Asymmetric Functional Divergence of Duplicate Genes in Yeast

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

Download Full-text

Learning retention mechanisms and evolutionary parameters of duplicate genes from their expression data

10.1101/2020.06.19.162107 ◽

2020 ◽

Author(s):

Michael DeGiorgio ◽

Raquel Assis

Keyword(s):

Gene Expression ◽

Gene Duplication ◽

Statistical Learning ◽

Gene Evolution ◽

Functional Divergence ◽

Duplicate Gene ◽

Duplicate Genes ◽

Evolutionary Mechanisms ◽

Retention Mechanisms ◽

Gene Copies

AbstractLearning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. To date, only one method—CDROM—has been developed with this goal in mind. In particular, CDROM employs gene expression distances as proxies for functional divergence, and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the underlying parameters of duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built upon a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents the best available method for classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby also highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.

Download Full-text

Rapid functional divergence of grass duplicate genes

10.1101/490524 ◽

2018 ◽

Author(s):

Xueyuan Jiang ◽

Raquel Assis

Keyword(s):

Expression Profiles ◽

Brachypodium Distachyon ◽

Functional Divergence ◽

Sequence Divergence ◽

Duplicate Gene ◽

Grass Species ◽

Small Scale ◽

Duplicate Genes ◽

Functional Conservation ◽

Gene Copies

AbstractGene duplication has played an important role in the evolution and domestication of flowering plants. Yet little is known about how plant duplicate genes evolve and are retained over long timescales, particularly those arising from small-scale duplication (SSD) rather than whole-genome duplication (WGD) events. Here we address this question in the Poaceae (grass) family by analyzing gene expression data from nine tissues of Brachypodium distachyon, Oryza sativa japonica (rice), and Sorghum bicolor (sorghum). Consistent with theoretical predictions, expression profiles of most grass genes are conserved after SSD, suggesting that functional conservation is the primary outcome of SSD in grasses. However, we also uncover support for widespread functional divergence, much of which occurs asymmetrically via the process of neofunctionalization. Moreover, neofunctionalization preferentially targets younger (child) duplicate gene copies, is associated with RNA-mediated duplication, and occurs quickly after duplication. Further analysis reveals that functional divergence of SSD-derived genes is positively correlated with both sequence divergence and tissue specificity in all three grass species, and particularly with anther expression in B. distachyon. Therefore, as found in many animal species, SSD-derived grass genes often undergo rapid functional divergence that may be driven by natural selection on male-specific phenotypes.

Download Full-text

Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast

Frontiers in Fungal Biology ◽

10.3389/ffunb.2021.642336 ◽

2021 ◽

Vol 2 ◽

Author(s):

Benjamin M. Heineike ◽

Hana El-Samad

Keyword(s):

Yeast Species ◽

Budding Yeast ◽

Kluyveromyces Lactis ◽

Functional Divergence ◽

Promoter Sequence ◽

Duplicate Genes ◽

Generating Functional ◽

Basal Expression ◽

Genes Expression ◽

Paralog Gene

Functional divergence of duplicate genes, or paralogs, is an important driver of novelty in evolution. In the model yeast Saccharomyces cerevisiae, there are 547 paralog gene pairs that survive from an interspecies Whole Genome Hybridization (WGH) that occurred ~100MYA. In this work, we report that ~1/6th (110) of these WGH paralogs pairs (or ohnologs) are differentially expressed with a striking pattern upon Protein Kinase A (PKA) inhibition. One member of each pair in this group has low basal expression that increases upon PKA inhibition, while the other has moderate and unchanging expression. For these genes, expression of orthologs upon PKA inhibition in the non-WGH species Kluyveromyces lactis and for PKA-related stresses in other budding yeasts shows unchanging expression, suggesting that lack of responsiveness to PKA was likely the typical ancestral phenotype prior to duplication. Promoter sequence analysis across related budding yeast species further revealed that the subsequent emergence of PKA-dependence took different evolutionary routes. In some examples, regulation by PKA and differential expression appears to have arisen following the WGH, while in others, regulation by PKA appears to have arisen in one of the two parental lineages prior to the WGH. More broadly, our results illustrate the unique opportunities presented by a WGH event for generating functional divergence by bringing together two parental lineages with separately evolved regulation into one species. We propose that functional divergence of two ohnologs can be facilitated through such regulatory divergence.

Download Full-text

Evolutionary mechanisms underlying the functional divergence of duplicate genes involved in vertebrates' circadian rhythm pathway

Gene ◽

10.1016/j.gene.2008.08.014 ◽

2008 ◽

Vol 426 (1-2) ◽

pp. 65-71 ◽

Cited By ~ 2

Author(s):

Mehdi Layeghifard ◽

Razieh Rabani ◽

Leila Pirhaji ◽

Bagher Yakhchali

Keyword(s):

Circadian Rhythm ◽

Functional Divergence ◽

Duplicate Genes ◽

Evolutionary Mechanisms

Download Full-text

Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data

Molecular Biology and Evolution ◽

10.1093/molbev/msaa267 ◽

2020 ◽

Author(s):

Michael DeGiorgio ◽

Raquel Assis

Keyword(s):

Gene Expression ◽

Gene Duplication ◽

Statistical Learning ◽

Gene Evolution ◽

Functional Divergence ◽

Duplicate Gene ◽

Previous Method ◽

Duplicate Genes ◽

Evolutionary Mechanisms ◽

Retention Mechanisms

Abstract Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. A previous method for achieving this goal, CDROM, employs gene expression distances as proxies for functional divergence and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the parameters driving duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built on a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents a major advancement in classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.

Download Full-text

Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis

DNA Research ◽

10.1093/dnares/dsy005 ◽

2018 ◽

Vol 25 (3) ◽

pp. 327-339 ◽

Cited By ~ 4

Author(s):

Kousuke Hanada ◽

Ayumi Tezuka ◽

Masafumi Nozawa ◽

Yutaka Suzuki ◽

Sumio Sugano ◽

...

Keyword(s):

Gene Duplication ◽

Functional Divergence ◽

Duplicate Genes

Download Full-text

In situ dissecting the evolution of gene duplication with different histone modification patterns based on high-throughput data analysis in Arabidopsis thaliana

PeerJ ◽

10.7717/peerj.10426 ◽

2021 ◽

Vol 9 ◽

pp. e10426

Author(s):

Jingjing Wang ◽

Yuriy L. Orlov ◽

Xue Li ◽

Yincong Zhou ◽

Yongjing Liu ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Gene Duplication ◽

Histone Modification ◽

Functional Divergence ◽

Genetic Regulation ◽

Sequence Divergence ◽

Single Copy ◽

Duplicate Genes ◽

Expression Divergence ◽

Sequencing Data

Background Genetic regulation is known to contribute to the divergent expression of duplicate genes; however, little is known about how epigenetic modifications regulate the expression of duplicate genes in plants. Methods The histone modification (HM) profile patterns of different modes of gene duplication, including the whole genome duplication, proximal duplication, tandem duplication and transposed duplication were characterized based on ChIP-chip or ChIP-seq datasets. In this study, 10 distinct HM marks including H2Bub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me2, H3K27me1, H3K27me3, H3K36me3 and H3K14ac were analyzed. Moreover, the features of gene duplication with different HM patterns were characterized based on 88 RNA-seq datasets of Arabidopsis thaliana. Results This study showed that duplicate genes in Arabidopsis have a more similar HM pattern than single-copy genes in both their promoters and protein-coding regions. The evolution of HM marks is found to be coupled with coding sequence divergence and expression divergence after gene duplication. We found that functionally selective constraints may impose on epigenetic evolution after gene duplication. Furthermore, duplicate genes with distinct functions have more divergence in histone modification compared with the ones with the same function, while higher expression divergence is found with mutations of chromatin modifiers. This study shows the role of epigenetic marks in regulating gene expression and functional divergence after gene duplication in plants based on sequencing data.

Download Full-text