Allodiplogaster sudhausi

Genome Assembly & Annotation

Assembly

The full assembly process is outlined in Wighard et al., (2022). Raw long-read data was assembled using Canu version 1.8. Sequence coverage distribution was investigated by aligning the genome against previously generated Illumina sequencing data from the European Nucleotide Archive (ENA) with BWA mem program (version 0.7.17).

Annotation

The full annotation process is outlined in Wighard et al., (2022). A transcriptome assembly of mixed-stage RNA-seq data from A. sudhausi was generated using the Trinity program (version 2.2.0, with the –normalize_reads option). The transcriptome assembly was then combined with community-curated gene annotations of P. pacificus (El Paco gene annotations version 3). The purpose of this was to create evidence-based gene annotations for A. sudhausi. Specifically, both datasets were aligned against the A. sudhausi assembly by the exonerate program (version 2.2.0) and processed by PPCAC software (version 1.0). The final gene annotations were assessed using BUSCO (version 3.0.1).

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

• Wighard SS, Athanasouli M, Witte H, Rödelsperger C, Sommer RJ. A New Hope: A Hermaphroditic Nematode Enables Analysis of a Recent Whole Genome Duplication Event. Genome Biol Evol, 2022;14(12):evac169

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree