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Genomics in the Journals: Jan 23, 2014

NEW YORK (GenomeWeb News) – A Nature Genetics study spelled out the spicy findings from a genome sequencing and analysis study of the hot pepper, Capsicum annuum.

For that paper, an international team led by investigators at Seoul National University generated a high-quality C. annuum genome sequence using genomic DNA from a plant in the commonly studied hot pepper cultivar Criollo de Morelas 334, obtained in the Mexican state of Morelas.

After cobbling the sequence data into a de novo assembly that covered the nearly 3.5 billion base hot pepper genome to a depth of almost 187-fold, on average, the researchers went on to analyze that reference genome and re-sequence two more C. annuum cultivars, known as Perennial and Dempsey.

The team's annotation of the hot pepper genomes, helped along by transcriptome sequence data, unearthed more than 34,900 predicted protein-coding genes in the hot pepper genome. That's similar to the gene repertoire found in other plants from the Solanaceae family such as potato and tomato, though the hot pepper genome is roughly four times as large as that of tomato.

The reference genome is already being used to begin unraveling biological and evolutionary patterns in the pepper. For instance, when investigators looked at the roots of pungent flavor production in the hot pepper lineage, they identified some of the expression and functional shifts that seem to have enabled the production of alkaloids called capsaicinoid.

In the early, online edition of the Proceedings of the National Academy of Sciences, University of Surrey researchers described the shifts in gene expression that they detected in individuals who had experienced changes to their typical sleep schedule.

The team took 22 healthy volunteers and tested their reactions to days with normal sleep-wake cycles followed by days with forced "desynchrony" in this schedule — achieved by a four hour delay in sleep times for three days in a row in an environment lacking normal daylight and darkness.

When they used custom microarrays to assess gene expression profiles in blood samples from the volunteers over time, the investigators detected a dramatic dip in the expression of circadian clock-related transcripts that normally rise and fall with a predictable rhythm. They also saw a drop in representation by transcripts that normally regulate more general gene expression features via transcription, translation, and chromatin modification pathways.

"This research may help us to understand the negative health outcomes associated with shift work, jet lag, and other conditions in which the rhythms of our genes are disrupted," senior author Derk-Jan Dijk, with the University of Surrey's Sleep Research Centre, said in a statement.

A special issue of the Annals of the American Thoracic Society focused on findings from studies centered on the lung microbiome.

The set of studies, lectures, reviews, and commentaries spanned related topics ranging from the typical composition of the lung microbiome and ways to assess it to factors that might influence or alter its composition, such as smoking and other environmental exposures.

Multiple papers in the collection touched on changes to lung microbial communities that may coincide with the presence of diseases such as asthma, cystic fibrosis, chronic obstructive pulmonary disease, and idiopathic pulmonary fibrosis, while other authors looked at ways in which lung microbial community profiles might foretell future health problems and/or disease progression.

Findings from an mBio study by investigators in the US and China suggest that European honeybees in the Apis mellifera species are prone to infection by an RNA virus that's better known as a plant pathogen.

The team sorted through sequence data generated from complementary DNA libraries of purified viral material —a search that turned up sequences from a Nepovirus called tobacco ringspot virus (TRSV).

Through a series of follow up experiments, the researchers found evidence that TRSVs can not only make their way into honeybees, but can also replicate within the insects, producing infectious virions that spread the RNA virus to other honeybees.

Moreover, the team's preliminary assessments revealed ongoing TRSV infection in four monitored bee colonies already classified as "weak," including colonies showing distinct population declines in the winter season. Together with results showing that the bee-infecting Varroa mites may also carry TRSV, such results hint that the RNA virus may play an unappreciated role in colony collapse disorder.

"This study represents the first evidence that honeybees exposed to virus-contaminated pollen could also be infected," US Department of Agriculture ARS Molecular Plant Pathology Laboratory researcher Yan Ping Chen, the study's corresponding author, and colleagues wrote, "and raises awareness of potential risks of new viral disease emergence due to host shift events."

The Wellcome Trust Sanger Institute's Michael Stratton and collaborators from centers in the UK, Australia, Brazil, and Italy sequenced the genomes of two canine transmissible venereal tumors in an effort to understand the infectious dog cancer — work that they presented in Science.

The team sequenced matched tumor and normal samples from two dogs infected with CTVT: an Aboriginal camp dog from Australia and an American cocker spaniel from Brazil. To that, they added cytogenetic data on additional tumor samples obtained from dogs with CTVT in Cape Verde and Italy.

An analysis of the genomes unearthed almost 2 million apparent somatic substitutions in the tumor genomes that were not found in matched normal tissue from the same animals.

Along with pronounced copy number changes, rearrangements, retrotransposon insertions, and gene losses, the team determined that clonal CTVTs tended to show a mutation signature similar to those found in tumor types that are associated with ultraviolet light exposure.

With the help of phylogenetic and other analyses, the study's authors determined that the transmissible cancer has probably persisted and been transmitted amongst dogs for thousands of years. Their analysis indicates that it originally cropped up in a lone dog — suspected to have been a Husky or Alaskan Malamute based on its genetic variant profile — roughly 11,000 years ago.

"The genome of the transmissible dog cancer will help us to understand the processes that allow cancers to become transmissible," Stratton said in a statement. "Although transmissible cancers are very rare, we should be prepared in case such a disease emerged in humans or other animals."

"Furthermore," he added, "studying the evolution of this ancient cancer can help us to understand factors driving cancer evolution more generally."