Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation

Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.

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Natural variation in CBF gene sequence, gene expression and freezing tolerance in the Versailles core collection of Arabidopsis thaliana

BMC Plant Biology ◽

10.1186/1471-2229-8-105 ◽

2008 ◽

Vol 8 (1) ◽

pp. 105 ◽

Cited By ~ 64

Author(s):

Heather I Mckhann ◽

Carine Gery ◽

Aurelie Berard ◽

Sylvie Leveque ◽

Ellen Zuther ◽

...

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Freezing Tolerance ◽

Core Collection ◽

Natural Variation ◽

Gene Sequence

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Sexual dimorphism in gene expression: coincidence and population genomics of two forms of differential expression in Drosophila melanogaster

10.1101/2021.02.08.429268 ◽

2021 ◽

Author(s):

Amardeep Singh ◽

Aneil F. Agrawal

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Sex Differences ◽

Drosophila Melanogaster ◽

Sexual Dimorphism ◽

Population Genomics ◽

The Body ◽

Species Selection ◽

Sexual Antagonism ◽

Opposite Pattern

AbstractIn most species, selection favours different phenotypes in the two sexes. This type of sexual antagonism can be resolved through the evolution of sexual dimorphism. Sex differences in gene regulation is a proximate mechanism by which this resolution can be achieved. One form of differential gene regulation is sex differences in the amount a gene is expressed, so called sex-biased gene expression (SBGE). Less attention has been given to sexual dimorphism in isoform usage (SDIU), resulting from sex-specific alternative splicing, which may be another way in which conflict between the sexes is resolved. Here, we use RNA-seq data from two tissue types (heads and bodies) from 18 genotypes of adult Drosophila melanogaster to investigate SDIU. In our data, SBGE and SDIU are both much more prevalent in the body than the head. SDIU is less common among sex-biased than unbiased genes in the body, though the opposite pattern occurs in the head. SDIU, but not SBGE, is significantly associated with reduced values of Tajima’s D, possibly indicating that such genes experience positive selection more frequently. SBGE, but not SDIU, is associated with increased πN/πS, possibly indicating weaker purifying selection. Together, these results are consistent with the idea that the SDIU and SBGE are alternative pathways towards the resolution of conflict between the sexes with distinct evolutionary consequences.

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Evolution of Gene Expression and Splicing in Parallel Cold-Adapted Fly Populations

10.1101/795716 ◽

2019 ◽

Author(s):

Yuheng Huang ◽

Justin B. Lack ◽

Grant T. Hoppel ◽

John E. Pool

Keyword(s):

Gene Expression ◽

Adaptive Evolution ◽

Parallel Evolution ◽

Population Variation ◽

Regulatory Evolution ◽

Cold Adapted ◽

Mitochondrial Functions ◽

Expression Evolution ◽

Gene Regulatory ◽

Trans Regulation

AbstractChanges in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find significant although somewhat limited evidence for parallel expression evolution between them, and less evidence for parallel splicing evolution. We find that genes with mitochondrial functions are particularly enriched among candidates for adaptive expression evolution. We also develop a method to estimate cis-versus trans-encoded contributions to expression or splicing differences that does not rely on the presence of fixed differences between parental strains. Applying this method, we infer important roles of both cis-and trans-regulation among our putatively adaptive expression and splicing differences. The apparent contributions of cis-versus trans-regulation to adaptive evolution vary substantially among population pairs, with an Ethiopian pair showing pervasive trans-effects, suggesting that basic characteristics of regulatory evolution may depend on biological context. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.

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Influence of the microbiota on epigenetics in colorectal cancer

National Science Review ◽

10.1093/nsr/nwy160 ◽

2018 ◽

Vol 6 (6) ◽

pp. 1138-1148 ◽

Cited By ~ 1

Author(s):

Danfeng Sun ◽

Yingxuan Chen ◽

Jing-Yuan Fang

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Fatty Acids ◽

Gene Sequence ◽

Short Chain Fatty Acids ◽

Epigenetic Modifications ◽

Host Cells ◽

Cancer Development ◽

Cancer Death ◽

Clear Link

Abstract Colorectal cancer is one of the most common malignancies and is the second leading cause of cancer death worldwide. Generally, there are three categories of colorectal cancer development mechanism—genetic, epigenetic and aberrant immunological signaling pathways—all of which may be initiated by an imbalanced gut microbiota. Epigenetic modifications enable host cells to change gene expression without modifying the gene sequence. The microbiota can interact with the host genome dynamically through the interface presented by epigenetic modifications. In particular, bacterially derived short-chain fatty acids have been identified as one clear link in the interaction of the microbiota with host epigenetic pathways. This review discusses recent findings relating to the cross talk between the microbiota and epigenetic modifications in colorectal cancer.

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Corrigendum to “VEGF gene sequence variation defines VEGF gene expression status and angiogenic activity in non-small cell lung cancer” [Lung Cancer 46 (2003) 293–298]

Lung Cancer ◽

10.1016/j.lungcan.2004.11.009 ◽

2005 ◽

Vol 48 (2) ◽

pp. 297

Author(s):

Michael I. Koukourakis ◽

Dimitrios Papazoglou ◽

Alexandra Giatromanolaki ◽

George Bougioukas ◽

Efstratios Maltezos ◽

...

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Small Cell Lung Cancer ◽

Sequence Variation ◽

Gene Sequence ◽

Small Cell ◽

Vegf Gene ◽

Small Cell Lung ◽

Angiogenic Activity ◽

Expression Status

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Cloning of Gonadotropin-Releasing Hormone I Complementary DNAs in Songbirds Facilitates Dissection of Mechanisms Mediating Seasonal Changes in Reproduction

Endocrinology ◽

10.1210/en.2008-1435 ◽

2009 ◽

Vol 150 (4) ◽

pp. 1826-1833 ◽

Cited By ~ 33

Author(s):

T. J. Stevenson ◽

K. S. Lynch ◽

P. Lamba ◽

G. F. Ball ◽

D. J. Bernard

Keyword(s):

Gene Expression ◽

Seasonal Changes ◽

Gene Sequence ◽

Amino Acid Identity ◽

Open Reading Frames ◽

Mrna Levels ◽

European Starlings ◽

Important Exception ◽

Reading Frames

Temperate zone animals exhibit seasonal variation in reproductive physiology. In most cases, seasonal changes in reproductive states are regulated by changes in GnRH1 secretion, rather than synthesis, from the preoptic area (POA)/anterior hypothalamus. An important exception occurs in some songbirds that become photorefractory to the stimulatory effects of long days and show profound decreases in brain GnRH1 protein content. Whether this decline reflects changes in gene expression is unknown because of past failures to measure GNRH1 mRNA levels, due in large part to the absence of available GNRH1 gene sequence in this taxon. Here, we report the first cloning of GNRH1 cDNAs in two songbirds: European starlings and zebra finches. Consistent with the size of the prepro-hormone in other avian and non-avian species, the open-reading frames predict proteins of 91 and 92 amino acids, respectively. Whereas the decapeptide in both species is perfectly conserved with chicken GnRH1, the amino acid identity in the signal peptide and GNRH associated peptide subdomains are significantly less well conserved. At the nucleotide level, the starling and zebra finch coding sequences are approximately 88% identical to each other but only approximately 70% identical to chicken GNRH1. In situ hybridization using radiolabeled cRNA probes demonstrated GNRH1 mRNA expression primarily in the POA, consistent with previous studies on the distribution of the GnRH1-immunoreactive cell bodies. Furthermore, we provide evidence for photoperiod-dependent regulation of GNRH1 mRNA in male starlings. Declines in GNRH1 mRNA levels occur in parallel with testicular involution. Thus, photorefractoriness is associated with decreases in GNRH1 gene expression in the medial POA.

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