About Caenorhabditis auriculariae
Caenorhabditis auriculariae is a free-living, rare, neglected species which was reported only once in 1999 as an associate of the fruiting bodies of the basidiomycota fungus Auricularia polytricha. The species has a short stoma, bifurcated metastegostomatal teeth, a spicule structure similar to the drosophilae super group, and closed bursa similar to several species in the drosophilae and elegans super group species. C. auriculariae is phylogenetically placed at the basal position of the genus.
Genome Assembly & Annotation
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.
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).
- 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
|Data Source||University of Miyazaki|
This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh