scholarly journals Rapid functional divergence of grass duplicate genes

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.

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

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.

scholarly journals Gradual divergence and diversification of mammalian duplicate gene functions

2014 ◽  
Author(s):  
Raquel Assis ◽  
Doris Bachtrog
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Duplicate Gene ◽  
Raw Material ◽  
Duplicate Genes ◽  
New Genes ◽  
Using Data

Gene duplication provides raw material for the evolution of functional innovation. We recently developed a phylogenetic method to classify the evolutionary processes underlying the retention and functional evolution of duplicate genes by quantifying divergence of their gene expression profiles. Here, we apply our method to pairs of duplicate genes in eight mammalian genomes, using data from 11 distinct tissues to construct spatial gene expression profiles. We find that young mammalian duplicates are often functionally conserved, and that functional divergence gradually increases with evolutionary distance between species. Examination of expression patterns in genes with conserved and new functions supports the ?out-of-testes? hypothesis, in which new genes arise with testis-specific functions and acquire functions in other tissues over time. While new functions tend to be tissue-specific, there is no bias toward expression in any particular tissue. Thus, duplicate genes acquire a diversity of functions outside of the testes, possibly contributing to the origin of a multitude of complex phenotypes during mammalian evolution.

scholarly journals Global Survey and Expressions of the Phosphate Transporter Gene Families in Brassica napus and Their Roles in Phosphorus Response

2020 ◽  
Vol 21 (5) ◽  
pp. 1752 ◽  
Author(s):  
Jin Yang ◽  
Jie Zhou ◽  
Hong-Jun Zhou ◽  
Mang-Mang Wang ◽  
Ming-Ming Liu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Functional Divergence ◽  
Gene Families ◽  
Small Scale ◽  
Transporter Gene ◽  
Promoter Regions ◽  
Network Analyses ◽  
Group I

Phosphate (Pi) transporters play critical roles in Pi acquisition and homeostasis. However, currently little is known about these genes in oil crops. In this study, we aimed to characterize the five Pi transporter gene families (PHT1-5) in allotetraploid Brassica napus. We identified and characterized 81 putative PHT genes in B. napus (BnaPHTs), including 45 genes in PHT1 family (BnaPHT1s), four BnaPHT2s, 10 BnaPHT3s, 13 BnaPHT4s and nine BnaPHT5s. Phylogenetic analyses showed that the largest PHT1 family could be divided into two groups (Group I and II), while PHT4 may be classified into five, Groups I-V. Gene structure analysis revealed that the exon-intron pattern was conservative within the same family or group. The sequence characteristics of these five families were quite different, which may contribute to their functional divergence. Transcription factor (TF) binding network analyses identified many potential TF binding sites in the promoter regions of candidates, implying their possible regulating patterns. Collinearity analysis demonstrated that most BnaPHTs were derived from an allopolyploidization event (~40.7%) between Brassica rapa and Brassica oleracea ancestors, and small-scale segmental duplication events (~39.5%) in the descendant. RNA-Seq analyses proved that many BnaPHTs were preferentially expressed in leaf and flower tissues. The expression profiles of most colinearity-pairs in B. napus are highly correlated, implying functional redundancy, while a few pairs may have undergone neo-functionalization or sub-functionalization during evolution. The expression levels of many BnaPHTs tend to be up-regulated by different hormones inductions, especially for IAA, ABA and 6-BA treatments. qRT-PCR assay demonstrated that six BnaPHT1s (BnaPHT1.11, BnaPHT1.14, BnaPHT1.20, BnaPHT1.35, BnaPHT1.41, BnaPHT1.44) were significantly up-regulated under low- and/or rich- Pi conditions in B. napus roots. This work analyzes the evolution and expression of the PHT family in Brassica napus, which will help further research on their role in Pi transport.

scholarly journals Complexity of Gene Expression Evolution after Duplication: Protein Dosage Rebalancing

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Igor B. Rogozin
Keyword(s):  
Gene Expression ◽  
Gene Dosage ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Sequence Divergence ◽  
Functional Similarity ◽  
Gene Dosage Effect ◽  
Cellular Context ◽  
Expression Evolution ◽  
Gene Expression Evolution

Ongoing debates about functional importance of gene duplications have been recently intensified by a heated discussion of the “ortholog conjecture” (OC). Under the OC, which is central to functional annotation of genomes, orthologous genes are functionally more similar than paralogous genes at the same level of sequence divergence. However, a recent study challenged the OC by reporting a greater functional similarity, in terms of gene ontology (GO) annotations and expression profiles, among within-species paralogs compared to orthologs. These findings were taken to indicate that functional similarity of homologous genes is primarily determined by the cellular context of the genes, rather than evolutionary history. Subsequent studies suggested that the OC appears to be generally valid when applied to mammalian evolution but the complete picture of evolution of gene expression also has to incorporate lineage-specific aspects of paralogy. The observed complexity of gene expression evolution after duplication can be explained through selection for gene dosage effect combined with the duplication-degeneration-complementation model. This paper discusses expression divergence of recent duplications occurring before functional divergence of proteins encoded by duplicate genes.

scholarly journals The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes

2015 ◽  
Vol 112 (33) ◽  
pp. 10185-10191 ◽  
Author(s):  
Zhiqiang Wu ◽  
Jocelyn M. Cuthbert ◽  
Douglas R. Taylor ◽  
Daniel B. Sloan
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Divergence ◽  
Duplicate Gene ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Gene Copies ◽  
Repeated Evolution ◽  
Multiple Species ◽  
Gain Loss ◽  
High Degree

Across eukaryotes, mitochondria exhibit staggering diversity in genomic architecture, including the repeated evolution of multichromosomal structures. Unlike in the nucleus, where mitosis and meiosis ensure faithful transmission of chromosomes, the mechanisms of inheritance in fragmented mitochondrial genomes remain mysterious. Multichromosomal mitochondrial genomes have recently been found in multiple species of flowering plants, including Silene noctiflora, which harbors an unusually large and complex mitochondrial genome with more than 50 circular-mapping chromosomes totaling ∼7 Mb in size. To determine the extent to which such genomes are stably maintained, we analyzed intraspecific variation in the mitochondrial genome of S. noctiflora. Complete genomes from two populations revealed a high degree of similarity in the sequence, structure, and relative abundance of mitochondrial chromosomes. For example, there are no inversions between the genomes, and there are only nine SNPs in 25 kb of protein-coding sequence. Remarkably, however, these genomes differ in the presence or absence of 19 entire chromosomes, all of which lack any identifiable genes or contain only duplicate gene copies. Thus, these mitochondrial genomes retain a full gene complement but carry a highly variable set of chromosomes that are filled with presumably dispensable sequence. In S. noctiflora, conventional mechanisms of mitochondrial sequence divergence are being outstripped by an apparently nonadaptive process of whole-chromosome gain/loss, highlighting the inherent challenge in maintaining a fragmented genome. We discuss the implications of these findings in relation to the question of why mitochondria, more so than plastids and bacterial endosymbionts, are prone to the repeated evolution of multichromosomal genomes.

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

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.

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

PeerJ ◽  
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.

scholarly journals Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots

2017 ◽  
Author(s):  
He Huang ◽  
Malia A. Gehan ◽  
Sarah E. Huss ◽  
Sophie Alvarez ◽  
Cesar Lizarraga ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Clock Genes ◽  
Expression Profiles ◽  
Affinity Purification ◽  
Brachypodium Distachyon ◽  
Sequence Divergence ◽  
Plant Responses ◽  
Crop Species ◽  
Physiological Level ◽  
High Sequence Divergence

ABSTRACTPlant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant Arabidopsis thaliana and crop species, circadian clock factors have been identified as critical for growth, flowering and circadian rhythms. Outside of A. thaliana, however, little is known about the molecular function of clock genes. Therefore, we sought to compare the function of Brachypodium distachyon and Seteria viridis orthologs of EARLY FLOWERING3, a key clock gene in A. thaliana. To identify both cycling genes and putative ELF3 functional orthologs in S. viridis, a circadian RNA-seq dataset and online query tool (Diel Explorer) was generated as a community resource to explore expression profiles of Setaria genes under constant conditions after photo- or thermo-entrainment. The function of ELF3 orthologs from A. thaliana, B. distachyon, and S. viridis were tested for complementation of an elf3 mutation in A. thaliana. Despite comparably low sequence identity versus AtELF3 (less than 37%), both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time and arrhythmic clock phenotypes. Molecular analysis using affinity purification and mass spectrometry to compare physical interactions also found that BdELF3 and SvELF3 could be integrated into similar complexes and networks as AtELF3, including forming a composite evening complex. Thus, we find that, despite 180 million years of separation, BdELF3 and SvELF3 can functionally complement loss of ELF3 at the molecular and physiological level.One Sentence SummaryOrthologs of a key circadian clock component ELF3 from grasses functionally complement the Arabidopsis counterpart at the molecular and physiological level, in spite of high sequence divergence.

scholarly journals Analysis of Sequence Divergence in Mammalian ABCGs Predicts a Structural Network of Residues That Underlies Functional Divergence

2021 ◽  
Vol 22 (6) ◽  
pp. 3012
Author(s):  
James I. Mitchell-White ◽  
Thomas Stockner ◽  
Nicholas Holliday ◽  
Stephen J. Briddon ◽  
Ian D. Kerr
Keyword(s):  
Substrate Specificity ◽  
Functional Divergence ◽  
3D Structure ◽  
Sequence Divergence ◽  
Conformational Flexibility ◽  
Substrate Selectivity ◽  
Multiple Sequence ◽  
Atp Binding Cassette Transporters ◽  
Structural Network ◽  
Wide Substrate Specificity

The five members of the mammalian G subfamily of ATP-binding cassette transporters differ greatly in their substrate specificity. Four members of the subfamily are important in lipid transport and the wide substrate specificity of one of the members, ABCG2, is of significance due to its role in multidrug resistance. To explore the origin of substrate selectivity in members 1, 2, 4, 5 and 8 of this subfamily, we have analysed the differences in conservation between members in a multiple sequence alignment of ABCG sequences from mammals. Mapping sets of residues with similar patterns of conservation onto the resolved 3D structure of ABCG2 reveals possible explanations for differences in function, via a connected network of residues from the cytoplasmic to transmembrane domains. In ABCG2, this network of residues may confer extra conformational flexibility, enabling it to transport a wider array of substrates.

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