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Genomics in the Journals Sep 4, 2014

NEW YORK (GenomeWeb) – A University of Maryland team used transcriptome sequencing to uncover possible pest control targets in the brown marmorated stink bug Halyomorpha halys.

As they reported in BMC Genomics, the researchers did RNA sequencing on pooled samples from multiple brown marmorated stink bug representatives at each stage of development, using a shotgun strand-specific sequencing approach. The critter is common to the mid-Atlantic region in the US, they explained, where it is notorious for damaging crops and infiltrating homes and gardens.

The team identified almost 54,000 apparent transcripts in the stink bug samples, which it subsequently whittled down to just over 13,211 higher confidence transcripts. These include sequences that coincided with brown marmorated stink bug genes as well as those that seemed to stem from bacterial endosymbionts living in the insect.

"We are excited to identify highly abundant bacterial genes with properties suggesting that they are functional parts of the stink bug genome," corresponding author Julie Dunning Hotopp, a microbiology and immunology researcher with the University of Maryland's Institute for Genome Sciences, said in a statement.

In Nature Genetics, three independent research groups published papers describing variants that dial up the risk of developing glaucoma.

For one of these studies, Chinese and American researchers embarked on a genome-wide association study that involved more than 1,000 southern Chinese individuals with a form of glaucoma called primary open-angle glaucoma and another 1,000 or so individuals from the same population with high-pressure glaucoma.

When they compared genotype patterns in the glaucoma patients with those present in around 1,000 unaffected controls from the same population, the investigators found four SNPs in a chromosome 9 cluster that were over-represented in individuals with primary open-angle glaucoma and two SNPs on chromosome 16 with more tenuous ties to the same condition.

A follow-up analysis in thousands more primary open-angle glaucoma and high-pressure glaucoma cases and controls from China or Singapore shored up the apparent association between primary open-angle glaucoma and SNPs at these chromosome 9 and 16 sites, which fell in or around the ABCA1 and PMM2 genes.

Variants near the ABCA1 gene were linked to primary open-angle glaucoma in a GWAS of individuals from Australia and the US as well, as were common SNPs in and around the AFAP1 and GMDS genes. For that study, investigators from Australia and elsewhere started by genotyping 1,155 Australian individuals with the primary open-angle glaucoma sub-type, along with 1,992 unaffected controls from the same population.

After replicating the most promising variant associations in another 932 cases and 6,962 controls from Australia, the team tested the variants in two replication cohorts from the US that comprised 2,616 individuals with primary open-angle glaucoma and 2,634 without.

By looking at results from these cohorts together and in combination, the investigators identified primary open-angle glaucoma-associated loci in three regions: a site upstream of the ABCA1 gene and two more falling in the GMDS and AFAP1 genes, respectively.

Finally, an international team led by investigators in the UK presented findings from a GWAS meta-analysis that focused on variants related to elevated intraocular pressure, a heritable trait that can increase the risk of developing glaucoma.

Using data collected for tens of thousands of individuals from a range of ancestries as part of the International Glaucoma Genetics Consortium, the researchers confirmed associations for loci linked to primary open-angle glaucoma and/or intraocular pressure in the past. They also uncovered ties between intraocular pressure and variants not identified previously, including SNPs at four sites in or near the ABCA1, FNDC3B, and ABO genes.

Through additional testing on almost 4,300 cases and more than 95,500 controls, that group linked three of the four same loci to primary open-angle glaucoma itself.

A genome re-sequencing and re-assembly paper appearing in the journal Bioinformatics expanded the gene and protein resources available for the naked mole rat, Heterocephalus glaber, a creature noted for its longevity and cancer resistance that was first sequenced in 2011.

A team from the UK, US, and Sweden used Illumina's HiSeq instrument to sequence several libraries produced with DNA from an inbred female naked mole rat raised at a University of Rochester colony. The resulting assembly — freely available through a Broad Institute portal known as the Naked Mole Rat Genome Resource — reportedly has longer scaffolds and contigs than the genome available in the past.

When they annotated and analyzed this improved assembly, the researchers described 42,117 predicted protein-coding genes, almost 42,000 naked mole rat proteins, and 1,779 non-coding sequences. They also saw signs of selection at sites in the naked mole rat genome, including sequences coding for the notorious cancer-related protein p53.

"The new study provides a fundamental resource for research on the naked mole rat and its many evolutionary adaptations, including longevity and resistance to diseases, as well as other traits (metabolic regulation, development, pain, and behavior)," senior author João Pedro de Magalhães, an integrative biology researcher at the University of Liverpool, said in a statement.

A transcriptome sequencing study published in Cell revealed consequences of rare non-coding variants identified in the genomes of individuals from a large multi-generational family of northern or western European ancestry.

Researchers based at Stanford University and the University of Washington did RNA sequencing on lymphocyte cell lines generated for 17 members of a three generational family who'd already had their genomes sequenced by Complete Genomics.

Their analysis of expression quantitative trait loci and splicing quantitative trait loci indicated that rare variants involved in regulating gene expression or transcript splicing tended to show the most pronounced effects in the family. Moreover, they noted that many of the most pronounced eQTLS and splicing QTLs affected essential genes or genes implicated in complex diseases through prior genome-wide association studies.

"These results highlight that rare non-coding variants are important contributors to gene expression profiles," Stanford pathology, genetics, and computer science researcher Stephen Montgomery, the study's senior author, and his colleagues wrote.