De novo identification of satellite DNAs in the sequenced genomes of Drosophila virilis and D. americana using the RepeatExplorer and TAREAN pipelines

Abstract

Satellite DNAs are among the most abundant repetitive DNAs found in eukaryote genomes, where they participate in a variety of biological roles, from being components of important chromosome structures to gene regulation. Experimental methodologies used before the genomic era were insufficient, too laborious and time-consuming to recover the collection of all satDNAs from a genome. Today, the availability of whole sequenced genomes combined with the development of specific bioinformatic tools are expected to foster the identification of virtually all the “satellitome” of a particular species. While whole genome assemblies are important to obtain a global view of genome organization, most of them are incomplete and lack repetitive regions. We applied short-read sequencing and similarity clustering in order to perform a de novo identification of the most abundant satellite families in two Drosophila species from the virilis group: Drosophila virilis and D. americana, using the Tandem Repeat Analyzer (TAREAN) and RepeatExplorer pipelines. These species were chosen because they have been used as models to understand satDNA biology since the early 70’s. We combined the computational approach with data from the literature and chromosome mapping to obtain an overview of the major tandem repeat sequences of these species. The fact that all of the abundant tandem repeats (TRs) we detected were previously identified in the literature allowed us to evaluate the efficiency of TAREAN in correctly identifying true satDNAs. Our results indicate that raw sequencing reads can be efficiently used to detect satDNAs, but that abundant tandem repeats present in dispersed arrays or associated with transposable elements are frequent false positives. We demonstrate that TAREAN with its parent method RepeatExplorer may be used as resources to detect tandem repeats associated with transposable elements and also to reveal families of dispersed tandem repeats.

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

“…The amount of satDNA in these four archives of sequencing data ranges between 8.81% and 9.62%, closer to our estimate (8.05%) than that obtained from the assembled genome (5.6%) ( Supplementary Table S1, Figure S1 ). Notwithstanding, as already shown on other insect species [ 13 , 14 , 20 ], variations in the amount—and even the absence—of some satDNA families were found between individuals. In spite of this, the general aspect of the repeat landscape for each genome was conserved ( Supplementary Figure S1b–e ).…”

“…Since Triatomini and Rhodniini divergence was dated around 18–22 million years ago (Mya) [ 44 ], it represents a rather high divergence time under the library evolution hypothesis. Other insects showing similar satDNA families presented shorter divergence periods below 8 Mya, i.e., three species from the Drosophila obscura subgroup [ 45 ], Drosophila virilis and D. americana [ 20 ], or in several grasshopper species from the Schistocerca genus [ 46 ]. Nevertheless, there are also some exceptional cases of shared satDNAs among ant species, with great divergence time (74–80 Mya) [ 47 ].…”

“…In the last five years, more than 40 studies have been published describing satDNA families using those pipelines, among them, the satellitome analysis of T. infestans and H. histrio . Other successful examples of the employment of this methodology were the satellitome analyses of several grasshoppers [ 14 , 18 ], one cricket species [ 19 ], Drosophila [ 20 ] or beetles [ 21 ]. Outside the arthropods, satDNA characterization from low-coverage sequencing data have been published in fish [ 22 , 23 , 24 ] and mostly in plants [ 25 , 26 , 27 , 28 ], among several other species.…”

The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths

“…Only recently, this difficulty has been overcome by bioinformatic analysis of low-coverage sequenced genomes using RepeatExplorer ( Novák et al, 2013 ). This approach allowed the characterization of multiple satDNAs and generated valuable chromosomal and genomic information, for example in crickets ( Palacios-Gimenez et al, 2017 ), Drosophila species ( Silva et al, 2019 ), fishes ( Silva et al, 2017 ; Crepaldi and Parise-Maltempi, 2020 ), amphibians ( da Silva et al, 2020 ), and some plants ( Mata-Sucre et al, 2020 ; Zwyrtková et al, 2020 ). However, this approach has not yet been applied to Lepidoptera.…”

Identification and characterization of repetitive DNA in the genus Didelphis Linnaeus, 1758 (Didelphimorphia, Didelphidae) and the use of satellite DNAs as phylogenetic markers

“…The advent of high-throughput next-generation sequencing (NGS) provided a fast and cost-effective manner to produce sequence data that can be used to identify the most frequent genome components in a single sequencing run ( Ansorge, 2009 ; Novák et al, 2010 ). This NGS output serves then as input for similarity and graph-based in silico analyses that have been proven to be an efficient strategy for de novo identification and characterization of repetitive DNAs ( Garrido-Ramos, 2017 ; Novák et al ., 2010 , 2013 , 2017 ; Silva et al, 2019 ).…”