Abstract
Satellite DNA is a class of repetitive sequences that are organized in long arrays of tandemly repeated units in most eukaryotes. Long considered as selfish DNA, satellite sequences are now proposed to contribute to genome integrity. Despite their potential impact on the architecture and evolution of the genome, satellite DNAs have not been investigated in oomycetes due to the paucity of genomic data and the difficulty of assembling highly conserved satellite arrays. Yet gaining knowledge on the structure and evolution of genomes of oomycete pathogens is crucial to understanding the mechanisms underlying adaptation to their environment and to proposing efficient disease control strategies. A de novo assembly of the genome of Phytophthora parasitica, an important oomycete plant pathogen, led to the identification of several families of tandemly repeated sequences varying in size, copy number, and sequence conservation. Among them, two abundant families, designated as PpSat1 and PpSat2, displayed typical features of satellite DNA and were collectively designated as PpSat. These two satellite families differ by their length, sequence, organization, genomic environment, and evolutionary dynamics. PpSat1, but not PpSat2, presented homologs among oomycetes. This observation, as well as the characterization of transcripts of PpSat families, suggested that these satellite DNA families likely play a conserved role within this important group of pathogens.
Highlights
Most eukaryotic genomes are mainly composed of repetitive sequences which may take into account a main proportion of total nuclear DNAs (Charlesworth et al, 1994; Haas et al, 2009; Lee and Kim, 2014)
The length and nucleotide composition as well as the repetitive nature of the sequences constituting these scaffolds were characteristic of satellite DNA, which prompted us to evaluate the relative proportion of satellite DNA in the new P. parasitica assembly
We searched tandemly repeated sequences with a monomer size ranging from 100 to 500 bp, which is the common range for most satellite DNA families and present in the assembly in ≥100 copies
Summary
Most eukaryotic genomes are mainly composed of repetitive sequences which may take into account a main proportion of total nuclear DNAs (Charlesworth et al, 1994; Haas et al, 2009; Lee and Kim, 2014). These sequences generally include multigene families, as well as two major groups that are classified according to their abundance and genomic organization: tandem repeats, including micro-, mini, and satellite DNA (SatDNA), and transposable elements (TEs), which are, by definition, mobile and tend to spread across the genome (Padeken et al, 2015). SatDNA is like TEs, considered as an important driver of genome architecture and plasticity, as well as evolution and speciation (Presting, 2018; Louzada et al, 2020)
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