Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination

Underwood, Charles J; Choi, Kyuha

doi:10.1007/s00412-019-00718-4

Cited by 35 publications

(23 citation statements)

References 144 publications

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“…The salmon louse is heterochiasmic as genetic recombination is predominantly found in the homogametic males. As the topoisomerase-like Spo11 protein is involved in genetic recombination by inducing double stranded breaks [80, 81] and is present as a single copy gene in the salmon louse genome, we investigated the possible involvement of the LsSpo11 protein in the recombination profile observed. The LsSpo11 gene is highly expressed in testes compared to ovaries with a difference exceeding 100-fold (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The salmon louse is heterochiasmic as genetic recombination is predominantly found in the homogametic males. As the topoisomerase-like Spo11 is involved in genetic recombination by inducing double stranded breaks [80,81] and is present as a single copy gene in the salmon has XX-XY type sex chromosomes, two regular chromosomes that recombine in the females only and a small "dot" chromosome that does not recombine in either sex [82][83][84][85]. Interestingly, in similarity to the D. melanogaster 'dot' chromosome the salmon louse also has a chromosome sheltered from recombination in both sexes; the chromosome corresponding to LG12 (Fig.…”

Section: Genomic Structure and Recombinationmentioning

confidence: 99%

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The salmon louse genome: copepod features and parasitic adaptations

Skern‐Mauritzen

Malde

Eichner

et al. 2021

Preprint

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Arthropods comprise the most populous groups of animals and show an astonishing diversity. Aquatic arthropods belonging to the sub-class Copepoda encompass a range of ecological roles from endo- and ectoparasites to grazers of phytoplankton that link primary producers to higher trophic levels. Despite the important role of copepods in central ecosystem services and their impact as parasites, representative genomic data and genome assemblies are scarce. This limits our opportunities to understand both the specific biology of individual species and unifying copepod genomic features that may govern their capacities to, for example, adapt to a changing environment. Among the copepod parasites we find Lepeophtheirus salmonis, an important ectoparasite that represents a threat to wild salmonid stocks and causes large annual losses to the salmon farming industry. Here we present the salmon louse genome - the first genome of a parasitic copepod that is fully sequenced and annotated. The 695.4 Mbp assembly was validated by a genetic linkage map and comprises 13 autosomes that recombine almost exclusively in males, one autosome that is shielded from recombination in both sexes and a ZZ-ZW style sex chromosome system. The genome assembly contains approximate 60% repetitive regions and comprise 13081 annotated predicted protein-coding genes. The predicted gene set appears to be quite complete as 92.4% of the expected Arthropod genes were found by a BUSCO. The gene annotations were validated by transcriptome sequencing that corresponds to the expected function of selected tissues. Transcriptome sequencing further revealed a marked shift in the gene expression pattern at the transition from the planktonic dispersal phase to the parasitic lifestyle after host attachment. Among other features, genes related to circadian rhythm are downregulated upon attaching to a host - probably reflecting abandoning a planktonic life with diurnal migration. The genome shows several evolutionary signatures including a large expansion of FNII domains, commonly considered vertebrate specific, and an incomplete heme homeostasis pathway suggesting that heme proteins are obtained from the host. The salmon louse has repeatedly demonstrated a large capacity to develop resistance against chemical treatments. Nonetheless, it exhibits low reduced numbers of several genes commonly involved in detoxification; cytochrome P450, ATP-Binding Cassette type transporters and Glutathione S-transferases. Interestingly, only one gene family with a putative detoxification role was expanded: the major vault proteins. Finally, the salmon louse has lost the ability to sustain peroxisomes, a loss apparently shared in the Caligid family but not among copepods in general.

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Section: Resultsmentioning

confidence: 99%

Section: Genomic Structure and Recombinationmentioning

confidence: 99%

The salmon louse genome: copepod features and parasitic adaptations

Skern‐Mauritzen

Malde

Eichner

et al. 2021

Preprint

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“…These values are slightly lower than those in the green puffer fish T. nigroviridis, where SSRs account for 3.21% of the genome [40] but higher than that found in the genome of the fugu puffer fish T. rubripes (1.29%) [41]. The relationship between meiotic recombination and TEs has been discussed recently [42], and its role in the coverage and distribution of TEs in particular chromosome regions of S. senegalensis could provide insights into their genome dynamics and evolution.…”

Section: Discussionmentioning

confidence: 78%

Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis

Rodríguez

Cross

Arias‐Pérez

et al. 2021

IJMS

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Cytogenomics, the integration of cytogenetic and genomic data, has been used here to reconstruct the evolution of chromosomes 2 and 4 of Solea senegalensis. S. senegalensis is a flat fish with a karyotype comprising 2n = 42 chromosomes: 6 metacentric + 4 submetacentric + 8 subtelocentric + 24 telocentric. The Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (FISH-BAC ) technique was applied to locate BACs in these chromosomes (11 and 10 BACs in chromosomes 2 and 4, respectively) and to generate integrated maps. Synteny analysis, taking eight reference fish species (Cynoglossus semilaevis, Scophthalmus maximus, Sparus aurata, Gasterosteus aculeatus, Xiphophorus maculatus, Oryzias latipes, Danio rerio, and Lepisosteus oculatus) for comparison, showed that the BACs of these two chromosomes of S. senegalensis were mainly distributed in two principal chromosomes in the reference species. Transposable Elements (TE) analysis showed significant differences between the two chromosomes, in terms of number of loci per Mb and coverage, and the class of TE (I or II) present. Analysis of TE divergence in chromosomes 2 and 4 compared to their syntenic regions in four reference fish species (C. semilaevis, S. maximus, O. latipes, and D. rerio) revealed differences in their age of activity compared with those species but less notable differences between the two chromosomes. Differences were also observed in peaks of divergence and coverage of TE families for all reference species even in those close to S. senegalensis, like S. maximus and C. semilaevis. Considered together, chromosomes 2 and 4 have evolved by Robertsonian fusions, pericentric inversions, and other chromosomal rearrangements mediated by TEs.

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“…Generally, meiotic crossover is suppressed in highly repetitive regions to prevent deleterious nonallelic homologous recombination events. However, intriguing relationships between meiotic recombination initiation and repairing, involving TEs have been detected (Underwood & Choi, 2019). In addition, TEs can be activated in germline or in embryonic phase where the most deleterious mutations are often suppressed by selection during fertilization or in the early stages of development.…”

Section: Introductionmentioning

confidence: 99%

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

Fambrini

Usai

Vangelisti

et al. 2020

Genesis

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Transposable elements (TEs) are DNA sequences that can change their position within genomes. TEs are present in most organisms and can be an important genomic component. Their activities are manifold: restructuring of genome size, chromosomal rearrangements, induction of gene mutations, and alteration of gene activity by insertion near or within promoters, intronic regions, or enhancer. There are several examples of mutations and other genetic variations determined by the activity of TEs, associated with the evolution of prokaryotic and eukaryotic organisms and the domestication of plants. Generally, TE mobilization occurs when the organism is subjected to stress, which can include both biotic and abiotic stresses, polyploidy conditions, and interspecific hybridizations, very common events in plants. TEs are widely distributed among organisms. TEs also play essential roles in evolution, but most of them are either dormant or inactive. This is mainly determined by epigenetic silencing mechanisms, regulatory systems, and control systems that aim to limit its proliferation. Furthermore, the host has recruited many genes originated from TEs as transcriptional regulators, especially in defense against pathogens and invasive genetic elements; this phenomenon is called molecular domestication. Therefore, TEs are responsible for horizontal gene transfer and the movement of genetic material between organisms, even phylogenetically distant, with a consequent remixing of their gene pools.

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Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination

Cited by 35 publications

References 144 publications

The salmon louse genome: copepod features and parasitic adaptations

The salmon louse genome: copepod features and parasitic adaptations

Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

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