Mosquitoes LTR Retrotransposons: A Deeper View into the Genomic Sequence of Culex quinquefasciatus

Marsano, Renè Massimiliano; Leronni, Daniela; D’Addabbo, Pietro; Viggiano, Luigi; Tarasco, Eustachio; Caizzi, Ruggiero

doi:10.1371/journal.pone.0030770

Cited by 14 publications

(10 citation statements)

References 52 publications

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“…aegypti ), the principal vector of yellow fever, and Culex quinquefasciatus ( Cu. quinquefasciatus ), the main vector of the nematode Wuchereria bancrofti have a high repeat content (about 55% and about 60%, respectively) and are relatively rich in transposable element [ 34 – 37 ], whereas Ch. tentans has very few transposable elements (Additional file 1 : Table S3 and Table S4).…”

Section: Resultsmentioning

confidence: 99%

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

et al. 2014

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BackgroundThe polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes.ResultsThe genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150–250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations.ConclusionsWe show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-819) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

et al. 2014

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“…Similar noncoding, nonautonomous members of LTR‐retrotransposon families that rely on their intact cousins for mobility have been identified in plants and insects (Havecker, Gao, & Voytas, ; Marsano et al, ). They have been called large retrotransposon derivatives (LARDs; Kalendar et al, ) or terminal repeat retrotransposons in miniature (TRIMs; Witte, Le, Bureau, & Kumar, ).…”

Section: Resultsmentioning

confidence: 74%

“…Unusually for a minisatellite, the level of sequence homogenization among the repeat units within each chromosome is lower than the homogenization between the copies of the microsatellite array (and the whole LARD containing it) on different chromosomes. Similar minisatellite repeats are a feature of LARDs in the genome of the insect Culex quinquefasciatus (Marsano et al, ) and may perhaps play a role in the element's mobilization cycle.…”

Section: Resultsmentioning

confidence: 94%

The reported point centromeres of Scheffersomyces stipitis are retrotransposon long terminal repeats

Coughlan

Wolfe

2019

Yeast

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Point centromeres, found in some ascomycete yeasts such Saccharomyces cerevisiae, are very different in structure from the centromeres of other eukaryotes. They are tiny and nonrepetitive and contain only two short conserved sequence motifs. Until recently, point centromeres were thought to have a single evolutionary origin, in the budding yeast family Saccharomycetaceae. Most yeasts outside this family have centromeres that are many kilobases in size. Some have centromeres consisting of a large inverted repeat sequence, others have centromeric clusters of retrotransposons, and a third group including Candida albicans has centromeres with no conserved sequence features. It was recently reported that Scheffersomyces stipitis has point centromeres with a strongly conserved 125-bp core sequence, which is unexpected because S. stipitis is only distantly related to the known point-centromere species.We show here that the 125-bp core sequence is actually part of the long terminal repeat (LTR) of the Ty5-like retrotransposon Tps5, which forms a cluster in the centromeric region of each S. stipitis chromosome. Thus, the LTR of a centromereassociated retrotransposon confers centromere-like mitotic stability when cloned into a plasmid. The centromeric regions of S. stipitis contain three types of Tps5 element (Tps5a, Tps5b, and Tps5c) and a noncoding nonautonomous large retrotransposon derivative.

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“…2002; Fernández-Medina et al 2011), Culex quinquefasciatus (Arensburguer et al 2010; Marsano et al 2012), Rhodnius prolixus (Mesquita et al 2015), and Tribolium castaneum (Wang et al 2008), among others; however, less is known about these elements at the transcription level (de Araujo et al 2005; Deloger et al 2009; Mourier and Willerslev 2010; Iorizzo et al 2011; Jiang et al 2012; Sze et al 2012). TEs are not only relevant due to the bulk of the genome occupied by them, but also due to the impact they have at the transcription level, by inserting into coding or regulatory regions, by influencing alternative mRNA processing or as sources of small regulatory RNAs (Kines and Belancio 2012; Mourier and Willerslev 2010; Cowley and Oakey 2013; de Araujo et al.…”

Section: Introductionmentioning

confidence: 99%

Transposable elements in the Anopheles funestus transcriptome

et al. 2017

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Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in A. funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized. Interestingly, we have identified a full-length putative active element (including the presence of full length TIRs in the genomic sequence) belonging to the hAT superfamily, which presents active members in other insect genomes. This work contributes to a comprehensive understanding of the landscape of transposable elements in A. funestus transcriptome. Our results reveal that TEs are abundant and diverse in the mosquito and that most of the TE families found in the genome are represented in the mosquito transcriptome, a fact that could indicate activity of these elements. The vast diversity of TEs expressed in A. funestus suggests that there is ongoing amplification of several families in this organism.

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Mosquitoes LTR Retrotransposons: A Deeper View into the Genomic Sequence of Culex quinquefasciatus

Cited by 14 publications

References 52 publications

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

The reported point centromeres of Scheffersomyces stipitis are retrotransposon long terminal repeats

Transposable elements in the Anopheles funestus transcriptome

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