News/GMOD Paper Cuts, Jan 24th, 2014

Jump to: navigation, search

After a break for the festive season, PAG XXII, and the GMOD community meeting in San Diego, GMOD Paper Cuts is back with a selection of scholarly publications for your reading pleasure.

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.

CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips [1]

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. [...] CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics.

A new bacterial resource that uses JBrowse for genome visualization. The justification for using JBrowse is interesting:

We chose JBrowse for CoryneBase for the following main reasons: (1) most of the traditional genome browsers, e.g., GBrowse, are implemented using the Common Gateway Interface (CGI) protocol—the use of CGI-based genome browsers will inadvertently incurs unnecessary delays since the whole-genome browser page need to be reloaded when users change how the data are displayed; and (2) with the advances in next-generation sequencing technologies and bioinformatic tools, we would expect more corynebacterial genomes will be sequenced and annotated. Therefore a user-friendly genome browser that allows rapid and seamless browsing of the huge genomic data will be a major advantage to the research communities.

The Genome Sequence of the Fungal Pathogen Fusarium virguliforme That Causes Sudden Death Syndrome in Soybean [2]

Fusarium virguliforme causes sudden death syndrome (SDS) of soybean, a disease of serious concern throughout most of the soybean producing regions of the world. Despite the global importance, little is known about the pathogenesis mechanisms of F. virguliforme. Thus, we applied Next-Generation DNA Sequencing to reveal the draft F. virguliforme genome sequence and identified putative pathogenicity genes to facilitate discovering the mechanisms used by the pathogen to cause this disease.

A new draft sequence of the fungal disease Fusarium virguliforme. The genome sequence can be browsed online using GBrowse.

Palaeosymbiosis revealed by genomic fossils of Wolbachia in a strongyloidean nematode

Georgios Koutsovoulos, Benjamin Makepeace, Vincent N. Tanya, Mark Blaxter; published on

Wolbachia are common endosymbionts of terrestrial arthropods, and are also found in nematodes, the animal-parasitic filaria, and the plant-parasite Radopholus similis. Lateral transfer of Wolbachia

DNA to the host genome is common. We generated a draft genome sequence for the strongyloidean nematode parasite Dictyocaulus viviparus, the cattle lungworm. In the assembly, we identified nearly 1 Mb of sequence with similarity to Wolbachia. The fragments were unlikely to derive from a live Wolbachia infection: most were short, and the genes were disabled through inactivating mutations. Many fragments were co-assembled with definitively nematode-derived sequence. We found limited evidence of expression of the Wolbachia-derived genes. The D. viviparus Wolbachia genes were most similar to filarial strains, and strains from the host-promiscuous clade F. We conclude that D. viviparus was infected by Wolbachia in the past. Genome sequence based surveys are a powerful tool for revealing the genome archaeology of infection and symbiosis.

A fascinating study that uses genetic techniques to dig into the history of a host-parasite relationship. The D. viviparus genome was annotated using the MAKER pipeline.

Genome of the human hookworm Necator americanus [3]

The hookworm Necator americanus is the predominant soil-transmitted human parasite. Adult worms feed on blood in the small intestine, causing iron-deficiency anemia, malnutrition, growth and development stunting in children, and severe morbidity and mortality during pregnancy in women. We report sequencing and assembly of the N. americanus genome (244 Mb, 19,151 genes). Characterization of this first hookworm genome sequence identified genes orchestrating the hookworm's invasion of the human host, genes involved in blood feeding and development, and genes encoding proteins that represent new potential drug targets against hookworms. N. americanus has undergone a considerable and unique expansion of immunomodulator proteins, some of which we highlight as potential treatments against inflammatory diseases. We also used a protein microarray to demonstrate a postgenomic application of the hookworm genome sequence. This genome provides an invaluable resource to boost ongoing efforts toward fundamental and applied postgenomic research, including the development of new methods to control hookworm and human immunological diseases.

Another somewhat gruesome parasite, the human hookworm, which is responsible for causing more disease than any other soil-based helminth. The genome was annotated using MAKER and can be viewed online at and Wormbase.

Happy reading!

  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086318
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0081832
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1038.2Fng.2875
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.

Posted to the GMOD News on 2014/01/24