Paragonimus skrjabinimiyazakii

Genome Assembly & Annotation

Assembly

The full assembly process is outlined in Rosa et al., (2020). Sequences were generated on the Illumina platform and assembled using Allpaths_LG. An in-house tool, Pygap, was used to improve scaffolding. L_RNA_scaffolder which uses transcript alignments to improve contiguity was also used.

Annotation

The full annotation process is outlined in Rosa et al., (2020). The nuclear genome was annotated using the MAKER pipeline v2.31.8. RNA-seq reads were aligned to their respective genome assemblies and assembled using StringTie v1.2.4. 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.

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