Bunonema rgd898

Genome Assembly & Annotation

Assembly

As described in Casasa S et al., 2021, raw reads of Bunonema sp. (Illumina NextSeq 500 - short-read sequencing technology) were trimmed and quality-filtered using Trimmomatic, followed by a SPAdes assembly and bacterial contamination removal.

Annotation

As described in Casasa S et al., 2021, gene predictions were annotated using Augustus with protein sequences from P. pacificus and C. elegans used as training set. Mitochondrial genomes were annotated using MITOS2.

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

• Casasa S, Biddle JF, Koutsovoulos GD, Ragsdale EJ. Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks. Mol Biol Evol, 2021;38(2):331-343

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree