Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

Abstract

Highly repetitive satellite DNA (satDNA) repeats are found in most eukaryotic genomes. SatDNAs are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses a challenge for genome assembly and makes progress on the detailed study of satDNA structure difficult. Here, we use single-molecule sequencing long reads from Pacific Biosciences (PacBio) to determine the detailed structure of all major autosomal complex satDNA loci in Drosophila melanogaster, with a particular focus on the 260-bp and Responder satellites. We determine the optimal de novo assembly methods and parameter combinations required to produce a high-quality assembly of these previously unassembled satDNA loci and validate this assembly using molecular and computational approaches. We determined that the computationally intensive PBcR-BLASR assembly pipeline yielded better assemblies than the faster and more efficient pipelines based on the MHAP hashing algorithm, and it is essential to validate assemblies of repetitive loci. The assemblies reveal that satDNA repeats are organized into large arrays interrupted by transposable elements. The repeats in the center of the array tend to be homogenized in sequence, suggesting that gene conversion and unequal crossovers lead to repeat homogenization through concerted evolution, although the degree of unequal crossing over may differ among complex satellite loci. We find evidence for higher-order structure within satDNA arrays that suggest recent structural rearrangements. These assemblies provide a platform for the evolutionary and functional genomics of satDNAs in pericentric heterochromatin.

Dynamic Evolution of Euchromatic Satellites on the X Chromosome in Drosophila melanogaster and the simulans Clade

“…To prepare the data for cluster age estimation, we extracted repeat monomers from the assemblies of D. melanogaster [2] and each species of the simulans clade [3]. We aligned repeats for each cluster using ClustalO [4] and MUSCLE [5], followed by manual curation of alignments to correct for mis-alignment or mis-annotations in Geneious v8.1.6.…”

Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

“…For non-model organisms, assemblies often contain even less information making the study of repetitive regions laborious (Peona et al, 2018). The availability of thirdgeneration long reads opens the way to solve genomic and evolutionary questions targeting satellite and ribosomal DNAs, such as array length, abundance and organisation in higher-15 order structures or head-to-head arrangements (Sevim et al, 2016, Khost et al, 2017, Symonová et al, 2017, Lower et al, 2018, Cechova et al, 2019, Vondrak et al, 2019. For C. quinoa, we identified arrays of the satellite families ChenSat-1a, ChenSat-1b, ChenSat-2b, ChenSat-2c, ChenSat-2d, and ChenSat-2e on SMRT reads; all were arranged in short or long homogeneous arrays, but also in structures of higher order (ChenSat-1a, ChenSat-1b, ChenSat-2c, and ChenSat-2e) and head-to-head arrangements (ChenSat-1a, ChenSat-2b, and ChenSat-2e).…”

The wide distribution and horizontal transfers of beta satellite DNA in eukaryotes

“…Highly homogenized arrays of tandem repeats, known as satDNAs, are enriched in centromeric, pericentromeric, subtelomeric regions and interstitial positions (Yunis, Yasmineh 1971;Greig, Willard 1992). SatDNAs have recently been reconsidered to have various functions, such as playing roles in genome stability, chromosome segregation (Khost, Eickbush, Larracuente 2017) and even gene regulations (Tomilin 2008). Beta satDNAs were considered to be unique in the primates.…”