Characterization of Two Satellite DNA Families in the Genome of the Oomycete Plant Pathogen Phytophthora parasitica

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.

Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica

“…There is compelling evidence that epigenetics, especially small RNA-based silencing, plays a major role in the biology of Phytophthora. Recent studies have shown that this mechanism targets protein coding genes like effectors and also TEs and other repetitive sequences like satellite DNA families (Vetukuri et al, 2012;Åsman et al, 2016;Panabières et al, 2020). Finally, viral genes may be silenced through fusion with TEs.…”

“…Repetitive sequences including TEs are known to frequently escape identification in genomes. Indeed, their repetitive nature and their size, longer than the average read length generated by the Illumina technique, prevent their identification and lead to collapsing them in most genome assemblies (Panabières et al, 2020). Consequently, a substantial proportion of the contig length was made of N-stretches of unassembled regions, introducing numerous gaps in the assembly.…”

Neofunctionalization of Glycolytic Enzymes: An Evolutionary Route to Plant Parasitism in the Oomycete Phytophthora nicotianae

“…Conversely, the GKI and GKII members were frequently located on boundaries of their respective contigs and scaffolds, so that only partial sequences could be resolved. They were generally retrieved in short-read derived genome assemblies, so the repetitive nature of these sequences can make them refractory to assembly [52].…”

A Comprehensive Assessment of the Secretome Responsible for Host Adaptation of the Legume Root Pathogen Aphanomyces euteiches

“…Long-read sequencing allows to obtain a continuous assembly, which can help to resolve localization of repeated regions and to improve gene annotations, notably for large families of genes such as effectors, which are often located in repeat-rich regions [36]. One example is the resequencing of the oomycete Phytophthora parasitica that helped to identify a new class of repeats corresponding to satellite DNA, which could not be identified in a short-read-based assembly [37]. Using long-read technology has helped to resolve the organization of repeated pathogenicity loci in the wheat fungal pathogen Pyrenophora tritici [38].…”