The challenges of predicting transposable element activity in hybrids

Hénault, Mathieu

doi:10.1007/s00294-021-01169-0

Cited by 7 publications

(3 citation statements)

References 57 publications

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“…The nature of TE repression mechanisms in yeast may provide limited opportunity for the deregulation of TE activity levels in hybrids (Hénault, 2021 ). TE overexpression has been mostly observed in species regulating TE propagation at the transcriptional level.…”

Section: Discussionmentioning

confidence: 99%

Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids

Drouin

Hénault

Hallin

et al. 2021

Front. Fungal Biol.

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Transposable element (TE) insertions are a source of structural variation and can cause genetic instability and gene expression changes. A host can limit the spread of TEs with various repression mechanisms. Many examples of plant and animal interspecific hybrids show disrupted TE repression leading to TE propagation. Recent studies in yeast did not find any increase in transposition rate in hybrids. However, this does not rule out the possibility that the transcriptional or translational activity of TEs increases following hybridization because of a disruption of the host TE control mechanisms. Thus, whether total expression of a TE family is higher in hybrids than in their parental species remains to be examined. We leveraged publically available RNA-seq and ribosomal profiling data on yeast artificial hybrids of the Saccharomyces genus and performed differential expression analysis of their LTR retrotransposons (Ty elements). Our analyses of total mRNA levels show that Ty elements are generally not differentially expressed in hybrids, even when the hybrids are exposed to a low temperature stress condition. Overall, only 2/26 Ty families show significantly higher expression in the S. cerevisiae × S. uvarum hybrids while there are 3/26 showing significantly lower expression in the S. cerevisiae x S. paradoxus hybrids. Our analysis of ribosome profiling data of S. cerevisiae × S. paradoxus hybrids shows similar translation efficiency of Ty in both parents and hybrids, except for Ty1_cer showing higher translation efficiency. Overall, our results do not support the hypothesis that hybridization could act as a systematic trigger of TE expression in yeast and suggest that the impact of hybridization on TE activity is strain and TE specific.

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Section: Discussionmentioning

confidence: 99%

Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids

Drouin

Hénault

Hallin

et al. 2021

Front. Fungal Biol.

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“…In fact, recent hybrids between incipient yeast species [304] or between well-differentiated species [304,305] have failed to detect any evidence of TE de-repression. Thus the role of TEs in mediating post-zygotic isolation remains unclear and will require further studies [306].…”

Section: The Role Of Tes In the Diversification Of Lifementioning

confidence: 99%

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Almojil

Bourgeois

Falis

et al. 2021

Genes

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Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.

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“…Irregular chromosome pairing during meiosis also explains hybrid sterility in many taxa (Kamstra et al ., 1999 ; Bhattacharyya et al ., 2013 ; Torgasheva & Borodin, 2016 ; Liang & Sharakhov, 2019 ). In addition, the mismatch between divergent transposable elements (TEs) and TE‐suppressors (Parisod et al ., 2010 ; Hénault, 2021 ) and nuclear‐cytoplasmic conflicts (Bogdanova & Galieva, 2009 ) can also generate expression novelties and affect fitness in hybrids.…”

Section: Introductionmentioning

confidence: 99%

Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole‐genome duplication

2022

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Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization.To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization.Hybridization played a major role in shaping the relative expression pattern of the neoallopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility.In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.

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The challenges of predicting transposable element activity in hybrids

Cited by 7 publications

References 57 publications

Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids

Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole‐genome duplication

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