Journal: PLoS Biology
Article Title: The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny ChromosomesTantalizing Glimpses into a Fragmented Genome
Figure Lengend Snippet: Extreme nanochromosomal fragmentation. Contig14329.0 is shown with coordinates in bp. Predicted genes, coding sequences, and introns are indicated by horizontal green, yellow, and white arrows, respectively. 5′ and 3′ fragmentation sites predicted from telomeric read pairs are indicated by red and navy arrows, respectively, with upward pointing solid arrows for sites predicted by 454 telomeric reads and downward pointing dashed arrows for sites predicted by Illumina telomeric reads. Numbers above/below the arrows indicate the number of telomeric reads found at each site for the two telomeric read sources. Alternative nanochromosome isoforms predicted from the 454 telomeric reads (isoforms B–O) are shown below the main locus, with the number of supporting read pairs next to each form. One additional isoform missed by our prediction method but documented in the 454 telomeric read pairs is indicated in pale green. Since the two fragmentation positions at 3,762 and 3,806 bp are in close proximity to each other, they were treated as a single point during alternative isoform prediction. Additional nanochromosome isoforms that were not detected by 454-telomeric reads, including the full eight-gene nanochromosome, but were detected by Southern blotting are indicated by stars (isoforms A, P, Q, and R). Sequence coverage, indicated by the cyan graph, shows the cumulative DNA amplification for all the nanochromosome isoforms. Sequence coverage is calculated from both Illumina telomereless and telomeric reads; telomeric read pairs appear as twin peaks ∼300 bp apart.
Article Snippet: We did not split contigs with missing spans 400 bp from either end of the contig, as the size selection procedure we employed in the Illumina DNA-sequence library construction eliminated most of the sequence coverage in a 160 bp span starting at 100 bp upstream of telomeres.
Techniques: Southern Blot, Sequencing, Amplification