Whole-genome sequence of the oriental lung fluke Paragonimus westermani

Abstract

BackgroundFoodborne infections caused by lung flukes of the genus Paragonimus are a significant and widespread public health problem in tropical areas. Approximately 50 Paragonimus species have been reported to infect animals and humans, but Paragonimus westermani is responsible for the bulk of human disease. Despite their medical and economic importance, no genome sequence for any Paragonimus species is available.ResultsWe sequenced and assembled the genome of P. westermani, which is among the largest of the known pathogen genomes with an estimated size of 1.1 Gb. A 922.8 Mb genome assembly was generated from Illumina and Pacific Biosciences (PacBio) sequence data, covering 84% of the estimated genome size. The genome has a high proportion (45%) of repeat-derived DNA, particularly of the long interspersed element and long terminal repeat subtypes, and the expansion of these elements may explain some of the large size. We predicted 12,852 protein coding genes, showing a high level of conservation with related trematode species. The majority of proteins (80%) had homologs in the human liver fluke Opisthorchis viverrini, with an average sequence identity of 64.1%. Assembly of the P. westermani mitochondrial genome from long PacBio reads resulted in a single high-quality circularized 20.6 kb contig. The contig harbored a 6.9 kb region of non-coding repetitive DNA comprised of three distinct repeat units. Our results suggest that the region is highly polymorphic in P. westermani, possibly even within single worm isolates.ConclusionsThe generated assembly represents the first Paragonimus genome sequence and will facilitate future molecular studies of this important, but neglected, parasite group.

The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala)

“…Nevertheless, in a larger phylogenetic context, the gene repertoire seems to have experienced a reduction in acanthocephalan evolution. Thus, we detected only 73% of the expected metazoan genes in the P. laevis transcriptome, a dimension that was reported also for parasitic helminths [161,162]. The reduction in gene repertoire was also reflected in a reduced complement of proteins regulating development, as expected for a parasite with comparably simple body organization [159].…”

“…The reduced number of usually conserved metazoan genes presumably reflects gene loss on the lineage to P. laevis, as it is common in parasite evolution [63,[158][159][160]. This is indeed very likely considering that almost identical percentages of metazoan genes (74% to 77%) were detected by BUSCO in the genome assemblies of four parasitic trematodes [161]. Although these counts refer to the subset of usually conserved metazoan genes, the relation could apply to the entire gene repertoire, as illustrated again by other taxa.…”

Molecular phylogenetics and mitogenomics of three avian dicrocoeliids (Digenea: Dicrocoeliidae) and comparison with mammalian dicrocoeliids

“…Similar regions in other studies of mt genomes have also been shown as problematic [46,47]. Therefore, the PacBio single-molecule real-time sequencing method has been used by researchers in recent studies to characterize long and difficult to sequence repetitive regions of flatworm mitogenomes [48,49]. Nonetheless, the coding regions of the mt genomes of Brachylecithum sp.…”

First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach

“…All 12 protein-encoding genes, 22 tRNAs and two rRNAs had high sequence similarities (> 99.2%) to those in published mitochondrial genomes and occurred in the same order. However, there is clear evidence [17,18,38] that conventional sequencing methods are not suited to the sequencing of long non-coding regions in mitochondrial genomes. This obstacle has been overcome through the use of nanopore-sequencing, which bodes well for future mitochondrial genome investigations.…”