Halicephalobus mephisto

Genome Assembly & Annotation

Assembly

As described in Weinstein et al (2019), a TruSeq library was paired-end sequenced on an Illumina HiSeq2500 with 215 bp reads. This data was assembled with Platanus. For PacBio, 30 lanes were run on the RS II system using libraries generated off the same DNA sample used in Illumina.

Annotation

As described in Weinstein et al (2019), Maker2 version 2.38.1 was utilized to run Augustus and SNAP as ab initio predictors to make comprehensive gene predictions for H. mephisto, and incorporating 28 nematode proteomes as hints along with the RNA-seq data.

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

• Borgonie G, García-Moyano A, Litthauer D, Bert W, Bester A, van Heerden E, Möller C, Erasmus M, Onstott TC. Nematoda from the terrestrial deep subsurface of South Africa. Nature, 2011;474(7349):79-82
• Weinstein DJ, Allen SE, Lau MCY, Erasmus M, Asalone KC, Walters-Conte K, Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR. The genome of a subterrestrial nematode reveals adaptations to heat. Nat Commun, 2019;10(1):5268

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression