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This Week in Genome Biology: Oct 20, 2010

In a Genome Biology paper published online in advance this week, researchers at Penn State University and their colleagues suggest Eschscholzia californica as a reference tool for floral evolutionary development studies. Using comparative transcriptomics via expressed sequenced tag set on microarrays, the team identified "differentially expressed genes in flower buds with pre-meiotic and meiotic cells, four floral organs at pre-anthesis stages (sepals, petals, stamens, and carpels), developing fruits, and leaves," which they say "provide a foundation for comparative gene expression studies between eudicots and basal angiosperms."

A team led by investigators at the Wellcome Trust Sanger Institute reports the "first paired-end sequencing of tumors from genetically engineered mouse models of ... Trp53-mutated breast cancer, Brca1- and Brca2-associated hereditary breast cancer, and E-cadherin-mutated lobular breast cancer," which they performed in an effort "to determine how faithfully these models recapitulate the landscape of somatic rearrangements found in human tumors," they write. The team found that the mouse models, while they showed "significant heterogeneity in their profiles," also showed "fewer rearrangements than cognate human mammary tumors," the authors write.

Nils Homer and Stanley Nelson at the University of California, Los Angeles, describe a method for "improved variant discovery through local realignment of short-read next-generation sequencing data using SRMA." As with other alignment approaches, Homer and Nelson's approach maps each short read to the reference genome independently, however it leverages the correlation between "reads that observe the same non-reference DNA sequence" via a micro re-aligner, SRMA.

Also in Genome Biology this week, invited speakers from the recent Beyond the Genome meeting held in Boston present recaps of their talks. The University of Maryland's Mihaela Pertea and Steven Salzberg justify their estimation that the human gene count is 22,333, which puts the human genome somewhere between those of a chicken and a grape.

The Scan

Possibly as Transmissible

Officials in the UK say the B.1.617.2 variant of SARS-CoV-2 may be as transmitted as easily as the B.1.1.7 variant that was identified in the UK, New Scientist reports.

Gene Therapy for SCID 'Encouraging'

The Associated Press reports that a gene therapy appears to be effective in treating severe combined immunodeficiency syndrome.

To Watch the Variants

Scientists told US lawmakers that SARS-CoV-2 variants need to be better monitored, the New York Times reports.

Nature Papers Present Nautilus Genome, Tool to Analyze Single-Cell Data, More

In Nature this week: nautilus genome gives peek into its evolution, computational tool to analyze single-cell ATAC-seq data, and more.