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WormBase ParaSite HomeVersion: WBPS19 (WS291)-  Archive: WBPS18

Halicephalobus mephisto

BioProject PRJNA528747 | Data Source American University | Taxonomy ID 2559892

About Halicephalobus mephisto

The nematode Halicephalobus mephisto is a free-living worm feeding on subterranean bacteria. It was first found in ore recovered from deep rock fracture water in South African goldmines. It is able to survive as deep as 3.6 km under the surface of Earth, resisting temperatures as high as 37°C.

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.

Key Publications

Assembly Statistics

Assemblymephisto_omega, GCA_009193035.1
Strainm2B
Database VersionWBPS19
Genome Size61,422,354
Data SourceAmerican University
Annotation Version2023-10-WormBase

Gene counts

Coding genes12,540
Pseudogenes66
Gene transcripts28,056

Learn more about this widget in our help section

This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh