Genome‐wide adaptive evolution to underground stresses in subterranean mammals: Hypoxia adaption, immunity promotion, and sensory specialization

SummaryDomestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity.We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (P. armeniaca), plum (P. salicina), and peach (P. persica). Based on their genome-wide single nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume.Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution.These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selection.

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Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations

Human Molecular Genetics ◽

10.1093/hmg/ddn399 ◽

2008 ◽

Vol 18 (4) ◽

pp. 779-784 ◽

Cited By ~ 4

Author(s):

Joanna L. Kelley ◽

Kayley Turkheimer ◽

Margo Haney ◽

Willie J. Swanson

Keyword(s):

Positive Selection ◽

Adaptive Evolution ◽

Targeted Resequencing ◽

Genome Wide ◽

A Genome ◽

Genome Wide Scan

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Genome-wide Identification ofWRKYGenes in the Desert PoplarPopulus euphraticaand Adaptive Evolution of the Genes in Response to Salt Stress

Evolutionary Bioinformatics ◽

10.4137/ebo.s22067 ◽

2015 ◽

Vol 11s1 ◽

pp. EBO.S22067 ◽

Cited By ~ 7

Author(s):

Jianchao Ma ◽

Jing Lu ◽

Jianmei Xu ◽

Bingbing Duan ◽

Xiaodong He ◽

...

Keyword(s):

Salt Stress ◽

Adaptive Evolution ◽

Genome Wide

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Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions

10.1101/217646 ◽

2017 ◽

Cited By ~ 2

Author(s):

Han Chen ◽

Haidong Shu ◽

Liyuan Wang ◽

Fan Zhang ◽

Xi Li ◽

...

Keyword(s):

Adaptive Evolution ◽

Plant Pathogens ◽

Phytophthora Sojae ◽

Genome Architecture ◽

Epigenetic Mark ◽

Gene Body ◽

Gene Body Methylation ◽

Methylated Dna ◽

Genome Wide

AbstractFilamentous plant pathogen genomes often display a bipartite architecture with gene sparse, repeat-rich compartments serving as a cradle for adaptive evolution. However, the extent to which this “two-speed” genome architecture is associated with genome-wide epigenetic modifications is unknown. Here, we show that the oomycete plant pathogens Phytophthora infestans and Phytophthora sojae possess functional adenine N6- methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine (5mC) could not be detected in the two Phytophthora species. Methylated DNA IP Sequencing (MeDIP-seq) of each species revealed that 6mA is depleted around the transcriptional starting sites (TSS) and is associated with low expressed genes, particularly transposable elements. Remarkably, genes occupying the gene-sparse regions have higher levels of 6mA compared to the remainder of both genomes, possibly implicating the methylome in adaptive evolution of Phytophthora. Among three putative adenine methyltransferases, DAMT1 and DAMT3 displayed robust enzymatic activities. Surprisingly, single knockouts of each of the 6mA methyltransferases in P. sojae significantly reduced in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the damt3 mutant revealed uneven patterns of 6mA methylation across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Our findings provide evidence that 6mA modification is an epigenetic mark of Phytophthora genomes and that complex patterns of 6mA methylation by the expanded 6mA methyltransferases may be associated with adaptive evolution in these important plant pathogens.

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Does Adaptive Protein Evolution Proceed by Large or Small Steps at the Amino Acid Level?

10.1101/379073 ◽

2018 ◽

Cited By ~ 1

Author(s):

Juraj Bergman ◽

Adam Eyre-Walker

Keyword(s):

Amino Acids ◽

Adaptive Evolution ◽

Evolutionary Biology ◽

Amino Acid Level ◽

Neutral Evolution ◽

Relative Contribution ◽

Mutational Step ◽

Genome Wide ◽

Genome Wide Data ◽

Evolution Of Proteins

AbstractA longstanding question in evolutionary biology is the relative contribution of large and small effect mutations to the adaptive process. We have investigated this question in proteins by estimating the rate of adaptive evolution between all pairs of amino acids separated by one mutational step using a McDonald-Kreitman type approach and genome-wide data from several Drosophila species. We find that the rate of adaptive evolution is higher amongst amino acids that are more similar. This is partly due to the fact that the proportion of mutations that are adaptive is higher amongst more similar amino acids. We also find that the rate of neutral evolution between amino acids is higher amongst similar amino acids. Overall our results suggest that both the adaptive and non-adaptive evolution of proteins is dominated by substitutions between amino acids that are more similar.

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The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms

10.1101/2020.05.29.122895 ◽

2020 ◽

Author(s):

Shubham K. Jaiswal ◽

Abhisek Chakraborty ◽

Shruti Mahajan ◽

Sudhir Kumar ◽

Vineet K. Sharma

Keyword(s):

Drought Stress ◽

Stress Response ◽

Adaptive Evolution ◽

Genome Sequence ◽

Genetic Basis ◽

Draft Genome ◽

Aloe Vera ◽

The Other ◽

Plant Family ◽

Genome Wide

ABSTRACTAloe vera is a species from Asphodelaceae plant family having unique characteristics such as drought resistance and also possesses numerous medicinal properties. However, the genetic basis of these phenotypes is yet unknown, primarily due to the unavailability of its genome sequence. In this study, we report the first Aloe vera draft genome sequence comprising of 13.83 Gbp and harboring 86,177 coding genes. It is also the first genome from the Asphodelaceae plant family and is the largest angiosperm genome sequenced and assembled till date. Further, we report the first genome-wide phylogeny of monocots with Aloe vera using 1,440 one-to-one orthologs that resolves the genome-wide phylogenetic position of Aloe vera with respect to the other monocots. The comprehensive comparative analysis of Aloe vera genome with the other available high-quality monocot genomes revealed adaptive evolution in several genes of the drought stress response, CAM pathway, and circadian rhythm in Aloe vera. Further, genes involved in DNA damage response, a key pathway in several biotic and abiotic stress response mechanisms, were found to be positively selected. This provides the genetic basis of the evolution of drought stress tolerance capabilities of Aloe vera. This also substantiates the previously suggested notion that the evolution of unique characters in this species is perhaps due to selection and adaptive evolution rather than the phylogenetic divergence or isolation.

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A Genome-Wide Identification of Genes Undergoing Recombination and Positive Selection inNeisseria

BioMed Research International ◽

10.1155/2014/815672 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 6

Author(s):

Dong Yu ◽

Yuan Jin ◽

Zhiqiu Yin ◽

Hongguang Ren ◽

Wei Zhou ◽

...

Keyword(s):

Positive Selection ◽

Adaptive Evolution ◽

Molecular Mechanisms ◽

Acid Sites ◽

Gram Negative Bacteria ◽

Orthologous Genes ◽

Genome Wide ◽

A Genome ◽

History Of ◽

Functional Analyses

Currently, there is particular interest in the molecular mechanisms of adaptive evolution in bacteria.Neisseriais a genus of gram negative bacteria, and there has recently been considerable focus on its two human pathogenic speciesN. meningitidisandN. gonorrhoeae. Until now, no genome-wide studies have attempted to scan for the genes related to adaptive evolution. For this reason, we selected 18Neisseriagenomes (14N. meningitidis, 3N. gonorrhoeaeand 1 commensalN. lactamics) to conduct a comparative genome analysis to obtain a comprehensive understanding of the roles of natural selection and homologous recombination throughout the history of adaptive evolution. Among the 1012 core orthologous genes, we identified 635 genes with recombination signals and 10 genes that showed significant evidence of positive selection. Further functional analyses revealed that no functional bias was found in the recombined genes. Positively selected genes are prone to DNA processing and iron uptake, which are essential for the fundamental life cycle. Overall, the results indicate that both recombination and positive selection play crucial roles in the adaptive evolution ofNeisseriagenomes. The positively selected genes and the corresponding amino acid sites provide us with valuable targets for further research into the detailed mechanisms of adaptive evolution inNeisseria.

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Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

eLife ◽

10.7554/elife.25884 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 58

Author(s):

Raghavendran Partha ◽

Bharesh K Chauhan ◽

Zelia Ferreira ◽

Joseph D Robinson ◽

Kira Lathrop ◽

...

Keyword(s):

Adaptive Evolution ◽

Strong Evidence ◽

Evolutionary Rate ◽

Regulatory Sequences ◽

Phenotypic Evolution ◽

Transcriptional Enhancers ◽

Ocular Disorders ◽

Subterranean Mammals ◽

Subterranean Species ◽

Subterranean Environment

The underground environment imposes unique demands on life that have led subterranean species to evolve specialized traits, many of which evolved convergently. We studied convergence in evolutionary rate in subterranean mammals in order to associate phenotypic evolution with specific genetic regions. We identified a strong excess of vision- and skin-related genes that changed at accelerated rates in the subterranean environment due to relaxed constraint and adaptive evolution. We also demonstrate that ocular-specific transcriptional enhancers were convergently accelerated, whereas enhancers active outside the eye were not. Furthermore, several uncharacterized genes and regulatory sequences demonstrated convergence and thus constitute novel candidate sequences for congenital ocular disorders. The strong evidence of convergence in these species indicates that evolution in this environment is recurrent and predictable and can be used to gain insights into phenotype–genotype relationships.

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