draft genome sequencing of isolates  (Novogene)

Journal: Microbiology Spectrum

Article Title: Chromosomally and Plasmid-Located mcr in Salmonella from Animals and Food Products in China

doi: 10.1128/spectrum.02773-22

Figure Lengend Snippet: Characteristics of mcr -carrying Salmonella isolates in this study

Article Snippet: Interestingly, an analysis of mcr -positive contigs from the draft genomes of Salmonella isolates sequenced by Illumina revealed that six S . Indiana strains had incomplete mcr-1 , which thus retained susceptibility to colistin.

Techniques: Plasmid Preparation

Journal: G3: Genes|Genomes|Genetics

Article Title: Molecular Characterization of a Heterothallic Mating System in Pseudogymnoascus destructans , the Fungus Causing White-Nose Syndrome of Bats

doi: 10.1534/g3.114.012641

Figure Lengend Snippet: Isolates of Pseudogymnoascus used in this study

Article Snippet: BLAST searches were conducted using the draft genome sequence of the North American isolate 20631-21 of P. destructans ( Geomyces destructans Sequencing Project, Broad Institute of Harvard and MIT; http://www.broadinstitute.org/ ).

Techniques: Sequencing

Journal: G3: Genes|Genomes|Genetics

Article Title: Molecular Characterization of a Heterothallic Mating System in Pseudogymnoascus destructans , the Fungus Causing White-Nose Syndrome of Bats

doi: 10.1534/g3.114.012641

Figure Lengend Snippet: Homothallic species of Pseudogymnoascus produced gymnothecia and contain a MAT locus consisting of the conserved regulators MAT1-2-1 , MAT1-1-3 , and MAT1-1-1 . (A) Gymnothecia of Pseudogymnoascus WSF 3629 grown at 25° for 4 wk on solid oatmeal medium in the dark. Scale bars are drawn on each of the images. (B) Gymnothecia of WSF 3629 are composed of loosely woven, pigmented peridial hyphae, and among the peridial hyphae there are asci. (C and D) Higher magnification of asci containing ascospores and ascospores liberated from asci. (E) Schematic of the mating-type locus ( MAT ) for the homothallic species Pseudogymnoascus sp. WSF 3629 and Pseudogymnoascus sp. 23342-1-I1. The North American genome reference strain of P. destructans (20631-21) is the MAT1-1 mating type, whereas the MAT locus of MAT1-2 strains is depicted by the Czech strain of P. destructans CCF3942.

Article Snippet: BLAST searches were conducted using the draft genome sequence of the North American isolate 20631-21 of P. destructans ( Geomyces destructans Sequencing Project, Broad Institute of Harvard and MIT; http://www.broadinstitute.org/ ).

Techniques: Produced

Journal: G3: Genes|Genomes|Genetics

Article Title: Molecular Characterization of a Heterothallic Mating System in Pseudogymnoascus destructans , the Fungus Causing White-Nose Syndrome of Bats

doi: 10.1534/g3.114.012641

Figure Lengend Snippet: Central European isolates of P. destructans have two mating types ( MAT1-1 or MAT1-2 ). (A) Southern blot of the MAT locus of the North American isolate (20631-21) and 23 isolates from central Europe. Expected banding patterns for an EcoRI digestion of MAT1-1 strains is a single band of 3.183 kb. Expected banding pattern for EcoRI digestion using MAT1-2 as a probe is three bands of 2.6 kb, 2.063 kb, and 0.699 kb. European isolates of P. destructans collected from the same hibernaculum and date, different individual bats, but opposite mating types are demarcated with a red line above the isolate name. (B) Schematic of the two MAT idiomorphs in P. destructans illustrating the gene prediction structure and restriction enzyme cut sites. Radio-labeled probes used in the Southern blot are indicated by a black line.

Article Snippet: BLAST searches were conducted using the draft genome sequence of the North American isolate 20631-21 of P. destructans ( Geomyces destructans Sequencing Project, Broad Institute of Harvard and MIT; http://www.broadinstitute.org/ ).

Techniques: Southern Blot, Labeling

Journal: G3: Genes|Genomes|Genetics

Article Title: Molecular Characterization of a Heterothallic Mating System in Pseudogymnoascus destructans , the Fungus Causing White-Nose Syndrome of Bats

doi: 10.1534/g3.114.012641

Figure Lengend Snippet: Putative genes involved in sexual reproduction are expressed in laboratory culture. (A) Semi-quantitative reverse-transcriptase PCR was used to measure gene expression of genes predicted to be involved in sexual reproduction. All PCR reactions were conducted with 32 amplification cycles except for those marked with an asterisk (*), where 42 amplification cycles were used. Mating type MAT1-1 is required for expression of the precursor to alpha-pheromone ( ppg1 ), whereas MAT1-2 is required for expression of the G-protein-coupled receptors pre1 and pre2 . Expression of MAT1-1-3 is only found when both mating types were co-cultured. (B) Proposed diagram of genes involved in sexual reproduction in P. destructans based on homology and expression in laboratory culture.

Article Snippet: BLAST searches were conducted using the draft genome sequence of the North American isolate 20631-21 of P. destructans ( Geomyces destructans Sequencing Project, Broad Institute of Harvard and MIT; http://www.broadinstitute.org/ ).

Techniques: Reverse Transcription, Gene Expression, Amplification, Expressing, Cell Culture

Journal: BMC Microbiology

Article Title: The cross-pathway control system regulates production of the secondary metabolite toxin, sirodesmin PL, in the ascomycete, Leptosphaeria maculans

doi: 10.1186/1471-2180-11-169

Figure Lengend Snippet: A) The cpcA locus of Leptosphaeria maculans . The conserved leucine zipper region at the C-terminus of cpcA is dark grey. The open boxes indicate the upstream Open Reading Frames uORF1 and uORF2 in the 5' leader region. The black dot preceding them represents the putative cross-pathway control element (CPRE) whose sequence is 5'TGACTCA3'. B) Alignment of the deduced amino acid sequence of uORF2 with counterparts in the leader sequences of Aspergillus fumigatus (Af) cpcA (GenBank XP_751584.1 ) and A. nidulans (An) cpcA (GenBank AF302935 ). Black boxes with white text denote amino acids identical in two of the three fungal species. Grey boxes with white text mark conserved changes. Gaps are introduced to optimize alignment. C) Alignment of the deduced amino acid sequence of the C-terminus conserved leucine zipper region with that of A. fumigatus CpcA and A. nidulans CpcA. The thick black line denotes the bZIP transcription factors basic domain signature (PS00036). Asterisks mark positions where conserved leucine residues characteristic of a leucine zipper (L-x(6)-L-x(6)-L-x(6)-L) should be found.

Article Snippet: The sequences of the resulting plasmids were compared to the draft genome sequence of L. maculans isolate JN3 (Genoscope and Unité de Recherche Génomique Info, France) and 10 kb regions flanking these DNA fragments were analysed by FGENESH for presence of ORFs.

Techniques: Control, Sequencing

Journal: BMC Microbiology

Article Title: The cross-pathway control system regulates production of the secondary metabolite toxin, sirodesmin PL, in the ascomycete, Leptosphaeria maculans

doi: 10.1186/1471-2180-11-169

Figure Lengend Snippet: Quantitative Reverse Transcription PCR analysis of (A) cpcA, trpC and aroC , (B) sirZ and sirP in wild type (wt) and a cpcA -silenced (cpcA-sil) isolate of Leptosphaeria maculans . Six replicates of each isolate were grown in Tinline for eight days and then mycelia were washed and then transferred to fresh Tinline media for 5 h with 5 mM 3AT (+) or without 3AT (-). RNA was isolated from all treatments, cDNA prepared and q RT-PCR carried out. Transcript level is normalised to that of actin. Values are means ± SE of triplicate reactions of three independent biological samples. Asterisks mark values that have a significant increase (p < 0.05) in mean transcription levels compared to controls without 3AT.

Article Snippet: The sequences of the resulting plasmids were compared to the draft genome sequence of L. maculans isolate JN3 (Genoscope and Unité de Recherche Génomique Info, France) and 10 kb regions flanking these DNA fragments were analysed by FGENESH for presence of ORFs.

Techniques: Reverse Transcription, Isolation, Reverse Transcription Polymerase Chain Reaction

Journal: BMC Microbiology

Article Title: The cross-pathway control system regulates production of the secondary metabolite toxin, sirodesmin PL, in the ascomycete, Leptosphaeria maculans

doi: 10.1186/1471-2180-11-169

Figure Lengend Snippet: Sirodesmin PL levels in culture filtrates of in wild type (wt) and a cpcA -silenced (cpcA-sil) isolate of Leptosphaeria maculans . Cultures were grown for eight days in Tinline media (8d) and the culture filtrate isolated and sirodesmin PL levels were quantified by HPLC. Mycelia were washed then transferred to fresh Tinline medium with water (+H 2 O) or 5 mM 3AT (+3AT), or Tinline medium with no carbon or nitrogen sources (-C/N) for a further eight days. Culture filtrates from the three treatments (+H 2 O, +3AT, -C/N) were extracted and sirodesmin PL levels were quantified by HPLC. Values are means ± SE of three independent biological samples. Asterisks mark values that have a significant increase or decrease (p < 0.05) in sirodesmin PL production compared to water controls (+H 2 O).

Article Snippet: The sequences of the resulting plasmids were compared to the draft genome sequence of L. maculans isolate JN3 (Genoscope and Unité de Recherche Génomique Info, France) and 10 kb regions flanking these DNA fragments were analysed by FGENESH for presence of ORFs.

Techniques: Isolation