Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species.

Eugenia E Montiel,Sebastián Pita,Francisco Panzera,Teresa Palomeque,Pedro Lorite

doi:10.3390/ijms22116052

Eugenia E Montiel, Sebastián Pita + Show 3 more

Open Access

https://doi.org/10.3390/ijms22116052

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Abstract

The triatomine Rhodnius prolixus is the main vector of Chagas disease in countries such as Colombia and Venezuela, and the first kissing bug whose genome has been sequenced and assembled. In the repetitive genome fraction (repeatome) of this species, the transposable elements represented 19% of R. prolixus genome, being mostly DNA transposon (Class II elements). However, scarce information has been published regarding another important repeated DNA fraction, the satellite DNA (satDNA), or satellitome. Here, we offer, for the first time, extended data about satellite DNA families in the R. prolixus genome using bioinformatics pipeline based on low-coverage sequencing data. The satellitome of R. prolixus represents 8% of the total genome and it is composed by 39 satDNA families, including four satDNA families that are shared with Triatoma infestans, as well as telomeric (TTAGG)n and (GATA)n repeats, also present in the T. infestans genome. Only three of them exceed 1% of the genome. Chromosomal hybridization with these satDNA probes showed dispersed signals over the euchromatin of all chromosomes, both in autosomes and sex chromosomes. Moreover, clustering analysis revealed that most abundant satDNA families configured several superclusters, indicating that R. prolixus satellitome is complex and that the four most abundant satDNA families are composed by different subfamilies. Additionally, transcription of satDNA families was analyzed in different tissues, showing that 33 out of 39 satDNA families are transcribed in four different patterns of expression across samples.

Highlights

Rhodnius prolixus, due to its medical importance as one of the main Chagas disease vector species, was the first Triatominae species to be sequenced [1]
The kissing bug R. prolixus is the main vector of Chagas diseases in countries such as Colombia and Venezuela in Latin America [39], and the first Triatomine species whose genome has been sequenced and assembled [1]
We described its satellitome, which is composed by 39 satellite DNA (satDNA) families, 34 of which were detected by RepeatExplorer2 analysis, and 5 were detected by RepeatMasker mapping

Summary

Introduction

Due to its medical importance as one of the main Chagas disease vector species, was the first Triatominae species to be sequenced [1]. Using the same raw data obtained in the genome assembly project, Castro et al [4] estimated that the amount of TEs in the R. prolixus genome ranged between 19% and 23%, that is, three to four times higher than the original quantification of Mesquita et al [1] They evaluated other sibling species, R. montenegrensis and R. marabaensis (formerly R. robustus II and III, respectively [6]), with similar results. SatDNA characterization from lowcoverage sequencing data have been published in fish [22,23,24] and mostly in plants [25,26,27,28], among several other species Those studies have paved the way for understanding satDNA organization and analyzing new roles in the genomes.

Results and Discussion

Materials and Methods

DNA Sequencing and Graph-Based Clustering of Sequencing Reads

Transcription of Satellite DNA

Cytogenetic Mapping

Rhodnius Prolixus Genome Assembly satDNA Families Searches