High-throughput analysis of the satellitome revealed enormous diversity of satellite DNAs in the neo-Y chromosome of the cricket Eneoptera surinamensis

Abstract

Satellite DNAs (satDNAs) constitute large portion of eukaryote genomes, comprising non-protein-coding sequences tandemly repeated. They are mostly found in heterochromatic regions of chromosomes such as around centromere or near telomeres, in intercalary heterochromatin, and often in non-recombining segments of sex chromosomes. We examined the satellitome in the cricket Eneoptera surinamensis (2n = 9, neo-X1X2Y, males) to characterize the molecular evolution of its neo-sex chromosomes. To achieve this, we analyzed illumina reads using graph-based clustering and complementary analyses. We found an unusually high number of 45 families of satDNAs, ranging from 4 bp to 517 bp, accounting for about 14% of the genome and showing different modular structures and high diversity of arrays. FISH mapping revealed that satDNAs are located mostly in C-positive pericentromeric regions of the chromosomes. SatDNAs enrichment was also observed in the neo-sex chromosomes in comparison to autosomes. Especially astonishing accumulation of satDNAs loci was found in the highly differentiated neo-Y, including 39 satDNAs over-represented in this chromosome, which is the greatest satDNAs diversity yet reported for sex chromosomes. Our results suggest possible involvement of satDNAs in genome increasing and in molecular differentiation of the neo-sex chromosomes in this species, contributing to the understanding of sex chromosome composition and evolution in Orthoptera.

Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair

“…Nevertheless, high-throughput sequencing contributed significantly to increase our knowledge regarding satDNA sequences [63]. Next generation sequencing (NGS; e.g., Illumina), allied to newly developed bioinformatics tools capable of identifying satDNA sequences in unassembled data (e.g., RepeatExplorer) [64][65][66], helped uncover the extent of satDNAs present in the genome of different species, revealing unpredicted levels of satDNA diversity (e.g., [34,[67][68][69][70][71]). For instances, 62 satDNA families were identified in the genome of the migratory locust, leading to the coining of the term 'satellitome' to refer to the whole collection of satDNA families found in a single genome [34], a part of the 'repeatome', a term proposed previously [33] to refer to the collection of all repetitive sequences in a genome (TEs, satDNAs, etc.).…”

Great Abundance of Satellite DNA in <b><i>Proceratophrys</i></b> (Anura, Odontophrynidae) Revealed by Genome Sequencing

“…Since they are composed of tandemly repeated sequences, satDNAs comprise long matrices located in highly compacted heterochromatin, generally in the centromeres and telomeres of the chromosomes, although they have also been reported in euchromatic regions [López-Flores and Garrido-Ramos, 2012]. In addition, there are specific sat-DNAs present in certain chromosomes, for example in sex chromosomes or B chromosomes [Mestriner et al, 2000;Ziegler et al, 2003;Vittorazzi et al, 2014;Ruiz-Ruano et al, 2016;Palacios-Gimenez et al, 2017;Gatto et al, 2018].…”

Sex chromosome repeats tip the balance towards speciation

“…For example, despite shared satellites at centromere loci across autosomes, the distribution of satellites varies across the X and Y chromosomes of wallabies (Bulazel, Ferreri, Eldridge, & O'Neill, ) (Figure ). Examples of novel transposable element and/or satellite distribution across sex chromosomes have been reported in many systems, including plants (Charlesworth, ; Cunado et al., ; Hobza et al., , ; Mariotti, Manzano, Kejnovsky, Vyskot, & Jamilena, ; Mariotti et al., ; Navajas‐Pérez et al., ; Shibata, Hizume, & Kuroki, , ; Steflova et al., ; Vyskot & Hobza, ), insects (Blackmon, Ross, & Bachtrog, ; DiBartolomeis, Tartof, & Jackson, ; Khost et al., ; Kuhn & Heslop‐Harrison, ; Palacios‐Gimenez et al., ; Steinemann & Steinemann, ) and vertebrates (Bulazel et al., ; Cioffi, Camacho, & Bertollo, ; Cioffi, Kejnovsky, & Bertollo, ; Cioffi, Molina, Moreira‐Filho, & Bertollo, ; Delany, Gessaro, Rodrigue, & Daniels, ; Ezaz & Deakin, ; Forster et al., ; Kawai et al., ; Kortschak, Tsend‐Ayush, & Grutzner, ; Macdonald et al., ; Miyaki, Hanotte, Wajntal, & Burke, ; Murtagh et al., ; de Oliveira et al., ; Pokorna, Kratochvil, & Kejnovsky, ; Suda, Uno, Mori, Matsuda, & Nakamura, ; Tomaszkiewicz, Medvedev, & Makova, ; Tone, Sakaki, Hashiguchi, & Mizuno, ; Wilson & Makova, ,b; Young, O'Meally, Sarre, Georges, & Ezaz, ), including human (Lander et al., ; Miga et al., ; Ross et al., ; Skaletsky et al., ).…”