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Genomics In The Journals: Nov 29, 2012

NEW YORK (GenomeWeb News) – In Nature Genetics, researchers based in China, Singapore, and the US outline findings from their effort to sequence and analyze a draft genome for sweet orange, Citrus sinensis.

After putting together a preliminary genome assembly using sequence data generated from a dihaploid sweet orange line, the team added in diploid sweet orange sequences to flesh out the genome's heterozygosity. From the assembly, which covers just over 87 percent of the 367 million bases estimated to make up the total sweet orange genome sequence, investigators identified more than a million SNPs, nearly 177,000 small insertions and deletions, and 29,445 predicted protein-coding genes (half of which seem to be in a heterozygous state). Through comparisons with other citrus sequences, the team also found clues about the origins of sweet orange, which apparently descended from a pummelo-mandarin hybrid that was itself crossed with mandarin.

At the annual Plant and Animal Genomes meeting earlier this year, members of another team, known as the International Citrus Genomics Consortium, announced that they had sequenced the diploid genome of sweet orange and a haploid genome for the Clementine mandarin.

The genetic variation present in protein-coding parts of the human genome has shifted dramatically within the past several thousand years, according to a study in Nature.

Researchers from the University of Washington and elsewhere determined the ages of 1.1 million autosomal single nucleotide variants using coding sequence data for 15,536 genes in a cohort of 6,515 European American and African American individuals assessed through the National Heart, Lung, and Blood Institute's Exome Sequencing Project. They found that just over 81 percent of SNVs in European-American protein-coding sequences and nearly 59 percent of SNVs in African-American coding sequences arose within the past 5,000 to 10,000 years.

When they looked specifically at coding variants that are potentially deleterious, meanwhile, investigators saw that the average age of those SNVs differed depending on the type of genes considered, but tended to be younger in the European Americans. For example, the study's authors wrote, "European Americans had an excess of deleterious variants in essential and Mendelian disease genes compared to African Americans, consistent with weaker purifying selection due to the Out-of-Africa dispersal."

A new PLOS ONE study suggests that bubonic plague outbreaks caused by the Yersinia pestis pathogen may have sprung up long before Europe's famous Black Death outbreak in the mid-1300s.

The University of Tübingen's Johannes Krause and colleagues from Germany, France, and Canada brought together genome sequence data for ancient Y. pestis strains isolated from Black Death remains, publicly available genome sequence data for 18 present-day Y. pestis strains, and SNP data for another 311 modern strains. Though most of the strains grouped into two main lineages with divergence times resembling the Black Death strains, the team also uncovered a cluster of 11 Y. pestis strains that seem to share a common ancestor going back much further, diverging sometime around the 7th century to 10th century. That hints that Y. pestis may have been behind a 6th century to 8th century outbreak in the Roman Empire known as the Plague of Justinian, as some have suspected.

Still, study authors cautioned that additional data is needed to directly pin that outbreak on the bug, noting that "Y. pestis data from human mass burials data to the Justinian era may hold pertinent information to permit a more thorough evaluation of the evolutionary history of this notorious human pathogen."

Glitches in the ubiquitination-related gene UBE3B can cause a rare neurodevelopmental disorder called blepharophimosis-ptosis-intellectual disability, or BPID, syndrome, according to an American Journal of Human Genetics study.

An international team led by researchers in Germany and Israel performed exome sequencing on children from two separate families affected by autosomal recessively inherited BPID. When they focused in on mutations within stretches of extended homozygosity in the first affected individual, who came from a consanguineous family, researchers found rare changes to UBE3B — a ubiquitin ligase gene that was also altered in the other individual, from a non-consanguineous family, whose exome was also sequenced. Follow-up analyses on an affected sibling from the second family and an unrelated child from a third — coupled with model experiments in organisms — indicate that loss-of-function changes to UBE3B are plausible BPID culprits.

Based on their findings, those involved in the study suspect that such UBE3B mutations lead to ubiquitination deficits, upending a pathway that normally degrades proteins damaged by oxidative stress or other processes.

"[N]euronal dysfunction associated with UBE3B deficiency might be a consequence of a genetically determined vulnerability toward oxidative stress," University of Ulm human genetics researcher Guntram Borck, the study's senior author, and colleagues said.

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

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.