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De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

Figure 2

Synteny between the genomes of S. macrospora and N. crassa.

(A) Synteny of contigs from the S. macrospora genome with the N. crassa genome before scaffolding along the N. crassa chromosomes. Dot plot of a comparison of the five largest contigs from the Velvet assembly (contigs 3467, 1588, 19727, 3369, and 12432, length given on the y-axis in descending order, total size of the five contigs 3.4 Mb, note that the Velvet contig numbers do not correspond to the contigs of the final assembly) against the Neurospora linkage groups (supercontigs I to VII in finished genome sequence, http://www.broadinstitute.org/annotation/genome/neurospora/Regions.html). The linkage group numbers for N. crassa are given above the dot plot. (B) Dot plot of a comparison of the S. macrospora scaffolds which cover 93% of the genomic sequence against the N. crassa supercontigs corresponding to linkage groups I to VII from the finished genome sequence. Comparisons for both analyses was done with BLASTN with e-value <10−150. Dot plot visualization was done with Combo [148].

Figure 2

doi: https://doi.org/10.1371/journal.pgen.1000891.g002