scholarly journals Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1972 ◽  
Author(s):  
Amy L. Longmuir ◽  
Peter L. Beech ◽  
Mark F. Richardson
Keyword(s):  
Plant Pathogen ◽  
Phytophthora Cinnamomi ◽  
Gene Prediction ◽  
Single Copy ◽  
Control Methods ◽  
Draft Assembly ◽  
Protein Encoding ◽  
Evolutionary Studies ◽  
Pathogen Control ◽  
Encoding Genes

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The currently available genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, more robust assemblies of the genomes of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings:  Some 308 million raw reads were generated for the two strains. Independent genome assembly produced final genomes of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 82.5% and 81.8% of the eukaryote universal single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analysis and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

scholarly journals Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1972 ◽  
Author(s):  
Amy L. Longmuir ◽  
Peter L. Beech ◽  
Mark F. Richardson
Keyword(s):  
Plant Pathogen ◽  
Reference Genome ◽  
Phytophthora Cinnamomi ◽  
Gene Prediction ◽  
Single Copy ◽  
Draft Assembly ◽  
Protein Encoding ◽  
Pathogen Control ◽  
Genome Assemblies ◽  
Encoding Genes

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The current reference genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, robust genome assemblies of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings:  Some 308 million raw reads were generated for the two strains, DU054 and WA94.26. Independent genome assembly produced final genome sequences of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 94.4% and 91.5% of the stramenopile single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analyses and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

scholarly journals What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes

2021 ◽  
Vol 9 (2) ◽  
pp. 299
Author(s):  
Angela Conti ◽  
Laura Corte ◽  
Debora Casagrande Pierantoni ◽  
Vincent Robert ◽  
Gianluigi Cardinali
Keyword(s):  
Single Copy ◽  
Sensu Stricto ◽  
Fungal Species ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Protein Encoding ◽  
The Many ◽  
Next Generation Sequencing Ngs ◽  
Encoding Genes

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.

scholarly journals What’s all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry

2021 ◽  
Author(s):  
Blase Matthew LeBlanc ◽  
Rosamaria Yvette Moreno ◽  
Edwin Escobar ◽  
Mukesh Kumar Venkat Ramani ◽  
Jennifer S Brodbelt ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Phosphorylation State ◽  
Terminal Domain ◽  
Carboxy Terminal Domain ◽  
Protein Encoding ◽  
Small Nuclear Rnas ◽  
Rnap Ii ◽  
Carboxy Terminal ◽  
Encoding Genes

RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and...

scholarly journals Autotransporter Protein-Encoding Genes of Diarrheagenic Escherichia coli Are Found in both Typical and Atypical Enteropathogenic E. coli Strains

2012 ◽  
Vol 79 (1) ◽  
pp. 411-414 ◽  
Author(s):  
Afonso G. Abreu ◽  
Vanessa Bueris ◽  
Tatiane M. Porangaba ◽  
Marcelo P. Sircili ◽  
Fernando Navarro-Garcia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Virulence Markers ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Specific Virulence

ABSTRACTAutotransporter (AT) protein-encoding genes of diarrheagenicEscherichia coli(DEC) pathotypes (cah,eatA,ehaABCDJ,espC,espI,espP,pet,pic,sat, andtibA) were detected in typical and atypical enteropathogenicE. coli(EPEC) in frequencies between 0.8% and 39.3%. Although these ATs have been described in particular DEC pathotypes, their presence in EPEC indicates that they should not be considered specific virulence markers.

Enhanced surface display efficiency of β-glucosidase in Saccharomyces cerevisiae by disruption of cell wall protein-encoding genes YGP1 and CWP2

2021 ◽  
pp. 108305
Author(s):  
Jantima Arnthong ◽  
Jatupong Ponjarat ◽  
Piyada Bussadee ◽  
Pacharawan Deenarn ◽  
Parichat Prommana ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Wall ◽  
Surface Display ◽  
Cell Wall Protein ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Enhanced Surface

Evaluation of DNA vaccination of spotted sand bass (Paralabrax maculatofasciatus) with two major outer-membrane protein-encoding genes from Aeromonas veronii

2005 ◽  
Vol 19 (2) ◽  
pp. 153-163 ◽  
Author(s):  
Roberto Carlos Vazquez-Juarez ◽  
Marta Gomez-Chiarri ◽  
Hugo Barrera-Saldaña ◽  
Norma Hernandez-Saavedra ◽  
Silvie Dumas ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
Dna Vaccination ◽  
Major Outer Membrane Protein ◽  
Aeromonas Veronii ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Spotted Sand Bass ◽  
Paralabrax Maculatofasciatus

scholarly journals Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica)

2017 ◽  
Vol 5 (7) ◽  
Author(s):  
Yannick Lara ◽  
Benoit Durieu ◽  
Luc Cornet ◽  
Olivier Verlaine ◽  
Rosmarie Rippka ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Axenic Strain ◽  
Larsemann Hills ◽  
Freshwater Cyanobacterium ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. Its draft genome is 5,684,389 bp long. It contains a total of 5,604 protein-encoding genes, of which 22.2% have no clear homologues in known genomes. To date, this draft genome is the first one ever determined for an axenic cyanobacterium from Antarctica.

Prion Protein-Encoding Genes

Prion Biology ◽  
2013 ◽  
Author(s):  
Sead Chadi ◽  
Rachel Young ◽  
Sandrine Guillou ◽  
Gaelle Tilly ◽  
Frédérique Bitton ◽  
...  
Keyword(s):  
Prion Protein ◽  
Protein Encoding ◽  
Encoding Genes

scholarly journals The microRNA, miR-133b, functions to slow Duchenne muscular dystrophy pathogenesis

2020 ◽  
Author(s):  
Thomas Taetzsch ◽  
Dillon Shapiro ◽  
Randa Eldosougi ◽  
Tracey Myers ◽  
Robert Settlage ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Skeletal Muscles ◽  
Tibialis Anterior Muscle ◽  
Muscle Fibers ◽  
Progressive Degeneration ◽  
Protein Encoding ◽  
Small Muscle ◽  
Encoding Genes

AbstractDuchenne muscular dystrophy (DMD) is characterized by progressive degeneration of skeletal muscles. To date, there are no treatments available to slow or prevent the disease. Hence, it remains essential to identify molecular factors that promote muscle biogenesis since they could serve as therapeutic targets for treating DMD. While the muscle enriched microRNA, miR-133b, has been implicated in the biogenesis of muscle fibers, its role in DMD remains unknown. To assess the role of miR-133b in DMD-affected skeletal muscles, we genetically ablated miR-133b in the mdx mouse model of DMD. In the absence of miR-133b, the tibialis anterior muscle of juvenile and adult mdx mice is populated by small muscle fibers with centralized nuclei, exhibits increased fibrosis, and thickened interstitial space. Additional analysis revealed that loss of miR-133b exacerbates DMD-pathogenesis partly by altering the number of satellite cells and levels of protein-encoding genes, including previously identified miR-133b targets as well as genes involved in cell proliferation and fibrosis. Altogether, our data demonstrate that skeletal muscles utilize miR-133b to mitigate the deleterious effects of DMD.

scholarly journals Transcriptome Analysis Unveils the Effects of Proline on Gene Expression in the Yeast Komagataella phaffii

2021 ◽  
Vol 10 (1) ◽  
pp. 67
Author(s):  
Andrey Rumyantsev ◽  
Anton Sidorin ◽  
Artemii Volkov ◽  
Ousama Al Shanaa ◽  
Elena Sambuk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Recombinant Proteins ◽  
Gene Promoter ◽  
Energy Sources ◽  
Experimental Conditions ◽  
Komagataella Phaffii ◽  
Protein Encoding ◽  
Modern Biotechnology ◽  
Encoding Genes ◽  
Transcriptome Level

Komagataella phaffii yeast is one of the most important biocompounds producing microorganisms in modern biotechnology. Optimization of media recipes and cultivation strategies is key to successful synthesis of recombinant proteins. The complex effects of proline on gene expression in the yeast K. phaffii was analyzed on the transcriptome level in this work. Our analysis revealed drastic changes in gene expression when K. phaffii was grown in proline-containing media in comparison to ammonium sulphate-containing media. Around 18.9% of all protein-encoding genes were differentially expressed in the experimental conditions. Proline is catabolized by K. phaffii even in the presence of other nitrogen, carbon and energy sources. This results in the repression of genes involved in the utilization of other element sources, namely methanol. We also found that the repression of AOX1 gene promoter with proline can be partially reversed by the deletion of the KpPUT4.2 gene.

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