Identification and structure of nonribosomal peptide synthetases in <i>Cochliobolus miyabeanus</i> TG12bL2.

<p>Identification and structure of nonribosomal peptide synthetases in <i>Cochliobolus miyabeanus</i> TG12bL2.</p

Summary features of the <i>Cochliobolus miyabeanus Cm</i>TG12bL2 isolate genome assembly and annotation.

<p>Summary features of the <i>Cochliobolus miyabeanus Cm</i>TG12bL2 isolate genome assembly and annotation.</p

Schematic representation of hypothetical degradation of wildrice cell wall polysaccharides by CAZymes.

<p>A. Degradation of cellulose by cellulolytic enzymes: endo-β-1,4-glucanase, cellobiohydrolase, β-glucosidase, and lytic polysaccharide monooxygenase; B. Degradation of hemicellulose polysaccharides and substituted residues by hemicellulolytic enzymes. <i>Xylan</i>: endoxylanase, β-xylosidase, acetylxylan esterase, feruloyl esterase, α-L-arabinofuranosidase, α-glucuronidase; <i>Xyloglucan</i>: endo-β-1,4-endoglucanase, α-L-fucosidase, β-galactosidase, α-xylosidase; <i>Galactomannan</i>: endo-β-1,4-mannanase, β-mannoside, α-galactosidase. C. Degradation of pectin polysaccharides and substituted moieties by pectinolytic enzymes. <i>Homogalacturonan</i>: endo- and exopolygalacturonase, pectin and pectate lyase, pectin acetylesterase, pectin methylesterase; <i>Xylogalacturonan</i>: endo- and exogalacturonase, β-xylosidase; <i>Rhamnogalacturonan</i>: rhamnogalacturonase, rhamnogalacturonan lyase, rhamnogalacturonan acetylesterase, α-L-rhamnosidase, β-1,4-galactosidase, β-1,4-galactanase, β-glucuronidase, α-L-arabinofuranosidase, α-L-arabinanase, β-1,6-galactosidase, β-1,3-galactanase α-L-fucosidase. The glycan symbol nomenclature used was according to [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154122#pone.0154122.ref085" target="_blank">85</a>].</p

Predicted families within the major facilitator superfamily transporters in the <i>Cm</i>TG12bL2 genome.

<p>SP: Sugar Porter (2.A.1.1), DHA1: Drug:H⁺ Antiporter-1 (12 Spanner) (2.A.1.2), ACS: Anion:Cation Symporter (2.A.1.14), DHA2: Drug:H⁺ Antiporter-2 (14 Spanner) (2.A.1.3), MCP: Monocarboxylate Porter (2.A.1.13), V-BAAT: Vacuolar Basic Amino Acid Transporter (2.A.1.48), NAG-T: N-Acetylglucosamine Transporter (2.A.1.58), SIT: Siderophore-Iron Transporter (2.A.1.16), FHS: Fucose: H⁺ Symporter(2.A.1.7), PHS: Phosphate: H⁺ Symporter (2.A.1.9), VNT: Vesicular Neurotransmitter Transporter (2.A.1.22), UMF1: Unknown Major Facilitator-1 (2.A.1.24), D-cP: Domain-containing Protein (2.A.1.40), LAT3: L-Amino Acid Transporter-3 (2.A.1.44), SHS: Sialate:H⁺ Symporter (2.A.1.12), AAHS: Aromatic Acid:H⁺ Symporter (2.A.1.15), OCT: Organic Cation Transporter (2.A.1.19), PAT: Peptide-Acetyl-Coenzyme A (2.A.1.25), FLVR: Feline Leukemia Virus Subgroup C Receptor (2.A.1.28), OPA: Organophosphate:P_i Antiporter (2.A.1.4), Pht: Proteobacterial Intraphagosomal Amino Acid (2.A.1.53), NNP: Nitrate/Nitrite Porter (2.A.1.8).</p

Predicted families of ABC transporters in the <i>Cm</i>TG12bL2 genome.

<p>Black bars: ABC2 superfamily that includes: PDR, Pleiotropic Drug Resistance; Gld, Gliding Motility ABC transporter; EPP, Eye Pigment Precursor transporter; ThiW, Putative Thiamine Uptake transporter; ThiP, Thiamine Precursor; EVE, Ethyl Viologen Exporter. Gray bars: ABC1 superfamily with MDR, MultiDrug Resistance exporter; DCT, Drug Conjugate Transporter; HMT, Heavy Metal Transport; P-FAT, Peroxysomal Fatty Acyl-CoA Transporter; MPE, Mitochondrial Peptide Exporter; STE, α-Factor Sex Pheromone Exporter; CPR, Cholesterol/Phospholipid/Retinal (CPR) Flippase Family. White bar: Bact, Bacterial-like transporters.</p

Comparison of predicted carbohydrate protein modules present in 12 Ascomycete genomes.

<p>Comparison of predicted carbohydrate protein modules present in 12 Ascomycete genomes.</p

<i>Cochliobolus miyabeanus</i> TG12bL2 genes with similarity to genes involved plant-pathogen interactions in other <i>Cochliobolus</i> species.

<p><i>Cochliobolus miyabeanus</i> TG12bL2 genes with similarity to genes involved plant-pathogen interactions in other <i>Cochliobolus</i> species.</p

Co-infection and quasispecies population in different viral samples.

a<p>Nucleotide numbering begins at each ORF; R = A/G Y = C/T M = A/C K = T/G.</p

Phylogenetic analysis of HA and NA sequences from A/bald eagle/Virginia/Sg-00154/2008(H1N1/H2N1) show HA lineages of H1 (Panel 3A) and H2 (Panel 3B), and at least two lineages of N1 segment (Panel 3C).

<p>Evolutionary associations were inferred in MEGA 4.0 using the maximum parsimony algorithm with Kimura-2P correction and 1000 bootstrap replications (confidence of the branches are shown on branch bifurcations).</p

Summary of the 454 sequencing results.

a<p>Total genome size of influenza A is 13523–13645 bp (PB2 – 2341 bp; pb1 - 2341 bp, PA - 2233 bp; HA - 1728–1779 bp; NP - 1565 bp; NA - 1398–1469 bp; M - 1027 bp; NS - 890 bp).</p