scholarly journals Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection

2021 ◽  
Author(s):  
Yuan Huang ◽  
Jiahui Chen ◽  
Chuan Dong ◽  
Dylan Sosa ◽  
Shengqian Xia ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Duplication ◽  
Positive Selection ◽  
Specific Gene ◽  
Phenotypic Evolution ◽  
New Genes ◽  
Parental Gene ◽  
New Gene ◽  
Species Specific ◽  
Partial Gene Duplication

Abstract Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana. EXOV is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNA-seq analyses revealed that, despite its young age, EXOV has acquired many novel direct and indirect interactions in which the parental gene does not engage. This observation is consistent with the high, selection-driven substitution rate of its encoded protein, in contrast to the slowly evolving EXOVL, suggesting an important role for EXOV in phenotypic evolution. We observed significant differentiation of morphological changes for all phenotypes assessed in genome-edited and T-DNA insertional single mutants and in double T-DNA insertion mutants in EXOV and EXOVL. We discovered a substantial divergence of phenotypic effects by principal component analyses, suggesting neofunctionalization of the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological evolution in A. thaliana.

scholarly journals Species-specific gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection

2021 ◽  
Author(s):  
Yuan Huang ◽  
Jiahui Chen ◽  
Chuan Dong ◽  
Dylan Sosa ◽  
Shengqian Xia ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Morphological Traits ◽  
Morphological Changes ◽  
Specific Gene ◽  
Phenotypic Evolution ◽  
Parental Gene ◽  
Dna Insertion ◽  
New Gene ◽  
Species Specific ◽  
Insertion Mutants

Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, the ways in which new duplicate genes contribute to phenotypic evolution remain largely unknown, especially in plants, owing to a lack of experimental and phenotypic data. In this study, we identified the new gene Exov, derived from a partial gene region duplication of its parental gene Exov-L, which is a member of an exonuclease family, into a different chromosome in Arabidopsis thaliana. We experimentally investigated the phenotypic effects of Exov and Exov-L in an attempt to understand how the new gene diverged from the parental copy and contributes to phenotypic evolution. Evolutionary analysis demonstrated that Exov is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNAseq analyses reveal that the new gene, despite its young age, has acquired a large number of novel direct and indirect interactions in which the parental gene does not engage. This is consistent with a high, selection-driven substitution rate in the protein sequence encoded by Exov in contrast to the slowly evolving Exov-L, suggesting an important role for Exov in phenotypic evolution. We analyzed phenotypic effects of exov and exov-l single T-DNA-insertion mutants; double exov, exov-l T-DNA insertion mutants; and CRISPR/Cas9-mediated exovcrp and exov-lcrp knockouts on seven morphological traits in both the new and parental genes. We detected significant segregation of morphological changes for all seven traits when assessed in terms of single mutants, as well as morphological changes for seven traits associated with segregation of double exov, exov-l mutants. Substantial divergence of phenotypic effects between new and parental genes was revealed by principal component analyses, suggesting neofunctionalization in the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological and developmental evolution in Arabidopsis thaliana.

scholarly journals Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species

2020 ◽  
Author(s):  
Thomas M. Winkelmüller ◽  
Frederickson Entila ◽  
Shajahan Anver ◽  
Anna Piasecka ◽  
Baoxing Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Binding Sites ◽  
Microbial Control ◽  
Purifying Selection ◽  
Wrky Transcription Factor ◽  
Specific Gene ◽  
Specific Expression ◽  
Brassicaceae Species ◽  
Species Specific

AbstractPlants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species for PTI responses to the MAMP flg22, we identified a set of genes with expression changes under purifying selection in the Brassicaceae species and genes exhibiting species-specific expression signatures. Variation in flg22-triggered transcriptome and metabolome responses across Brassicaceae species was incongruent with their phylogeny while expression changes were strongly conserved within A. thaliana, suggesting directional selection for some species-specific gene expression. We found the enrichment of WRKY transcription factor binding sites in 5’-regulatory regions in conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene responses in PTI. Our findings advance our understanding of transcriptome evolution during biotic stress.

scholarly journals ARABIDILLO gene homologues in basal land plants: species-specific gene duplication and likely functional redundancy

Planta ◽  
2012 ◽  
Vol 236 (6) ◽  
pp. 1927-1941 ◽  
Author(s):  
Laura A. Moody ◽  
Younousse Saidi ◽  
Emma J. Smiles ◽  
Susan J. Bradshaw ◽  
Matthew Meddings ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Redundancy ◽  
Land Plants ◽  
Specific Gene ◽  
Species Specific

scholarly journals Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Duo Chen ◽  
Peng-Cheng Yan ◽  
Yan-Ping Guo
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Specific Gene ◽  
Differential Adaptation ◽  
Expression Bias ◽  
Parental Gene ◽  
Species Specific ◽  
Go Terms ◽  
Allotetraploid Species

Abstract Background Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsoniana arose independently from allopolyploidization between diploid A. acuminata and A. asiatica. The genetics and geography of these origins are clear from previous studies, providing a solid basis for comparing gene expression patterns of sibling allopolyploid species that arose independently. Results We conducted comparative RNA-sequencing analyses on the two Achillea tetraploid species and their diploid progenitors to evaluate: 1) species-specific gene expression and coexpression across the four species; 2) patterns of inheritance of parental gene expression; 3) parental contributions to gene expression in the allotetraploid species, and homeolog expression bias. Diploid A. asiatica showed a higher contribution than diploid A. acuminata to the transcriptomes of both tetraploids and also greater homeolog bias in these transcriptomes, possibly reflecting a maternal effect. Comparing expressed genes in the two allotetraploids, we found expression of ca. 30% genes were species-specific in each, which were most enriched for GO terms pertaining to “defense response”. Despite species-specific and differentially expressed genes between the two allotetraploids, they display similar transcriptome changes in comparison to their diploid progenitors. Conclusion Two independently originated Achillea allotetraploid species exhibited difference in gene expression, some of which must be related to differential adaptation during their post-speciation evolution. On the other hand, they showed similar expression profiles when compared to their progenitors. This similarity might be expected when pairs of merged diploid genomes in tetraploids are similar, as is the case in these two particular allotetraploids.

scholarly journals Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum

2020 ◽  
Vol 37 (9) ◽  
pp. 2601-2615 ◽  
Author(s):  
Rosa Fernández ◽  
Marina Marcet-Houben ◽  
Fabrice Legeai ◽  
Gautier Richard ◽  
Stéphanie Robin ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Acyrthosiphon Pisum ◽  
High Capacity ◽  
Chromatin Accessibility ◽  
Pea Aphid ◽  
Specific Gene ◽  
Gene Duplications ◽  
Evolutionary Mechanisms ◽  
Ancestral Gene ◽  
Species Specific

Abstract Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host–symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.

scholarly journals Isolation of botulinolysin, a thiol-activated hemolysin, from serotype D Clostridium botulinum : A species-specific gene duplication in Clostridia

2016 ◽  
Vol 193 ◽  
pp. 20-29
Author(s):  
Tomonori Suzuki ◽  
Thomas Nagano ◽  
Koichi Niwa ◽  
Shingo Mutoh ◽  
Masataka Uchino ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Clostridium Botulinum ◽  
Specific Gene ◽  
Species Specific

scholarly journals Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1819
Author(s):  
Haorong Li ◽  
Chunyan Chen ◽  
Zhongkai Wang ◽  
Kun Wang ◽  
Yongxin Li ◽  
...  
Keyword(s):  
De Novo ◽  
General Pattern ◽  
Gene Identification ◽  
Whole Genome ◽  
Genome Data ◽  
New Genes ◽  
Emergence Rate ◽  
New Gene ◽  
Species Specific ◽  
Lineage Specific Genes

Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo–origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.

scholarly journals Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes

2001 ◽  
Vol 11 (4) ◽  
pp. 555-565 ◽  
Author(s):  
I. King Jordan ◽  
Kira S. Makarova ◽  
John L. Spouge ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Gene Duplication ◽  
Average Score ◽  
Specific Gene ◽  
Tandem Gene Duplication ◽  
New Genes ◽  
A Genome ◽  
Prokaryotic Genomes ◽  
Bacterial Chromosomes ◽  
Large Clusters ◽  
Lineage Specific Gene

Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification of the major prokaryotic lineages (lineage-specific expansions) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (∼5%–33%) of their coding capacities. A positive correlation exists between the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that lineage-specific expansions are made up of relatively recently duplicated genes, >90% of the detected clusters consists of only two to four genes. The more common smaller clusters tend to include genes with higher pairwise similarity (as reflected by average score density) than larger clusters. Regardless of size, cluster members tend to be located more closely on bacterial chromosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes also contain rare large clusters of size ≥20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss.

scholarly journals Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum

2019 ◽  
Author(s):  
Rosa Fernández ◽  
Marina Marcet-Houben ◽  
Fabrice Legeai ◽  
Gautier Richard ◽  
Stéphanie Robin ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Acyrthosiphon Pisum ◽  
High Capacity ◽  
Chromatin Accessibility ◽  
Pea Aphid ◽  
Specific Gene ◽  
Gene Duplications ◽  
Evolutionary Mechanisms ◽  
Ancestral Gene ◽  
Species Specific

AbstractEcology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem-sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there is a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed to tackle the history of duplicated genes to pave the road towards understanding the role of gene duplication in ecological adaptation.

scholarly journals PiggyBac Transposable Element-derived 1 controls Neuronal Progenitor Identity, Stress Sensing and mammal-specific paraspeckles

2021 ◽  
Author(s):  
Tamas Rasko ◽  
Amit Pande ◽  
Kathrin Radscheit ◽  
Annika Zink ◽  
Manvendra Singh ◽  
...  
Keyword(s):  
Transposable Element ◽  
Neural Progenitor Cells ◽  
Functional Integration ◽  
Specific Gene ◽  
Protein Protein Interaction ◽  
Neuronal Progenitor ◽  
System A ◽  
New Genes ◽  
New Gene ◽  
Stress Sensing

The evolution and functional integration of new genes, especially those that become core to key functions, remains enigmatic. We consider the mammal-specific gene, piggyBac transposable element derived 1 (PGBD1), implicated in neuronal disorders. While it no longer recognises piggyBac transposon-like inverted repeats and transposase functionality having been lost, it has evolved a core role in neural homeostasis. Depletion of PGBD1 triggers accumulation of mammal-specific paraspeckles and neural differentiation. It acts by two modalities, DNA binding and protein-protein interaction. As a transcriptional repressor of (lnc)NEAT1, the backbone of paraspeckles, it inhibits paraspeckle formation in neural progenitor cells (NPCs). At the protein level it is associated with the stress response system, a function partially shared with (lnc)NEAT1. PGBD1 thus presents as an unusual exemplar of new gene creation, being a recently acquired multi-function, multi-modal gene. Mammalian specificity associated with control of a mammal-specific structure implies coevolution of new genes with new functions.

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