Vertebrate Genome Size and the Impact of Transposable Elements in Genome Evolution

Genome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations, but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogen’s center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.

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The Impact of Transposable Elements in Genome Evolution and Genetic Instability and Their Implications in Various Diseases

Genomics & Informatics ◽

10.5808/gi.2014.12.3.98 ◽

2014 ◽

Vol 12 (3) ◽

pp. 98 ◽

Cited By ~ 54

Author(s):

Selvam Ayarpadikannan ◽

Heui-Soo Kim

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

Genetic Instability ◽

The Impact

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The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

Gene ◽

10.1016/j.gene.2012.07.042 ◽

2012 ◽

Vol 509 (1) ◽

pp. 7-15 ◽

Cited By ~ 165

Author(s):

Benoît Chénais ◽

Aurore Caruso ◽

Sophie Hiard ◽

Nathalie Casse

Keyword(s):

Transposable Elements ◽

Genome Size ◽

Size Increase ◽

Genetic Adaptation ◽

The Impact ◽

Stressful Environments ◽

Eukaryotic Genomes

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Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defences

10.1101/2020.05.13.092635 ◽

2020 ◽

Cited By ~ 1

Author(s):

Cécile Lorrain ◽

Alice Feurtey ◽

Mareike Möller ◽

Janine Haueisen ◽

Eva Stukenbrock

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

Related Species ◽

Plant Pathogens ◽

De Novo ◽

Zymoseptoria Tritici ◽

Closely Related Species ◽

Fungal Plant Pathogens ◽

Wide Range ◽

The Impact

AbstractTransposable elements (TEs) impact genome plasticity, architecture and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defence mechanisms that can counter-balance TE expansion and spread. Closely related species can harbour drastically different TE repertoires, suggesting variation in the efficacy of genome defences. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and Repeat-Induced Point mutation signatures in thirteen genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The thirteen genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with distinct genome compartments in all Zymoseptoria species, including chromosomal rearrangements, genes showing presence/absence variation and effectors. European Z. tritici isolates have reduced signatures of Repeat-Induced Point mutations compared to Iranian isolates and closely related species. Our study supports the hypothesis that ongoing but moderate TE mobility in Zymoseptoria species shapes pathogen genome evolution.

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Genome in toto

Genome ◽

10.1139/g98-117 ◽

1999 ◽

Vol 42 (2) ◽

pp. 361-362 ◽

Cited By ~ 7

Author(s):

Alexander E Vinogradov

Keyword(s):

Cell Cycle ◽

Genome Evolution ◽

Genome Size ◽

Cycle Duration ◽

Noncoding Dna ◽

Cell Cycle Duration ◽

The Relationship

At a certain temperature, which is a compromise for temperatures at which the species are adapted, the relationship between genome size and cell cycle duration during synchronous cleavage divisions can be very strong (r = 1.00, P < 0.01) in four closely related frogs, suggesting a functional dependence.Key words: genome size, genome evolution, genome cytoecology, noncoding DNA, cell cycle duration.

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Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq)

Genes ◽

10.3390/genes12010124 ◽

2021 ◽

Vol 12 (1) ◽

pp. 124

Author(s):

Alessio Iannucci ◽

Alexey I. Makunin ◽

Artem P. Lisachov ◽

Claudio Ciofi ◽

Roscoe Stanyon ◽

...

Keyword(s):

Genome Evolution ◽

Karyotype Evolution ◽

Genomic Data ◽

Anolis Carolinensis ◽

Vertebrate Genome ◽

Single Chromosome ◽

Sequencing Technologies ◽

Novel Approaches ◽

Genome Assemblies ◽

Generation Sequencing

The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.

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Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

Genome Research ◽

10.1101/gr.275658.121 ◽

2021 ◽

pp. gr.275658.121

Author(s):

Yuyun Zhang ◽

Zijuan Li ◽

Yu'e Zhang ◽

Kande Lin ◽

Yuan Peng ◽

...

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

Regulatory Networks ◽

Transcriptional Regulatory Network ◽

Sequence Similarity ◽

Purifying Selection ◽

Wheat Genome ◽

Specific Gene ◽

High Sequence Similarity ◽

Wheat Genome Evolution

More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.

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Variation and Evolution of Genome Size in Gymnosperms

Silvae Genetica ◽

10.2478/sg-2021-0013 ◽

2021 ◽

Vol 70 (1) ◽

pp. 156-169

Author(s):

Deepak Ohri

Keyword(s):

Transposable Elements ◽

Genome Size ◽

Narrow Range ◽

Ltr Retrotransposons ◽

General Survey ◽

Efficient Mechanism ◽

Repeat Sequences ◽

Adaptive Value ◽

Epigenetic Machinery ◽

Large Genomes

Abstract Gymnosperms show a significantly higher mean (1C=18.16, 1Cx=16.80) and a narrow range (16.89-fold) of genome sizes as compared with angiosperms. Among the 12 families the largest ranges of 1C values is shown by Ephedraceae (4.73-fold) and Cupressaceae (4.45-fold) which are partly due to polyploidy as 1Cx values vary 2.41 and 1.37-fold respectively. In rest of the families which have only diploid taxa the range of 1C values is from 1.18-fold (Cycadaeae) to 4.36-fold (Podocarpaceae). The question is how gymnosperms acquired such big genome sizes despite the rarity of recent instances of polyploidy. A general survey of different families and genera shows that gymnosperms have experienced both increase and decrease in their genome size during evolution. Various genomic components which have accounted for these large genomes have been discussed. The major contributors are the transposable elements particularly LTR-retrotransposons comprising of Ty3gypsy, Ty1copia and gymny superfamilies which are most widespread. The genomes of gymnosperms have been acquiring diverse LTR-RTs in their long evolution in the absence of any efficient mechanism of their elimination. The epigenetic machinery which silences these large tracts of repeat sequences into the stretches of heterochromatin and the adaptive value of these silenced repeat sequences need further investigation.

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