Revisiting the Neurospora crassa mitochondrial genome.

The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64 839 bp revealed 21 protein-coding genes and several hypothetical open reading frames with no significant homology to any described gene. Five large repetitive regions were identified across the genome, including partial or complete genes. The largest repeated region holds a partial nd2 section that was also detected in Neurospora intermedia, suggesting a rearrangement that occurred before the N. crassa speciation. Interestingly, N. crassa has a palindrome adjacent to the partial nd2 repeated region possibly related to the genomic rearrangement, which is absent in N. intermedia. Finally, we compared the sequences of the three available N. crassa complete mtDNAs and found low levels of intraspecific variability. Most differences among strains were due to small indels in noncoding regions. The revisiting of the N. crassa mtDNA forms the basis for future studies on mitochondrial genome organization and variability.

A genomic distance for assembly comparison based on compressed maximal exact matches.

Genome assemblies are typically compared with respect to their contiguity, coverage, and accuracy. We propose a genome-wide, alignment-free genomic distance based on compressed maximal exact matches and suggest adding it to the benchmark of commonly used assembly quality metrics. Maximal exact matches are perfect repeats, without gaps or misspellings, which cannot be further extended to either their left- or right-end side without loss of similarity. The genomic distance here proposed is based on the normalized compression distance, an information-theoretic measure of the relative compressibility of two sequences estimated using multiple finite-context models. This measure exposes similarities between the sequences, as well as, the nesting structure underlying the assembly of larger maximal exact matches from smaller ones. We use four human genome assemblies for illustration and discuss the impact of genome sequencing and assembly in the final content of maximal exact matches and the genomic distance here proposed.