Caenorhabditis auriculariae

Genome Assembly & Annotation

Assembly

According to Dayi, M., et al. (2021), three de novo assemblers were used to generate initial assemblies. The Nanopore reads were assembled with Flye or Canu, both followed by base correction by Illumina DNA reads using Pilon. Spades (v.3.7.1) was separately used to generate a hybrid assembly of Nanopore, Illumina pair-end and mate-pair reads. The three assemblies were merged using MetaAssembler (v.1.5) with the Flye assembly as a reference. Haplomerger2 (20151106) was run on the merged assembly to remove remaining haplotypic sequences. Further base corrections were performed by ICORN253.

Annotation

According to Dayi, M., et al. (2021), RNA-seq read pairs were aligned to the ssembly using Hisat2 v2.1.056 with default parameters and used to generate intron hints using bam2hints script in Augustus v3.3.257. Protein-coding genes on the assembly were predicted using BRAKER with the intron hints and protein homology hints from ~ 78,000 proteins of 9 nematode species (Brugia malayi, Bursaphelenchus xylophilus, Caenorhabditis elegans, C. briggsae, Necator americanus, Pristionchus pacificus, Strongyloides ratti, Trichinella spiralis, and Trichuris muris).

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

• Dayi M, Kanzaki N, Sun S, Ide T, Tanaka R, Masuya H, Okabe K, Kajimura H, Kikuchi T. Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis. Sci Rep, 2021;11(1):6720

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree