BRIG alignment.

<p>BRIG alignments of the 5 study isolates and the references. (A) Relative to reference NC_018108.1 four major regions with poor alignment are visible. (B) A possible fifth region with poor alignment becomes visible when isolates are aligned with respect to NC_014914.1.</p

<i>Taylorella equigenitalis</i> isolate attributes.

<p><i>Taylorella equigenitalis</i> isolate attributes.</p

Genomic diversity of <i>Taylorella equigenitalis</i> introduced into the United States from 1978 to 2012

<div><p>Contagious equine metritis is a disease of worldwide concern in equids. The United States is considered to be free of the disease although sporadic outbreaks have occurred over the last few decades that were thought to be associated with the importation of horses. The objective of this study was to create finished, reference quality genomes that characterize the diversity of <i>Taylorella equigenitalis</i> isolates introduced into the USA, and identify their differences. Five isolates of <i>T</i>. <i>equigenitalis</i> associated with introductions into the USA from unique sources were sequenced using both short and long read chemistries allowing for complete assembly and annotation. These sequences were compared to previously published genomes as well as the short read sequences of the 200 isolates in the National Veterinary Services Laboratories’ diagnostic repository to identify unique regions and genes, potential virulence factors, and characterize diversity. The 5 genomes varied in size by up to 100,000 base pairs, but averaged 1.68 megabases. The majority of that diversity in size can be explained by repeat regions and 4 main regions of difference, which ranged in size from 15,000 to 45,000 base pairs. The first region of difference contained mostly hypothetical proteins, the second contained the CRISPR, the third contained primarily hemagglutinin proteins, and the fourth contained primarily segments of a type IV secretion system. As expected and previously reported, little evidence of recombination was found within these genomes. Several additional areas of interest were also observed including a mechanism for streptomycin resistance and other virulence factors. A SNP distance comparison of the <i>T</i>. <i>equigenitalis</i> isolates and <i>Mycobacterium tuberculosis complex</i> (MTBC) showed that relatively, <i>T</i>. <i>equigenitalis</i> was a more diverse species than the entirety of MTBC.</p></div

Mauve alignment.

<p>This alignment contains the 5 study isolates and NC_018108.1. Overall similarity among the 6 genomes with localized regions of variability is visible. No rearrangements are evident.</p

Percent identity and coverage calculated from Lastz output performing pairwise comparisons.

<p>Percent identity and coverage calculated from Lastz output performing pairwise comparisons.</p

<i>Taylorella equigenitalis</i> isolate information.

<p><i>Taylorella equigenitalis</i> isolate information.</p

Mean and variance of percent coverage by window.

<p>Mean percent coverage and variance of the percent coverage of each isolate at a minimum depth of 10X using the MiSeq reads from the 200 NVSL diagnostic isolates of <i>T</i>. <i>equigenitalis</i>. Results are given by 35,000 bp window.</p

Synteny of <i>Fusarium virguliforme</i> Mont1 sequences to the <i>Nectria haematococca</i> chromosomal sequences.

<p>The colored blocks show the alignment of <i>F. virguliforme</i> sequences to the sequences of the <i>N. haematococca</i> chromosomes. Blocks below the central line indicate the regions that align in the reverse complement orientation.</p

Heat-map depicting the Pfam domains in all <i>Fusarium</i> species.

<p><i>F. virguliforme</i> genome is rich in Pkinase_Tyr (Protein tyrosine kinase), Ank (Ankyrin repeat), and HET (Heterokaryon incompatibility proteins) as compared to the other <i>Fusarium</i> genomes.</p

Breadth of coverage of the transposon at a minimum depth of 25 reads¹.

<p>Breadth of coverage of the transposon at a minimum depth of 25 reads<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158183#t006fn001" target="_blank">¹</a>.</p