scholarly journals Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs (Xenopus)

2015 ◽  
Vol 145 (3-4) ◽  
pp. 243-252 ◽  
Author(s):  
Ben J. Evans ◽  
Taejoon Kwon
Keyword(s):  
Genome Duplication ◽  
Gene Dosage ◽  
Functional Divergence ◽  
Single Copy ◽  
Duplicated Genes ◽  
Genetic Redundancy ◽  
Molecular Polymorphism ◽  
Genome Wide ◽  
Extant Species ◽  
Almost All

Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost all extant species in this group evolved from a polyploid ancestor. To better understand the nature of selective constraints in a polyploid genome, we examined molecular polymorphism and divergence of duplicates and single-copy genes in 2 tetraploid African clawed frog species, Xenopus laevis and X. victorianus. We found that molecular polymorphism in the coding regions of putative duplicated genes was higher than in singletons, but not significantly so. Our findings also suggest that transcriptome evolution in polyploids is influenced by variation in the genome-wide mutation rate, and do not reject the hypothesis that gene dosage balance is also important.

scholarly journals Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

2017 ◽  
Author(s):  
Fiona M. Robertson ◽  
Manu Kumar Gundappa ◽  
Fabian Grammes ◽  
Torgeir R. Hvidsten ◽  
Anthony K. Redmond ◽  
...  
Keyword(s):  
Genome Duplication ◽  
Functional Divergence ◽  
Time Lag ◽  
Time Lags ◽  
Species Radiation ◽  
Evolutionary Diversification ◽  
Genome Wide ◽  
Physiological Adaptations ◽  
Lag Model ◽  
Functional Consequences

AbstractThe functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification is often highly temporally-detached from WGD. Salmonid fish, whose ancestor experienced WGD by autotetraploidization ~95 Ma (i.e. ‘Ss4R’), fit such a ‘time-lag’ model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model called ‘Lineage-specific Ohnologue Resolution’ (LORe) to address the phylogenetic and functional consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One quarter of each salmonid genome, harbouring at least 4,500 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions > 50 Myr post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that promoted salmonid species radiation. We show that LORe ohnologues are enriched for different functions than ‘older’ ohnologues that began diverging in the salmonid ancestor. LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear ‘explosively’, but can arise gradually over tens of Myr, promoting lineage-specific diversification regimes under prevailing ecological pressures.

scholarly journals Gene fractionation and function in the ancient subgenomes of maize

2016 ◽  
Author(s):  
Simon Renny-Byfield ◽  
Eli Rodgers-Melnick ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Gene Loss ◽  
Genome Duplication ◽  
Phenotypic Diversity ◽  
Single Copy ◽  
Maize Genome ◽  
Gene Deletions ◽  
Genome Wide ◽  
Association Data ◽  
Gene Fractionation ◽  
And Function

AbstractThe maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts. Furthermore, paralogous genes in the least-fractionated subgenome account for a greater degree of phenotypic diversity than those resident on the more-fractionated subgenome. We also show that the two subgenomes of maize are distinct in epigenetic characteristics. Intriguingly, analysis of singleton genes reveals that these differences persist even after fractionation is complete.

scholarly journals Conserved Molecular Function and Regulatory Subfunctionalization of the LORELEI Gene Family in Brassicaceae

2020 ◽  
Author(s):  
Jennifer A. Noble ◽  
Ming-Che James Liu ◽  
Thomas A. DeFalco ◽  
Martin Stegmann ◽  
Kara McNamara ◽  
...  
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Gene Families ◽  
Single Copy ◽  
Gene Family Evolution ◽  
Duplicated Genes ◽  
Evolutionary Mechanisms ◽  
Functional Conservation ◽  
Signaling Complex ◽  
And Function

AbstractA signaling complex comprising members of the LORELEI (LRE)-LIKE GPI-anchored protein (LLG) and Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) families perceive RAPID ALKALINIZATION FACTOR (RALF) peptides and regulate growth, development, reproduction, and immunity in Arabidopsis thaliana. Duplications in each component, which potentially could generate thousands of combinations of this signaling complex, are also evident in other angiosperms. Widespread duplication in angiosperms raises the question what evolutionary mechanisms underlie the expansion and retention of these gene families, as duplicated genes are typically rendered non-functional. As genetic and genomic resources make it a tractable model system, here we investigated this question using LLG gene family evolution and function in Brassicaceae. We first established that the LLG homologs in the Brassicaceae resulted from duplication events that pre-date the divergence of species in this family. Complementation of vegetative phenotypes in llg1 by LRE, LLG2, and LLG3 showed that the molecular functions of LLG homologs in A. thaliana are conserved. We next tested the possibility that differences in gene expression (regulatory subfunctionalization), rather than functional divergence, played a role in retention of these duplicated genes. For this, we examined the function and expression of LRE and LLG1 in A. thaliana and their single copy ortholog in Cleome violacea (Clevi LRE/LLG1), a representative species outside the Brassicaceae, but from the same order (Brassicales). We showed that expression of LLG1 and LRE did not overlap in A. thaliana and that Clevi-LRE/LLG1 expression in C. violacea encompassed all the expression domains of A. thaliana LRE + LLG1. Still, complementation experiments showed that LLG1 rescued reproductive phenotypes in lre and that Clevi LRE/LLG1 rescued both vegetative and reproductive phenotypes in llg1 and lre. Additionally, we found that expression of LLG2 and LLG3 in A. thaliana have also diverged from the expression of their corresponding single copy ortholog (Clevi LLG2/LLG3) in C. violacea. Our findings demonstrated how regulatory subfunctionalization, rather than functional divergence, underlies the retention of the LLG gene family in Brassicaceae. Our findings on the regulatory divergence and functional conservation provide an experimental framework to characterize the combinatorial assembly and function of this critical plant cell signaling complex.

scholarly journals Genome-Wide Analysis of Sex Disparities in the Genetic Architecture of Lung and Colorectal Cancers

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 686
Author(s):  
Alireza Nazarian ◽  
Alexander M. Kulminski
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Significance Level ◽  
Association Analyses ◽  
Complex Disorders ◽  
Specific Effects ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
Sex Disparities ◽  
Almost All

Almost all complex disorders have manifested epidemiological and clinical sex disparities which might partially arise from sex-specific genetic mechanisms. Addressing such differences can be important from a precision medicine perspective which aims to make medical interventions more personalized and effective. We investigated sex-specific genetic associations with colorectal (CRCa) and lung (LCa) cancers using genome-wide single-nucleotide polymorphisms (SNPs) data from three independent datasets. The genome-wide association analyses revealed that 33 SNPs were associated with CRCa/LCa at P < 5.0 × 10−6 neither males or females. Of these, 26 SNPs had sex-specific effects as their effect sizes were statistically different between the two sexes at a Bonferroni-adjusted significance level of 0.0015. None had proxy SNPs within their ±1 Mb regions and the closest genes to 32 SNPs were not previously associated with the corresponding cancers. The pathway enrichment analyses demonstrated the associations of 35 pathways with CRCa or LCa which were mostly implicated in immune system responses, cell cycle, and chromosome stability. The significant pathways were mostly enriched in either males or females. Our findings provided novel insights into the potential sex-specific genetic heterogeneity of CRCa and LCa at SNP and pathway levels.

scholarly journals Like wings of a bird: functional divergence and complementarity between HLA-A and HLA-B molecules

2020 ◽  
Author(s):  
Da Di ◽  
Jose Manuel Nunes ◽  
Wei Jiang ◽  
Alicia Sanchez-Mazas
Keyword(s):  
Balancing Selection ◽  
Functional Divergence ◽  
Peptide Binding ◽  
Human Leukocyte ◽  
Environmental Pressures ◽  
Protein Levels ◽  
Functional Complementarity ◽  
Vital Functions ◽  
Almost All ◽  
Immune Potential

Abstract Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations worldwide are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence and linear modelling) on 2,909 common and rare HLA-A, HLA-B and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defence. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intra-protein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.

scholarly journals Combinatorial CRISPR screen identifies fitness effects of gene paralogues

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicola A. Thompson ◽  
Marco Ranzani ◽  
Louise van der Weyden ◽  
Vivek Iyer ◽  
Victoria Offord ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Cell Lines ◽  
Unknown Function ◽  
Single Copy ◽  
Genetic Redundancy ◽  
Synthetic Lethal ◽  
Fitness Effects ◽  
Synthetic Lethal Interactions ◽  
Crispr Screen ◽  
Multiple Cell

AbstractGenetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. Our studies reveal the fitness effects of FAM50A/FAM50B in cancer cells.

scholarly journals Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gareth B. Gillard ◽  
Lars Grønvold ◽  
Line L. Røsæg ◽  
Matilde Mengkrog Holen ◽  
Øystein Monsen ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Whole Genome Duplication ◽  
Genome Stability ◽  
Genome Duplication ◽  
Gene Dosage ◽  
Whole Genome ◽  
Specific Expression ◽  
Tissue Specific ◽  
Genome Doubling ◽  
Expression Evolution

Abstract Background Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80–100 million years ago. Results We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of “toxic mutations”. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. Conclusions Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

Sign in / Sign up

Export Citation Format

Share Document