A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera

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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Effect of Bodily Fluids from Honey Bee (Apis mellifera) Larvae on Growth and Genome-Wide Transcriptional Response of the Causal Agent of American Foulbrood Disease (Paenibacillus larvae)

PLoS ONE ◽

10.1371/journal.pone.0089175 ◽

2014 ◽

Vol 9 (2) ◽

pp. e89175 ◽

Cited By ~ 1

Author(s):

Lina De Smet ◽

Dieter De Koker ◽

Alyse K. Hawley ◽

Leonard J. Foster ◽

Paul De Vos ◽

...

Keyword(s):

Apis Mellifera ◽

Honey Bee ◽

Transcriptional Response ◽

Causal Agent ◽

Paenibacillus Larvae ◽

American Foulbrood ◽

Bodily Fluids ◽

Genome Wide ◽

American Foulbrood Disease

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Genome-wide analysis of brain transcriptional changes in honey bee (Apis mellifera L.) queens exposed to carbon dioxide and physical manipulation

Insect Molecular Biology ◽

10.1111/j.1365-2583.2011.2011.01072.x ◽

2011 ◽

Vol 20 (3) ◽

pp. 387-398 ◽

Cited By ~ 17

Author(s):

E. L. Niño ◽

D. R. Tarpy ◽

C. Grozinger

Keyword(s):

Carbon Dioxide ◽

Apis Mellifera ◽

Honey Bee ◽

Genome Wide Analysis ◽

Genome Wide ◽

Transcriptional Changes ◽

Physical Manipulation

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Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

10.21203/rs.2.21482/v1 ◽

2020 ◽

Author(s):

Muhammad Zulfiqar Ahmad ◽

Xiangsheng Zeng ◽

Qiang Dong ◽

Sehrish Manan ◽

Huanan Jin ◽

...

Keyword(s):

Positive Selection ◽

Gene Family ◽

Expression Profiles ◽

Plant Defence ◽

Constitutive Expression ◽

Gene Families ◽

Strong Positive Selection ◽

Genome Wide ◽

A Genome ◽

Bahd Acyltransferase

Abstract Background: Members of the BAHD acyltransferase (ACT) family play important roles in plant defence against biotic and abiotic stresses. Previous genome-wide studies explored different acyltransferase gene families, but not a single study was found so far on the overall genome-wide or positive selection analyses of the BAHD family genes in Glycine max . A better understanding of the functions that specific members of this family play in stress defence can lead to better breeding strategies for stress tolerance. Results: A total of 103 genes of the BAHD family (GmACT genes) were mined from the soybean genome, which could be grouped into four phylogenetic clades (I- IV). Clade III was further divided into two sub-clades (IIIA and IIIB). In each clade, the constituent part of the gene structures and motifs were relatively conserved. These 103 genes were distributed unequally on all 20 chromosomes, and 16 paralogous pairs were found within the family. Positive selection analysis revealed important amino acids under strong positive selection, which suggests that the evolution of this gene family modulated soybean domestication. Most of the expression of ACT genes in soybean was repressed with Al 3+ and fungal elicitor exposure, except for GmACT84 , which expression increased in these conditions 2- and 3-fold, respectively. The promoter region of GmACT84 contains the maximum number of stress-responsive elements among all GmACT genes and is especially enriched in MYB-related elements. Some GmACT genes showed expression specific under specific conditions, while others showed constitutive expression in all soybean tissues or conditions analysed. Conclusions: This study provided a genome-wide analysis of the BAHD gene family and assessed their expression profiles. We found evidence of a strong positive selection of GmACT genes. Our findings will help efforts of functional characterisation of ACT genes in soybean in order to discover their involvement in growth, development, and defence mechanisms.

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P5050 A genome-wide scan for signature of positive selection in some Iranian sheep breeds

Journal of Animal Science ◽

10.2527/jas2016.94supplement4139b ◽

2016 ◽

Vol 94 (suppl_4) ◽

pp. 139-140

Author(s):

Z. Manzari ◽

H. Mehrabani Yeghaneh ◽

A. Nejati-Javaremi ◽

M. Gholizadeh ◽

M. H. Moradi

Keyword(s):

Positive Selection ◽

Sheep Breeds ◽

Genome Wide ◽

A Genome ◽

Genome Wide Scan

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The Genomes of the Livebearing Fish Species Poeciliopsis retropinna and Poeciliopsis turrubarensis Reflect Their Different Reproductive Strategies

Molecular Biology and Evolution ◽

10.1093/molbev/msaa011 ◽

2020 ◽

Vol 37 (5) ◽

pp. 1376-1386

Author(s):

Henri van Kruistum ◽

Michael W Guernsey ◽

Julie C Baker ◽

Susan L Kloet ◽

Martien A M Groenen ◽

...

Keyword(s):

Positive Selection ◽

Mammalian Species ◽

Rapid Evolution ◽

Gene Duplications ◽

Genome Wide ◽

Single Instance ◽

A Genome ◽

Livebearing Fish ◽

Genome Assemblies ◽

Genome Wide Scan

Abstract The evolution of a placenta is predicted to be accompanied by rapid evolution of genes involved in processes that regulate mother–offspring interactions during pregnancy, such as placenta formation, embryonic development, and nutrient transfer to offspring. However, these predictions have only been tested in mammalian species, where only a single instance of placenta evolution has occurred. In this light, the genus Poeciliopsis is a particularly interesting model for placenta evolution, because in this genus a placenta has evolved independently from the mammalian placenta. Here, we present and compare genome assemblies of two species of the livebearing fish genus Poeciliopsis (family Poeciliidae) that differ in their reproductive strategy: Poeciliopsis retropinna which has a well-developed complex placenta and P. turrubarensis which lacks a placenta. We applied different assembly strategies for each species: PacBio sequencing for P. retropinna (622-Mb assembly, scaffold N50 of 21.6 Mb) and 10× Genomics Chromium technology for P. turrubarensis (597-Mb assembly, scaffold N50 of 4.2 Mb). Using the high contiguity of these genome assemblies and near-completeness of gene annotations to our advantage, we searched for gene duplications and performed a genome-wide scan for genes evolving under positive selection. We find rapid evolution in major parts of several molecular pathways involved in parent–offspring interaction in P. retropinna, both in the form of gene duplications as well as positive selection. We conclude that the evolution of the placenta in the genus Poeciliopsis is accompanied by rapid evolution of genes involved in similar genomic pathways as found in mammals.

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A fully integrated machine learning scan of selection in the chimpanzee genome

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa061 ◽

2020 ◽

Vol 2 (3) ◽

Author(s):

Jessica Nye ◽

Mayukh Mondal ◽

Jaume Bertranpetit ◽

Hafid Laayouni

Keyword(s):

Machine Learning ◽

Positive Selection ◽

Demographic History ◽

Effective Population ◽

Fully Integrated ◽

Genome Wide ◽

A Genome ◽

Machine Learning Approach ◽

History Of ◽

The Impact

Abstract After diverging, each chimpanzee subspecies has been the target of unique selective pressures. Here, we employ a machine learning approach to classify regions as under positive selection or neutrality genome-wide. The regions determined to be under selection reflect the unique demographic and adaptive history of each subspecies. The results indicate that effective population size is important for determining the proportion of the genome under positive selection. The chimpanzee subspecies share signals of selection in genes associated with immunity and gene regulation. With these results, we have created a selection map for each population that can be displayed in a genome browser (www.hsb.upf.edu/chimp_browser). This study is the first to use a detailed demographic history and machine learning to map selection genome-wide in chimpanzee. The chimpanzee selection map will improve our understanding of the impact of selection on closely related subspecies and will empower future studies of chimpanzee.

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