Paragonimus westermani

Genome Assembly & Annotation

Assembly

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).

Annotation

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).

Downloads

• Genomic Sequence (FASTA)
• Hard-masked Genomic Sequence (FASTA)
• Soft-masked Genomic Sequence (FASTA)
• Annotations (GFF3)
• Proteins (FASTA)
• Full-length transcripts (FASTA)
• CDS transcripts (FASTA)

Tools

• Search for sequences in the genome and proteome using BLAST
• Work with lists of data using the WormBase ParaSite BioMart data-mining tool
• Programatically access WormBase ParaSite data using the REST API
• Predict the effects of variants using the Variant Effect Predictor

Key Publications

• Rosa BA, Choi YJ, McNulty SN, Jung H, Martin J, Agatsuma T, Sugiyama H, Le TH, Doanh PN, Maleewong W, Blair D, Brindley PJ, Fischer PU, Mitreva M. Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis. Gigascience, 2020;9(7):giaa073

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression