Genome Biology – highlights of the October issue

The October issue of Genome Biology is now available and, excitingly, it contains reports of three novel genome sequences.

Much attention has already surrounded our article from van Bakel et al. reporting the genome of Cannabis sativa. As well as sequencing and assembling the genome, the group also sequenced the transcriptomes of the Purple Kush marijuana strain and the Finola hemp strain to shed light on why marijuana is psychoactive and hemp is not. So as not to spoil the surprise, I won’t reveal the answer here – read the article, or our editorial by Naomi Attar, to find out.http://commons.wikimedia.org/wiki/File:Clonorchis_sinensis_2.png

The liver fluke Clonorchis sinensis is endemic in South East Asia and is the third most prevalent worm parasite of humans. The flukes are contracted through eating raw fish, and persistent infection has been linked with bile duct cancer. Xinbing Yu and colleagues have sequenced and assembled the genome of this parasite, which should lead to better therapies to combat worm infection and may provide insights into why colonization by the fluke is carcinogenic.

Anybody who has kept fish is probably familiar with the infectious disease white spot. The disease is caused by a ciliate protozoan called Ichthyophthirius multifiliis, or Ich for short, and is a major problem for the worldwide aquaculture industry. Coyne et al. have sequenced and assembled the Ich genome. The obligate parasitic nature of the Ich genome made this challenging, due to the difficulty in obtaining sufficient quantities for sequencing and the problem of contamination with fish DNA. Further complications were presented by the presence of bacterial endosymbionts, which provided another source of contaminating DNA. But Coyne and his co-workers overcame these problems to sequence the genome. Because Ich is closely related to the model ciliate Tetrahymena thermophila, comparison of the two genomes has shed light on the changes arising on adoption of the parasitic lifestyle, and it is hoped these could lead to therapeutic approaches against white spot.

Similar difficulties of obtaining uncontaminated nucleic acid from an obligate intracellular parasite were faced by Thomas Rudel and colleagues in their attempts to sequence the transcriptome of Chlamydia pneumoniae, and necessitated a complex methodology that included a sucrose gradient purification step and differential RNA-seq. The resulting transcriptome adds useful information on gene structure and expression to the existing genome sequence of this pathogen.

Other research articles this month include a study by Edwin Cuppen and colleagues looking at catastrophic chromosomal rearrangements in colorectal cancer and a transcriptomic study of Rhizobium leguminosarum by Philip Poole and colleagues, and we have also published several methods, including those for detecting condition-specific gene expression and for performing high-throughput shRNA screens. As well as genomes, October has also been a bumper month for reviews: among others, Julian Parkhill and Brendan Wren discuss what genome sequencing can tell us about bacterial epidemics, and Justin Borevitz and colleagues tell us about the success of GWAS in plants.

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