Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

AbstractHighly conserved noncoding elements (CNEs) comprise a significant proportion of the genomes of multicellular eukaryotes. The function of most CNEs remains elusive, but growing evidence indicates they are under some form of purifying selection. Noncoding regions in many species also harbor large numbers of transposable element (TE) insertions, which are typically lineage specific and depleted in exons because of their deleterious effects on gene function or expression. However, it is currently unknown whether the landscape of TE insertions in noncoding regions is random or influenced by purifying selection on CNEs. Here we combine comparative and population genomic data in Drosophila melanogaster to show that abundance of TE insertions in intronic and intergenic CNEs is reduced relative to random expectation, supporting the idea that selective constraints on CNEs eliminate a proportion of TE insertions in noncoding regions. However, we find no difference in the allele frequency spectra for polymorphic TE insertions in CNEs versus those in unconstrained spacer regions, suggesting that the distribution of fitness effects acting on observable TE insertions is similar across different functional compartments in noncoding DNA. Our results provide evidence that selective constraints on CNEs contribute to shaping the landscape of TE insertion in eukaryotic genomes, and provide further evidence supporting the conclusion that CNEs are indeed functionally constrained and not simply mutational cold spots.

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Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

Nature Communications ◽

10.1038/s41467-019-13730-0 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 9

Author(s):

Pierre Baduel ◽

Leandro Quadrana ◽

Ben Hunter ◽

Kirsten Bomblies ◽

Vincent Colot

Keyword(s):

Transposable Element ◽

Local Adaptation ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Purifying Selection ◽

Whole Genome ◽

Genome Resequencing ◽

Environmentally Responsive ◽

Main Driver ◽

Whole Genome Resequencing

AbstractPolyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leverage whole-genome resequencing data available for ~300 individuals of Arabidopsis arenosa, a well characterized natural diploid-autotetraploid plant species, to address these questions. Based on 43,176 TE insertions we detect in these genomes, we demonstrate that relaxed purifying selection rather than transposition bursts is the main driver of TE over-accumulation after WGD. Furthermore, the increased pool of TE insertions in tetraploids is especially enriched within or near environmentally responsive genes. Notably, we show that the major flowering-time repressor gene FLC is disrupted by a TE insertion specifically in the rapid-cycling tetraploid lineage that colonized mainland railways. Together, our findings indicate that tetrasomy leads to an enhanced accumulation of genic TE insertions, some of which likely contribute to local adaptation.

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DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity

10.1101/039602 ◽

2016 ◽

Author(s):

Steven R Eichten ◽

Tim Stuart ◽

Akanksha Srivastava ◽

Ryan Lister ◽

Justin O Borevitz

Keyword(s):

Dna Methylation ◽

Genetic Variation ◽

Transposable Element ◽

Brachypodium Distachyon ◽

Genomic Diversity ◽

Reference Sequence ◽

Epigenetic Mark ◽

Cereal Species ◽

Genome Bisulfite Sequencing ◽

Methylation Variation

DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon. Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertion or deletions are associated with nearby differential methylation. This study highlights the importance of genetic variation when assessing DNA methylation variation between samples and provides a valuable map of DNA methylation across diverse re-sequenced accessions of this model cereal species.

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Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley

Plants ◽

10.3390/plants9111439 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1439

Author(s):

Shazia Rehman ◽

Bodil Jørgensen ◽

Ejaz Aziz ◽

Riffat Batool ◽

Samar Naseer ◽

...

Keyword(s):

Gene Family ◽

Protease Inhibitors ◽

Brachypodium Distachyon ◽

In Silico Analysis ◽

Purifying Selection ◽

Serpin Gene ◽

Bioinformatic Tools ◽

Duplication Events ◽

Genome Level

Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2–P1′) identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

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Genome-Wide Identification, Evolution, and Expression Analysis of TPS and TPP Gene Families in Brachypodium distachyon

Plants ◽

10.3390/plants8100362 ◽

2019 ◽

Vol 8 (10) ◽

pp. 362 ◽

Cited By ~ 3

Author(s):

Song Wang ◽

Kai Ouyang ◽

Kai Wang

Keyword(s):

Stress Responses ◽

Brachypodium Distachyon ◽

Interaction Network ◽

Purifying Selection ◽

Gene Interaction ◽

Gene Families ◽

Gene Interaction Network ◽

Genome Wide ◽

Duplication Events ◽

Gene Structures

Trehalose biosynthesis enzyme homologues in plants contain two families, trehalose-6-phosphate synthases (TPSs) and trehalose-6-phosphate phosphatases (TPPs). Both families participate in trehalose synthesis and a variety of stress-resistance processes. Here, nine BdTPS and ten BdTPP genes were identified based on the Brachypodium distachyon genome, and all genes were classified into three classes. The Class I and Class II members differed substantially in gene structures, conserved motifs, and protein sequence identities, implying varied gene functions. Gene duplication analysis showed that one BdTPS gene pair and four BdTPP gene pairs are formed by duplication events. The value of Ka/Ks (non-synonymous/synonymous) was less than 1, suggesting purifying selection in these gene families. The cis-elements and gene interaction network prediction showed that many family members may be involved in stress responses. The quantitative real-time reverse transcription (qRT-PCR) results further supported that most BdTPSs responded to at least one stress or abscisic acid (ABA) treatment, whereas over half of BdTPPs were downregulated after stress treatment, implying that BdTPSs play a more important role in stress responses than BdTPPs. This work provides a foundation for the genome-wide identification of the B. distachyon TPS–TPP gene families and a frame for further studies of these gene families in abiotic stress responses.

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Molecular Characterization Revealed the Role of Thaumatin-Like Proteins of Bread Wheat in Stress Response

Frontiers in Plant Science ◽

10.3389/fpls.2021.807448 ◽

2022 ◽

Vol 12 ◽

Author(s):

Alok Sharma ◽

Himanshu Sharma ◽

Ruchika Rajput ◽

Ashutosh Pandey ◽

Santosh Kumar Upadhyay

Keyword(s):

Stress Response ◽

Recombinant Expression ◽

Brachypodium Distachyon ◽

Crop Improvement ◽

Purifying Selection ◽

Pathogenesis Related ◽

Duplication Events ◽

Improvement Programs ◽

Conserved Gene

Thaumatin-like proteins (TLPs) are related to pathogenesis-related-5 (PR-5) family and involved in stress response. Herein, a total of 93 TLP genes were identified in the genome of Triticum aestivum. Further, we identified 26, 27, 39, and 37 TLP genes in the Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Zea mays genomes for comparative characterization, respectively. They could be grouped into small and long TLPs with conserved thaumatin signature motif. Tightly clustered genes exhibited conserved gene and protein structure. The physicochemical analyses suggested significant differences between small and long TLPs. Evolutionary analyses suggested the role of duplication events and purifying selection in the expansion of the TLP gene family. Expression analyses revealed the possible roles of TLPs in plant development and abiotic and fungal stress response. Recombinant expression of TaTLP2-B in Saccharomyces cerevisiae provided significant tolerance against cold, heat, osmotic, and salt stresses. The results depicted the importance of TLPs in cereal crops that would be highly useful in future crop improvement programs.

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Population genetics of transposable element load: a mechanistic account of observed overdispersion

10.1101/2020.11.16.382945 ◽

2020 ◽

Author(s):

Ronald D. Smith ◽

Joshua R. Puzey ◽

Gregory D. Conradi Smith

Keyword(s):

Population Genetics ◽

Transposable Element ◽

Natural Populations ◽

Purifying Selection ◽

Death Process ◽

Stationary Population ◽

Population Distributions ◽

Evolutionary Genetic ◽

Genetic Mechanisms ◽

Copy And Paste

AbstractIn an empirical analysis of transposable element (TE) abundance within natural populations of Mimulus guttatus and Drosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 100). To obtain insight regarding those evolutionary genetic mechanisms that are may underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and it extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analysis of stationary population distributions of TE load reveal that overdispersion is most likely to arise via copy-and-paste (as opposed to cut-and-paste) dynamics. Parameter studies suggest that overdispersed population distributions of TE abundance are probably not a consequence of purifying selection on total element load.

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Asexual reproduction drives the reduction of transposable element load

10.1101/501361 ◽

2018 ◽

Cited By ~ 2

Author(s):

Jens Bast ◽

Kamil S. Jaron ◽

Donovan Schuseil ◽

Denis Roze ◽

Tanja Schwander

Keyword(s):

Saccharomyces Cerevisiae ◽

Transposable Element ◽

Sexual Reproduction ◽

Asexual Reproduction ◽

Direct Evidence ◽

Purifying Selection ◽

Load Reduction ◽

Over Time

AbstractTheory predicts that sexual reproduction can both facilitate and restrain transposable element (TE) accumulation by providing TEs with a means of spreading to all individuals in a population and facilitating TE load reduction via purifying selection. By quantifying genomic TE loads over time in experimental sexual and asexual Saccharomyces cerevisiae populations, we provide direct evidence that asexual reproduction drives a reduction of TE loads. We show, using simulations, that this reduction occurs via evolution of TE activity, most likely via increased excision rates. Thus, sex is a major driver of genomic TE loads and at the root of the success of TEs.

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Transposable element over-accumulation in autopolyploids results from relaxed purifying selection and provides variants for rapid local adaptation

10.1101/686584 ◽

2019 ◽

Author(s):

P. Baduel ◽

L. Quadrana ◽

B. Hunter ◽

K. Bomblies ◽

V. Colot

Keyword(s):

Transposable Element ◽

Local Adaptation ◽

Genome Duplication ◽

Purifying Selection ◽

Whole Genome ◽

Abiotic And Biotic Stress ◽

Genome Resequencing ◽

Stress Response Genes ◽

Main Driver ◽

Whole Genome Resequencing

AbstractPolyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leveraged whole-genome resequencing data of ∼300 individual Arabidopsis arenosa plants, a well characterized natural diploid-autotetraploid species, to address these questions. Based on 43,176 polymorphic TE insertions we detected in these genomes, we demonstrate that relaxed purifying selection rather than transposition bursts is the main driver of TE over-accumulation after WGD. Furthermore, the increased pool of TE insertions in tetraploids is especially enriched within or near abiotic and biotic stress response genes. Notably, we uncovered one such insertion in a major flowering-time repressor gene and found that the resulting allele is specific to the rapid-cycling tetraploid lineage that colonized mainland railways. Together, our findings indicate that tetrasomy by itself leads to an enhanced tolerance to accumulating genic TE variants, some of which can potentially contribute to local adaptation.

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Asexual reproduction reduces transposable element load in experimental yeast populations

eLife ◽

10.7554/elife.48548 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 13

Author(s):

Jens Bast ◽

Kamil S Jaron ◽

Donovan Schuseil ◽

Denis Roze ◽

Tanja Schwander

Keyword(s):

Saccharomyces Cerevisiae ◽

Transposable Element ◽

Sexual Reproduction ◽

Asexual Reproduction ◽

Direct Evidence ◽

Purifying Selection ◽

Load Reduction ◽

Over Time

Theory predicts that sexual reproduction can either facilitate or restrain transposable element (TE) accumulation by providing TEs with a means of spreading to all individuals in a population, versus facilitating TE load reduction via purifying selection. By quantifying genomic TE loads over time in experimental sexual and asexual Saccharomyces cerevisiae populations, we provide direct evidence that TE loads decrease rapidly under asexual reproduction. We show, using simulations, that this reduction may occur via evolution of TE activity, most likely via increased excision rates. Thus, sex is a major driver of genomic TE loads and at the root of the success of TEs.

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