WormBase ParaSite HomeVersion: WBPS19 (WS291)-  Archive: WBPS18

Paragonimus westermani

BioProject PRJNA219632 | Data Source The Genome Institute | Taxonomy ID 34504

About Paragonimus westermani

The lung fluke Paragonimus westermani is found in Southeast Asia and Japan, and is the most common cause of paragonimiasis. Infection is characterised by chronic inflammatory lung disease, though in severe cases the parasite can also infect the brain and CNS. P. westermani has two intermediate hosts: freshwater snails and crustaceans. The definitive host (such as humans) is infected upon ingestion of undercooked freshwater crabs and crayfish.

There is 1 alternative genome project for Paragonimus westermani available in WormBase ParaSite: PRJNA454344

Genome Assembly & Annotation


Illumina reads were assembled using Allpaths_LG. Scaffolding was improved using an in-house tool called Pygap, the Pyramid assembler with Illumina paired reads to close gaps and extend contigs, and L_RNA_scaffolder, which uses transcript alignments to improve contiguity. The assembly process is described in full in Rosa et al., (2020).


The genome was annotated using the MAKER pipeline v2.31.8. Ab initio gene predictions from BRAKER v2 and AUGUSTUS v3.2.2 (trained by BRAKER and run within MAKER) were refined using transcript and protein evidence. To reduce false-positives, gene predictions without supporting evidence were excluded, with the exception of those encoding Pfam domains, as detected by InterProScan v5.19. Gene products were named using PANNZER2 and sma3s v2. The annotation is described in full in Rosa et al., (2020).

Key Publications

Assembly Statistics

AssemblyP_westermani_1.0.allp.flsh.newb.jlly.lrna, GCA_015252655.1
Database VersionWBPS19
Genome Size923,276,502
Data SourceThe Genome Institute
Annotation Version2023-09-WormBase

Gene counts

Coding genes12,071
Non coding genes1,201
Small non coding genes1,201
Gene transcripts13,272

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