seas Ecology LaboratoriesSchool of Biological Sciences and the Environment InstituteDX 650 418The University of AdelaideAdelaideSAAustralia
| | - Sean D. Connell
- Southern Seas Ecology LaboratoriesSchool of Biological Sciences and the Environment InstituteDX 650 418The University of AdelaideAdelaideSAAustralia
| | - Celia Schunter
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong KongHong Kong SAR
| |
Collapse
|
25
|
Bittner NKJ, Mack KL, Nachman MW. Gene expression plasticity and desert adaptation in house mice. Evolution 2021; 75:1477-1491. [PMID: 33458812 PMCID: PMC8218737 DOI: 10.1111/evo.14172] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 12/10/2020] [Accepted: 12/27/2020] [Indexed: 12/26/2022]
Abstract
Understanding how organisms adapt to new environments is a key problem in evolution, yet it remains unclear whether phenotypic plasticity generally facilitates or hinders this process. Here we studied evolved and plastic responses to water-stress in lab-born descendants of wild house mice (Mus musculus domesticus) collected from desert and non-desert environments and measured gene expression and organismal phenotypes under control and water-stressed conditions. After many generations in the lab, desert mice consumed significantly less water than mice from other localities, indicating that this difference has a genetic basis. Under water-stress, desert mice maintained more weight than non-desert mice, and exhibited differences in blood chemistry related to osmoregulatory function. Gene expression in the kidney revealed evolved differences between mice from different environments as well as plastic responses between hydrated and dehydrated mice. Desert mice showed reduced expression plasticity under water-stress compared to non-desert mice. Importantly, non-desert mice under water-stress generally showed shifts toward desert-like expression, consistent with adaptive plasticity. Finally, we identify several co-expression modules linked to phenotypes of interest. These findings provide evidence for local adaptation after a recent invasion and suggest that adaptive plasticity may have facilitated colonization of the desert environment.
Collapse
Affiliation(s)
- Noëlle K J Bittner
- Deparment of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, 94720
| | - Katya L Mack
- Deparment of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, 94720
- Department of Biology, Stanford University, Stanford, California, 94305
| | - Michael W Nachman
- Deparment of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, 94720
| |
Collapse
|
26
|
Morgan K, Harr B, White MA, Payseur BA, Turner LM. Disrupted Gene Networks in Subfertile Hybrid House Mice. Mol Biol Evol 2021; 37:1547-1562. [PMID: 32076722 PMCID: PMC7253214 DOI: 10.1093/molbev/msaa002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Dobzhansky–Muller (DM) model provides a widely accepted mechanism for the evolution of reproductive isolation: incompatible substitutions disrupt interactions between genes. To date, few candidate incompatibility genes have been identified, leaving the genes driving speciation mostly uncharacterized. The importance of interactions in the DM model suggests that gene coexpression networks provide a powerful framework to understand disrupted pathways associated with postzygotic isolation. Here, we perform weighted gene coexpression network analysis to infer gene interactions in hybrids of two recently diverged European house mouse subspecies, Mus mus domesticus and M. m. musculus, which commonly show hybrid male sterility or subfertility. We use genome-wide testis expression data from 467 hybrid mice from two mapping populations: F2s from a laboratory cross between wild-derived pure subspecies strains and offspring of natural hybrids captured in the Central Europe hybrid zone. This large data set enabled us to build a robust consensus network using hybrid males with fertile phenotypes. We identify several expression modules, or groups of coexpressed genes, that are disrupted in subfertile hybrids, including modules functionally enriched for spermatogenesis, cilium and sperm flagellum organization, chromosome organization, and DNA repair, and including genes expressed in spermatogonia, spermatocytes, and spermatids. Our network-based approach enabled us to hone in on specific hub genes likely to be influencing module-wide gene expression and hence potentially driving large-effect DM incompatibilities. A disproportionate number of hub genes lie within sterility loci identified previously in the hybrid zone mapping population and represent promising candidate barrier genes and targets for future functional analysis.
Collapse
Affiliation(s)
- Katy Morgan
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Bettina Harr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI
| | - Leslie M Turner
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| |
Collapse
|
27
|
Ferris KG, Chavez AS, Suzuki TA, Beckman EJ, Phifer-Rixey M, Bi K, Nachman MW. The genomics of rapid climatic adaptation and parallel evolution in North American house mice. PLoS Genet 2021; 17:e1009495. [PMID: 33914747 PMCID: PMC8084166 DOI: 10.1371/journal.pgen.1009495] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America. First, we show that mice are genetically differentiated between transects, indicating that they have independently colonized similar environments in eastern and western North America. Next, we find genetically-based differences in body weight and nest building behavior between mice from the ends of the western transect which mirror differences seen in the eastern transect, demonstrating parallel phenotypic change. We then conduct genome-wide scans for selection and a genome-wide association study to identify targets of selection and candidate genes for body weight. We find some genomic signatures that are unique to each transect, indicating population-specific responses to selection. However, there is significant overlap between genes under selection in eastern and western house mouse transects, providing evidence of parallel genetic evolution in response to similar selection pressures across North America.
Collapse
Affiliation(s)
- Kathleen G. Ferris
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Andreas S. Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Taichi A. Suzuki
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Elizabeth J. Beckman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Megan Phifer-Rixey
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Michael W. Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| |
Collapse
|
28
|
Josephs EB. Gene expression links genotype and phenotype during rapid adaptation. Mol Ecol 2020; 30:30-32. [PMID: 33187015 DOI: 10.1111/mec.15729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/06/2020] [Indexed: 12/27/2022]
Abstract
Natural environments can change quickly and organisms living in these environments can either move, go extinct, or persist through rapid adaptation. Understanding the genetic and phenotypic changes that occur during rapid adaptation is crucial for predicting how populations will respond to sudden environmental changes. Since gene expression links genotype to phenotype, determining how rapid adaptation shapes the transcriptome will be useful for identifying both the traits and the genes important for adaptation, especially in cases where adaptation involves changes in quantitative traits. However, we lack a clear understanding of how rapid adaptation can cause and be caused by changes in gene expression. In this issue of Molecular Ecology, Hamann et al. (2020) investigate how gene expression has evolved during rapid adaptation to drought in two populations of the plant species Brassica rapa.
Collapse
Affiliation(s)
- Emily B Josephs
- Department of Plant Biology and the Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
29
|
North HL, Caminade P, Severac D, Belkhir K, Smadja CM. The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190540. [PMID: 32654648 PMCID: PMC7423270 DOI: 10.1098/rstb.2019.0540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2020] [Indexed: 12/24/2022] Open
Abstract
Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations of Mus musculus musculus that display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These 'Choosiness-associated' CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene, Sp110, that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice-the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Collapse
Affiliation(s)
- Henry L. North
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Pierre Caminade
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 5, France
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Carole M. Smadja
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| |
Collapse
|
30
|
Josephs EB, Lee YW, Wood CW, Schoen DJ, Wright SI, Stinchcombe JR. The Evolutionary Forces Shaping Cis- and Trans-Regulation of Gene Expression within a Population of Outcrossing Plants. Mol Biol Evol 2020; 37:2386-2393. [DOI: 10.1093/molbev/msaa102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Abstract
Understanding the persistence of genetic variation within populations has long been a goal of evolutionary biology. One promising route toward achieving this goal is using population genetic approaches to describe how selection acts on the loci associated with trait variation. Gene expression provides a model trait for addressing the challenge of the maintenance of variation because it can be measured genome-wide without information about how gene expression affects traits. Previous work has shown that loci affecting the expression of nearby genes (local or cis-eQTLs) are under negative selection, but we lack a clear understanding of the selective forces acting on variants that affect the expression of genes in trans. Here, we identify loci that affect gene expression in trans using genomic and transcriptomic data from one population of the obligately outcrossing plant, Capsella grandiflora. The allele frequencies of trans-eQTLs are consistent with stronger negative selection acting on trans-eQTLs than cis-eQTLs, and stronger negative selection acting on trans-eQTLs associated with the expression of multiple genes. However, despite this general pattern, we still observe the presence of a trans-eQTL at intermediate frequency that affects the expression of a large number of genes in the same coexpression module. Overall, our work highlights the different selective pressures shaping variation in cis- and trans-regulation.
Collapse
Affiliation(s)
- Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI
| | | | - Corlett W Wood
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Daniel J Schoen
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
31
|
Huang Y, Liu H, Zuo L, Tao A. Key genes and co-expression modules involved in asthma pathogenesis. PeerJ 2020; 8:e8456. [PMID: 32117613 PMCID: PMC7003696 DOI: 10.7717/peerj.8456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/24/2019] [Indexed: 12/31/2022] Open
Abstract
Machine learning and weighted gene co-expression network analysis (WGCNA) have been widely used due to its well-known accuracy in the biological field. However, due to the nature of a gene’s multiple functions, it is challenging to locate the exact genes involved in complex diseases such as asthma. In this study, we combined machine learning and WGCNA in order to analyze the gene expression data of asthma for better understanding of associated pathogenesis. Specifically, the role of machine learning is assigned to screen out the key genes in the asthma development, while the role of WGCNA is to set up gene co-expression network. Our results indicated that hormone secretion regulation, airway remodeling, and negative immune regulation, were all regulated by critical gene modules associated with pathogenesis of asthma progression. Overall, the method employed in this study helped identify key genes in asthma and their roles in the asthma pathogenesis.
Collapse
Affiliation(s)
- Yuyi Huang
- The State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui Liu
- The State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,School of Basic Medical Sciences, The Sixth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Zuo
- The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA.,College of Arts and Sciences, University of Maine Presque Isle Campus, Presque Isle, ME, USA
| | - Ailin Tao
- The State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
32
|
Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice. Genes (Basel) 2019; 10:genes10030225. [PMID: 30889893 PMCID: PMC6470930 DOI: 10.3390/genes10030225] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/10/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023] Open
Abstract
Interactions between genes can influence how selection acts on sequence variation. In gene regulatory networks, genes that affect the expression of many other genes may be under stronger evolutionary constraint than genes whose expression affects fewer partners. While this has been studied for individual tissue types, we know less about the effects of regulatory networks on gene evolution across different tissue types. We use RNA-sequencing and genomic data collected from Mus musculus domesticus to construct and compare gene co-expression networks for 10 tissue types. We identify tissue-specific expression and local regulatory variation, and we associate these components of gene expression variation with sequence polymorphism and divergence. We found that genes with higher connectivity across tissues and genes associated with a greater number of cross-tissue modules showed significantly lower genetic diversity and lower rates of protein evolution. Consistent with this pattern, “hub” genes across multiple tissues also showed evidence of greater evolutionary constraint. Using allele-specific expression, we found that genes with cis-regulatory variation had lower average connectivity and higher levels of tissue specificity. Taken together, these results are consistent with strong purifying selection acting on genes with high connectivity within and across tissues.
Collapse
|