About Cercopithifilaria johnstoni
Cercopithifilaria johnstoni is a filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. Its ability to infect such a broad host range is unusual for a filarial parasite. C. johnstoni infections can cause skin and ocular immunopathologies in native hosts and experimentally-infected laboratory rats that appear to be analogous to those seen in humans infected with related filarial parasite, Onchocerca volvulus.
Genome Assembly & Annotation
The draft genome assembly was produced by the Parasites & Microbes Programme at the Wellcome Trust Sanger Institute. The assembly uses Illumina paired-end sequencing followed by a genome assembly pipeline comprising various steps, including De novo genome assembly with SPAdes, decontamination with Redundans and BlobTools, scaffolding with OPERA-LG and more.
The mitochondrial genome was assembled independently by mapping all trimmed reads to mitochondrial genomes of closely related species. Aligned reads were assembled using Velvet followed by manual curation to produce a signle contig which was then validated by multiple sequence alignment to filarial mtDNA genomes using Mesquite.
The nuclear genome assembly was annotated using Braker v2. As no RNA-seq data were available, hints were generated for Braker using the ProtHint pipeline; spliced alignments were generated by mapping proteins from OrthoDB Metazoan protein database, from which evidence was used as an input to Braker.
The mtDNA genome sequence was initially annotated using MITOS. The annotation was further improved manually by comparing sequence alignments and GFF3 annotation files from C. johnstoni with the closely related filarial nematodes L. loa, D. immitis, A. viteae, B. malayi, O. ochengi, O. volvulus, W. bancrofti.
- McCann K, Grant W, Doyle SR. The genome sequence of the Australian filarial nematode, <i>Cercopithifilaria johnstoni</i>. Wellcome Open Res, 2021;6():259
|Wellcome Sanger Institute
|Non coding genes
|Small non coding genes
This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh