In Genome Research this week, Adam Ewing and Haig Kazazian at the University of Pennsylvania report their technique, using high-throughput sequencing "to determine the insertion sites of virtually all members of the human-specific L1 retrotransposon family in any human genome." In assaying 25 individuals at 1,139 sites, and using diagnostic nucleotides, the pair was able to locate "the approximately 800 L1Hs copies corresponding specifically to the pre-Ta, Ta-0, and Ta-1 L1Hs subfamilies," and found that "any two individual genomes differ at an average of 285 sires with respect to L1 insertion presence of absence."
A trio of researchers suggests that "the observed frequency of gene movements can explain the erosion of gene colinearity between plant genomes during evolution," in Genome Research this week. Namely, the University of Zurich team writes, genomic fragments of up to 50 kb containing non-colinear genes "are duplicated to acceptor sites elsewhere in the genome." They also found that gene movements can occur when double-strand breaks are repaired.
Investigators in France examine the dynamics of GC-content across 33 mammalian genomes. In their analysis of more than 1,000 orthologous genes in the fully sequenced genomes, the team was able to reconstruct their ancestral isochore organization, and explore the evolution of third-codon position GC-content. They refute the previously reported GC-rich isochore erosion trend, and correlated "GC-content evolution with species life-history traits and cytology."
Researchers in Spain and Germany report their strand-specific protocol for transcriptome sequencing — direct strand-specific sequencing, or DSSS. The authors tested their method using data containing strand-specific information from RNA from a prokaryotic and eukaryotic sample using single-read paired-end sequencing experiments. They compared those results with their strand-specific tiling array data set, and validated their method using qPCR. "The results of DSSS were very well supported by the results from tiling arrays and qPCR," the authors write, adding that "DSSS provided higher dynamic range and single-base resolution, thus enabling efficient antisense detection and the precise mapping of transcription start sites and untranslated regions."