Additional file 3: Table S3. of Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants

Overview of the flagellar locus found in C. clostridioforme. (XLSX 13 kb

Location of lincRNAs and single-exon intergenic non-coding transcripts.

<p>(a) We show the mapping of lincRNAs, broken down by sample across chromosome 1. (b) Histogram of distance from intergenic transcripts to the next known transcribed element in both the 5′ (left) and 3′ (right) direction. The average distance is around 150,000 nucleotides, suggesting that these loci are not closely associated with known genes.</p

Comparison of canFam2.0 and canFam3.1.

<p>Comparison of canFam2.0 and canFam3.1.</p

Distance trees of expression profiles.

<p>We constructed neighbor-joining trees based on the correlation between expression values (FPKM>1.0) between samples, with 1 minus Spearman's rho defining the distance. Colors denote library construction methods (poly-A: blue, DSN: red). We divided transcribed loci into (a) protein coding genes with RNA-Seq support, either annotated by EnsEMBL in dog or EnsEMBL in the human orthologous regions. Replicates cluster together, so do the library constructions methods poly-A and DSN, as well as related tissues, such as heart and muscle; (b) antisense transcripts, that overlap at least one exon of a protein coding gene, as defined in (a). With the exception of testis, poly-A and DSN separate the samples, with both the poly-A and DSN sub-trees maintaining closer relationships between the related tissues heart and muscle; (c) spliced intergenic loci, excluding sequences that have coding potential. Similar to protein coding genes, the poly-A and DSN group by tissue first, with the exception of kidney DSN; and (d) intergenic and uncharacterized single-exon transcript loci. In this set, DSN and poly-A are, similar to antisense loci, the most dominant factor when grouping samples.</p

Transcribed loci per tissue and library preparation.

<p>N/A, due to poor alignment performance, this library was excluded from subsequent analyses.</p