Check out the latest chapter in WormBook, GENETICS: Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs by Victor Ambros and Gary Ruvkun.
Data sets coming from high throughput experiments which reside in SPELL have now been updated with topics so that you can actually search by your favorite topic. You can see the topic search options by clicking the button ‘Options for Filtering Results by Dataset Tags‘ on the SPELL home page under the search box for Gene Name(s).
If you’re wondering which WormBase tool to use for your data needs, check out this updated list of tools with short descriptions for what to use them for. Click on the tool names to be taken directly to the tool.
This WS264 release of WormBase includes two new genome assemblies from both a free-living Caenorhabditis species (C. nigoni) and a whipworm parasite of mice (Trichuris muris).
The C. nigoni genome was assembled from both long-read (Pacific Biosciences) and short-read (Illumina) data, and then further scaffolded by genome-wide alignment with its very close relative, C. briggsae.
Despite the fact that C. nigoni and C. briggsae are closely enough related to produce partially fertile offspring, their lifestyles and genomes are quite different. C. briggsae, like C. elegans, is primarily a self-fertilizing hermaphrodite with roughly 1% males. C. nigoni, in contrast, is like most animal species (including humans) and has 50% males with 50% females. At the molecular level, C. nigoni‘s genome is larger than that of C. briggsae (130 Mb versus 108 Mb) and encodes 7,000 more genes, which appear to have been lost in C. briggsae after it evolved hermaphroditism, and which disproportionately encode small proteins with male-biased expression.
The T. muris genome was assembled from long-read (Pacific Biosciences) and short-read (Illumina) data, with the help of an optical map.
T. muris infects the caecum region of the mouse large intestine, and is very closely related to the human whipworm parasite T. trichiura, for which T. muris is a laboratory model. Adult whipworms have a highly unusual body shape for nematodes: their heads and front bodies have a whip-like shape that can be inserted into intestinal cells like a flexible needle, and that is easily mistaken as a “tail” rather than the worm’s head. Whipworm heads have a specific ultrastructure called a “stichosome” that allows them both to suck nutrients out of intestinal cells and to export immunosuppressive molecules into their hosts. This strategy is unfortunately effective: over 700 million human beings are currently infected by T. trichiura. Having a high-quality genome assembly for T. muris raises the hope of rational interventions against this worldwide parasite.
guest authors: Faye Rogers(1) and Erich Schwarz(2)
(1) Wellcome Sanger Institute
(2) Cornell University
The Eukaryotic Genomic Databases book has just been released by Springer (Editors: Kollmar, Martin) and contains detailed chapters related to the eukaryotic databases such as WormBase, FlyBase, the yeast databases, SGD and PomBase, etc. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research.