In a paper published in the online advance of Nature Genetics this week, an international research team reports a draft sequence of the domestic apple genome. "We show that a relatively recent (>50 million years ago) genome-wide duplication has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae," the authors write. The team suggests that in apple, MADS-box genes — involved in flower and fruit development — include 15 members. The apple genome also contains other expanded gene families, including those "involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol." See our sister publication GenomeWeb Daily News' coverage of the study here.
In another Nature Genetics paper published online in advance, researchers show that the minor allele of rs1835740 on chromosome 8q22.1 is associated with common migraine. The team investigated 2,721 migraine cases and 10,747 population-matched controls in a genome-wide association study. They replicated the association in 3,202 cases and 40,062 comtrols. "To our knowledge, our data establish rs1835740 as the first genetic risk factor for migraine," the authors write.
Researchers in Europe this week report their "identity-by-descent filtering of exome sequence data" study, which identified "PIGV mutations in hyperphosphatasia mental retardation syndrome." Specifically, the team sequenced the exomes of three siblings "of a nonconsanguineous union with HPMR and performed computational inference of regions identical by descent in all siblings." PIGV — which encodes a member of the GPI-anchor biosynthesis pathway — is to be the gene mutated in HMPR, the team writes. They also "identified homozygous or compound heterozygous mutations in PIGV in three additional families."
A paper appearing online in advance in Nature this week outlines "a quality-control mechanism for mRNA 5'-end capping." Rutgers University's Xinfu Jiao and colleagues show that "Rai1 possesses a novel de-capping endonuclease activity that can also remove the entire cap structure dinucleotide from an mRNA," both in vitro and in yeast cells. This Rai1 activity, the authors write, "is targeted preferentially towards mRNAs with unmethylated caps in contrast to the canonical de-capping enzyme, Dcp2, which targets mRNAs with a methylated cap." In this way, capped but unmethylated mRNAs from "yeast cell with a defect in the methyltransferase gene are more stable in a rai1-gene-disrupted background," Jiao et al. write.