Impact of transposable elements on genome size variation between two closely related crustacean species

Becking, Thomas; Gilbert, Clément; Cordaux, Richard

doi:10.1016/j.ab.2020.113770

Cited by 9 publications

(10 citation statements)

References 49 publications

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“…30,31,[54][55][56] Even in closely related species, such as those in the genus Armadillidium, the recent proliferation of TEs can also lead to an increase in genome size. 57 As expected, branchiopods and copepods generally have smaller genomes and lower levels of TEs, whereas some isopods (e.g., B. jamesi) and decapods (e.g., P. platypus, P. carinicauda and Synalpheus snapping shrimp) have larger genomes and higher levels of TEs (Table 3). 58 TEs can be applied to improve aquaculture production by manipulating the germ line to produce transgene, as well as for the development of new DNA vaccination vectors.…”

Section: Content Of Repeat Sequencessupporting

confidence: 60%

Recent advances in crustacean genomics and their potential application in aquaculture

Yuan

Zhang

et al. 2023

Reviews in Aquaculture

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Genomic resources are increasingly being used to improve the production efficiency and profitability of aquaculture. Crustaceans are a large group of invertebrates that encompasses some of the most important farmed species in the aquaculture industry. However, very few crustacean genomes have been published although an aquaculture genome project was proposed as early as 1997. Breakthroughs in next‐generation and third‐generation sequencing technologies and the development of high‐complexity sequence assembly strategies have promoted the publication of an increasing number of crustacean genomes, thus paving a broad way for biological and genetic studies and applications in aquaculture. In this review, we summarize recent advances in crustacean genomic research as of June 2022, including genome sequencing and assembly, genomic characteristics, and the genetic mechanisms underlying various biological phenotypes, such as environmental adaptation, lifestyle, development, and sex determination. This review also discusses the application of crustacean genomes in aquaculture, including genetic dissection of economic traits and genome‐based selective breeding via genome‐wide association studies and genomic selection. High‐quality genomes are important not only for understanding the genetic basis of biologically and economically important traits but also for the genetic improvement of aquaculture species. However, the utilization of crustacean genomics still lags far behind those in other animals. Therefore, additional multi‐omics studies and technological development are needed to accelerate the application of genomics in aquaculture.

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Section: Content Of Repeat Sequencessupporting

confidence: 60%

Recent advances in crustacean genomics and their potential application in aquaculture

Yuan

Zhang

et al. 2023

Reviews in Aquaculture

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“…We tested whether the expression of 14 diverse TEs was different between Wolbachia -infected and Wolbachia -free D. melanogaster flies of 25 distinct genotypes differing in Wolbachia loads and in number of TE insertions. We focused on TE expression, which is often used as a proxy for TE activity (e.g., Becking et al 2020 ; Torres et al 2021 ), reasoning that higher expression creates more opportunities for insertions. TE transcript levels were quantified using qPCR, with effort put into carrying out and explaining in detail data structure, quality control, and analyses (see Materials and Methods).…”

Section: Discussionmentioning

confidence: 99%

Effects ofWolbachiaon Transposable Element Expression Vary BetweenDrosophila melanogasterHost Genotypes

Eugénio

Marialva

Beldade

2023

Genome Biology and Evolution

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Transposable elements (TEs) are repetitive DNA sequences capable of changing position in host genomes, thereby causing mutations. TE insertions typically have deleterious effects but they can also be beneficial. Increasing evidence of the contribution of TEs to adaptive evolution further raises interest in understanding what factors impact TE activity. Based on previous studies associating the bacterial endosymbiont Wolbachia to changes in the abundance of piRNAs, a mechanism for TE repression, and to transposition of specific TEs, we hypothesized that Wolbachia infection would interfere with TE activity. We tested this hypothesis by studying expression of 14 TEs in a panel of 25 Drosophila melanogaster host genotypes, naturally infected with Wolbachia and annotated for TE insertions. The host genotypes differed significantly in Wolbachia titers inside individual flies, with broad-sense heritability around 20%, and in the number of TE insertions, which depended greatly on TE identity. By removing Wolbachia from the target host genotypes, we generated a panel of 25 pairs of Wolbachia-positive and Wolbachia-negative lines in which we quantified transcription levels our target TEs. We found variation in TE expression that was dependent on Wolbachia status, TE identity, and host genotype. Comparing between pairs of Wolbachia-positive and Wolbachia-negative flies, we found that Wolbachia removal affected TE expression in 21.1% of the TE-genotype combinations tested, with up to 2.3 times differences in median level of transcript. Our data shows that Wolbachia can impact TE activity in host genomes, underscoring the importance this endosymbiont can have in the generation of genetic novelty in hosts.

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“…As if often done (e.g., Becking et al 2020; Torres et al 2021), we used transcript level as a proxy for TE activity, reasoning that higher expression creates more opportunities for new insertions. However, transcription is only a necessary first step in TE mobilization, and it is conceivable that Wolbachia , or other factors, might impact TE integration post-transcription.…”

Section: Discussionmentioning

confidence: 99%

Effects ofWolbachiaon transposable element activity largely depend onDrosophila melanogasterhost genotype

Eugénio

Marialva

Beldade

2022

Preprint

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Transposable elements (TEs) are repetitive DNA sequences capable of changing position in host genomes, thereby causing mutations. TE insertions typically have deleterious effects but they can also be beneficial. Increasing evidence of the contribution of TEs to adaptive evolution further raises interest in understanding what factors impact TE activity. Based on previous studies associating the bacterial endosymbiont Wolbachia to changes in the abundance of piRNAs, a mechanism for TE repression, and to transposition of specific TEs, we hypothesized that Wolbachia infection would interfere with TE activity. We tested this hypothesis by studying expression of 14 TEs in a panel of 25 Drosophila melanogaster host genotypes, naturally infected with Wolbachia and annotated for TE insertions. The host genotypes differed significantly in Wolbachia titers inside individual flies, with broad-sense heritability around 20%, and in the number of TE insertions, which depended greatly on TE identity. By removing Wolbachia from the target host genotypes, we generated a panel of 25 pairs of Wolbachia-positive and Wolbachia-negative lines in which we quantified transcription levels our target TEs. We found variation in TE expression that was dependent on Wolbachia status, TE identity, and host genotype. Comparing between pairs of Wolbachia-positive and Wolbachia-negative flies, we found that Wolbachia removal affected TE expression in 23.7% of the TE-genotype combinations tested, with up to 4.6 times differences in median level of transcript. Our data shows that Wolbachia can impact TE activity in host genomes, underscoring the importance this endosymbiont can have in the generation of genetic novelty in hosts.

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Impact of transposable elements on genome size variation between two closely related crustacean species

Cited by 9 publications

References 49 publications

Recent advances in crustacean genomics and their potential application in aquaculture

Recent advances in crustacean genomics and their potential application in aquaculture

Effects ofWolbachiaon Transposable Element Expression Vary BetweenDrosophila melanogasterHost Genotypes

Effects ofWolbachiaon transposable element activity largely depend onDrosophila melanogasterhost genotype

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