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Genomics in the Journals: Mar 28, 2013

NEW YORK (GenomeWeb News) – In Nature Genetics, members of the International Peach Genome Initiative described findings from a project that produced a high-quality reference genome for peach, Prunus persica, as well as whole-genome resequencing data on 14 more accessions from the same genus.

Using Sanger sequencing, the researchers put together a 225 million base, chromosome-level assembly for the Lovell peach variety, starting with a doubled haploid (wholly homozygous) version of this plant. Their analyses of the sequence uncovered nearly 28,000 predicted protein-coding genes, including members of key biosynthetic and metabolic pathways.

Comparisons between the peach genome and sequences from previously sequenced plants offered a look at evolutionary patterns in the peach lineage, study authors explained. And by folding in genome sequence information for 10 more cultivated P. persica accessions — along with resequencing data on individual representatives from the P. ferganensis, P. kansuensis, P. davidiana, and P. mira species — the group learned more about some of the genetic events behind peach domestication.

Populations of aye-aye lemurs in Madagascar's north are genetically differentiated from those in other parts of the country, according to a study in the early, online edition of the Proceedings of the National Academy of Sciences, supporting the notion that there are significant and long-standing barriers to gene flow between the lemur populations.

Researchers from the US, Canada, and Singapore generated low-coverage, whole-genome sequence data for a dozen aye-ayes from northern, western, and eastern parts of Madagascar. From variant patterns in these genomes, they looked at aye-aye genetic diversity and relationships between populations of the nocturnal lemurs, uncovering a genetically distinct cluster of aye-ayes in Madagascar's north.

Going forward, the group argued that this and other genomic data might benefit efforts to understand aye-aye ecology and help in protecting lemur populations at elevated extinction risk.

"Aye-ayes have low population densities and extensive range requirements that could make this flagship species particularly susceptible to extinction," senior author Webb Miller, with Pennsylvania State University's Center for Comparative Genomics and Bioinformatics, and colleagues explained. "Therefore, knowledge of genetic diversity and differentiation among aye-aye populations is critical for conservation planning."

"To help facilitate future ecological- and conservation-motivated population genomic analyses by non-computational biologists," the authors added, "the analytical toolkit used in this study is available on the Galaxy website."

A Genome Biology study published this week looks at features in the genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, which may help explain the insect's biology and its destructive tendencies. The Canadian team behind the study put together a 204 million base draft version of the mountain pine beetle genome de novo, using short read, paired-end sequencing and DNA from a male pine beetle pupa.

To complement this genome information, the researchers generated transcript sequences from a pooled pupae sample. With this sequence collection, they then started searching for some of the key contributors to survival, spread, and success of the North American bark beetle species, which has wiped out millions of hectares of pine forests in British Columbia and other parts of western North America.

For instance, investigators identified representatives from enzyme families believed to help the beetles break down plant material and survive in nutrient-poor situations. They also found an enzyme-coding gene from a carbohydrate utilization pathway that the mountain pine beetle appears to have nabbed from an enterobacterial species via horizontal gene transfer.

A Chinese research team has developed a new scheme for determining species composition of environmental samples. As they reported in GigaScience, the researchers started with smashed up collections of insect material, which they subsequently assessed by cytochrome c oxidase subunit 1 mitochondrial DNA barcoding and deep sequencing. Instead of using PCR amplification to bolster representation of these COI barcodes, though, the group added an enrichment step that targeted the mitochondrial sequences.

The method appears to produce little in the way of false-positive species identifications, according to the study's authors. Even so, when they used this method to test samples from insect traps set up near the BGI Shenzhen lab in China, investigators detected an unanticipated level of species diversity, both within and between the samples.

"The two sampling sites were very close to each other, yet there were only around 10 percent of the total species being shared between them," corresponding author Xin Zhou, with BGI Shenzhen, said in a statement.

"The fact that only very few of our barcoded specimens received a sequence match from the Barcode of Life Data Systems, the world's largest barcode reference database, suggests that much of China's arthropod fauna still remains as a mystery" he added, "at least from a molecular aspect."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.