Halicephalobus mephisto
BioProject PRJNA528747 | Data Source American University, Washington, D.C. | 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.
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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
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Assembly Statistics
| Assembly | SWDT01000000, SWDT00000000 |
| Database Version | WBPS18 |
| Genome Size | 61,428,783 |
| Data Source | American University, Washington, D.C. |
| Annotation Version | 2019-05-WormBase |
Gene counts
| Coding genes | 12,546 |
| Pseudogenes | 66 |
| Gene transcripts | 28,062 |
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