Draft genomes of Perkinsus olseni and Perkinsus chesapeaki reveal polyploidy and regional differences in heterozygosity

• Published in: Genomics (San Diego, Calif.) Vol. 113; no. 1; pp. 677 - 688
• Main Authors: Bogema, Daniel R., Yam, Jerald, Micallef, Melinda L., Gholipourkanani, Hosna, Go, Jeffrey, Jenkins, Cheryl, Dang, Cecile
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.01.2021
• Subjects: Alveolata - genetics; Electron Transport Complex IV - genetics; Genome, Protozoan; Genomics; Heterozygosity; Loss of Heterozygosity; Perkinsus; Ploidy; Polymorphism, Genetic; Polyploidy; Protozoan Proteins - genetics; Ploidy; Genomics; Perkinsus; Heterozygosity
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2020.09.064

Perkinsus spp. parasites have significant impact on aquaculture and wild mollusc populations. We sequenced the genomes of five monoclonal isolates of Perkinsus olseni and one Perkinsus chesapeaki from international sources. Sequence analysis revealed similar levels of repetitive sequence within species, a polyploid genome structure, and substantially higher heterozygosity in Oceanian-sourced isolates. We also identified tandem replication of the rRNA transcriptional unit, with high strain variation. Characterized gene content was broadly similar amongst all Perkinsus spp. but P. olseni Oceanian isolates contained an elevated number of genes compared to other P. olseni isolates and cox3 could not be identified in any Perkinsus spp. sequence. Phylogenetics and average nucleotide identity scans were consistent with all P. olseni isolates being within one species. These are the first genome sequences generated for both P. olseni and P. chesapeaki and will allow future advances in diagnostic design and population genomics of these important aquatic parasites. •The first genome sequences have been generated for two species Perkinsus olseni and Perkinsus chesapeaki.•Cytochrome c oxidase subunit III was not identified in Perkinsus spp. genomes.•Comparative genome analysis reveals very low heterozygosity in isolates sourced from Europe and East Asia.•Analysis of heterozygous variants and flow cytometry indicates polyploidy.