Methyltransferases identified in the <i>Salmonella</i> serovars, but not assigned to a motif.

<p>^am5C MTases not included.</p><p>Methyltransferases identified in the <i>Salmonella</i> serovars, but not assigned to a motif.</p

Genome-Wide Methylation Patterns in <i>Salmonella enterica</i> Subsp. <i>enterica</i> Serovars

<div><p>The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. <i>Salmonella</i> is an important foodborne pathogen, and methylation in <i>Salmonella</i> is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven <i>Salmonella enterica</i> isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N⁶-methyladenine (m6A) methylated motifs, one N⁴-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases) associated with 13 of the motifs. Some motifs are conserved across all <i>Salmonella</i> serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems), indicating the high diversity of methylation patterns present in <i>Salmonella</i>.</p></div

The methylomes of eleven <i>Salmonella</i> serovars.

<p>Violet = MTase identified, light violet = MTase unknown, red = novel motif, orange = MTase present in genome, motif not observed. Light violet/red stripe = novel motif, MTase unknown. Roman numerals indicate MTase type (I – III). Note the majority of novel MTases are Type I systems.</p

Summary of motifs and methyltransferases found in each <i>Salmonella</i> genome.

<p>*A unique motif refers to one that has not been previously observed in any bacterial species.</p><p>Summary of motifs and methyltransferases found in each <i>Salmonella</i> genome.</p

Diagram of the interpulse duration (IPD) ratio of three novel motifs identified in three <i>Salmonella</i> serovars.

<p>Vertical axis = IPD ratio, horizontal axis = genome position. IPD ratio listed next to bar. A. Motif CC^m6AN₈<u>T</u>GAG in <i>S</i>. Anatum. B. Motif RA^m6ACN₅<u>T</u>GA in <i>S</i>. Cubana. C. Motif CG^m6AYN₆R<u>T</u>RTC in <i>S</i>. Montevideo.</p

Scaffolding using optical map, genetic map and synteny with closely related fish genomes produced chromosome-level assembly of the Asian seabass genome.

<p>(A) Comparison of <i>L</i>. <i>calcarifer</i> to two closely related fish species (<i>G</i>. <i>aculeatus</i>, and <i>D</i>. <i>labrax</i>) at the genome-wide level. Colours used for depicting assembled chromosomes are random for each of the three genomes. Different colours in a single <i>L</i>. <i>calcarifer</i> linkage group are used to represent the inter-chromosomal rearrangements. Black arcs show collinear blocks that are intra-chromosomally rearranged between the species. (B) Genome assembly (middle panel) shown anchored to two (LG15 and LG18) of the twenty four <i>L</i>. <i>calcarifer</i> linkage groups while the right panel represents the scaffolded assembly (regions in grey depict the additional contigs brought together by scaffolding).</p

<i>Lates calcarifer</i> has the best metrics from among the assembled fish genomes till date.

<p>The <i>L</i>. <i>calcarifer</i> genome contig N50 and scaffold N50 values were compared to the following fish genomes: <i>Anguilla japonica</i>, <i>Astatotilapia burtoni</i>, <i>Astyanax mexicanus</i>, <i>Boleophthalmus pectinirostris</i>, <i>Ctenopharyngodon idellus</i>, <i>Cynoglossus semilaevis</i>, <i>Cyprinus carpio</i>, <i>Danio rerio</i>, <i>Dicentrarchus labrax</i>, <i>Electrophorus electricus</i>, <i>Esox lucius</i>, <i>Gadus morhua</i>, <i>Gasterosteus aculeatus</i>, <i>Larimichthys crocea</i>, <i>Latimeria chalumnae</i>, <i>Metriaclima zebra</i>, <i>Neolamprologus brichardi</i>, <i>Notothenia coriiceps</i>, <i>Oncorhynchus mykiss</i>, <i>Oreochromis niloticus</i>, <i>Oryzias latipes</i>, <i>Pundamilia nyererei</i>, <i>Periophthalmodon schlosseri</i>, <i>Periophthalmus magnuspinnatus</i>, <i>Salmo salar</i>, <i>Scartelaos histophorus</i>, <i>Takifugu flavidus</i>, <i>Takifugu rubripes</i>, <i>Tetraodon nigroviridis</i>, <i>Thunnus orientalis</i>, and <i>Xiphophorus maculatus</i> (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005954#pgen.1005954.s002" target="_blank">S1 Table</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005954#pgen.1005954.s003" target="_blank">S2 Fig</a> for more details).</p

Survey of the <i>L</i>. <i>calcarifer</i> genome assembly identified long stretches of TRs lacking in the short read-based assembly and a continuous assembled telomeric region identified at the end of LG3.

<p>(A) Stretches of TRs were virtually missing from the <i>L</i>. <i>calcarifer</i> short read assembly (SRA) generated using 80X Illumina reads scaffolded with ~11,000 BAC ends (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005954#pgen.1005954.s016" target="_blank">S1 Table</a>) whereas the long read assembly (LRA) had a good representation of TRs (upper panel) and the different repeats were more fragmented in the SRA <i>vis-à-vis</i> the LRA (lower panel). (B) Arrangement of telomere monomer sequence (TTAGGG) on a single assembled contig, (unitig_1659; ~0.5 Mb) placed at the terminal end of LG3 (region indicated in orange). Every occurrence of the monomer is indicated by green bars. A highly dense region of (TTAGGG)n was observed between 455.5–466.9 kb, containing the monomer repeated in tandem 1,655 times. The region upstream to this dense region had short dispersed stretches of (TTAGGG)n and contained eight predicted genes (indicated by blue boxes).</p

Annotation statistics of the Asian seabass genome.

<p>Annotation statistics of the Asian seabass genome.</p

Fluorescence <i>in situ</i> hybridization revealed the localization of tandem repeats in centromeric/pericentromeric regions of the Asian seabass genome and characterization of B chromosomes.

<p>Labeled painting B chromosomes and tandem repeat probes were hybridized to metaphase chromosomes. The chromosomal position of three tandem repeats (green): (A) Sat_LM- centromeres; (B) Lca_217 and Lca_38 (C) pericentromeric region. (D) B chromosome-derived probes, ChB5 (green) and ChB6 (red), reveal the presence of a B chromosome in the <i>L</i>. <i>calcarifer</i> karyotype, as indicated by arrowhead. Chromosomes were counterstained with DAPI (blue). Bar is 10 μm for all images. (E) Association of B chromosomes with the linkage groups. Each linkage group is represented in coloured blocks, and the shadings delineate the genome superscaffolds (after optical mapping) that were assigned to the given linkage group. Rearrangements of portions from the four linkage groups, namely LG5, LG9, LG17 and LG19, together with regions without linkage group assignment (U) comprised the B chromosome.</p