scholarly journals Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design

2018 ◽  
Author(s):  
S. Daval ◽  
A. Belcour ◽  
K. Gazengel ◽  
L. Legrand ◽  
J. Gouzy ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Computational Analysis ◽  
Reference Genome ◽  
Plasmodiophora Brassicae ◽  
Functional Study ◽  
Spongospora Subterranea ◽  
Pathway Database ◽  
European Isolate ◽  
Genome Database ◽  
Brassicaceae Species

AbstractPlasmodiophora brassicae is an obligate biotrophic pathogenic protist responsible for clubroot, a root gall disease of Brassicaceae species. In addition to the reference genome of the P. brassicae European e3 isolate and the draft genomes of Canadian or Chinese isolates, we present the genome of eH, a second European isolate. Refinement of the annotation of the eH genome led to the identification of the mitochondrial genome sequence, which was found to be bigger than that of Spongospora subterranea, another plant parasitic Plasmodiophorid phylogenetically related to P. brassicae. New pathways were also predicted, such as those for the synthesis of spermidine, a polyamine up-regulated in clubbed regions of roots. A P. brassicae pathway genome database was created to facilitate the functional study of metabolic pathways in transcriptomics approaches. These available tools can help in our understanding of the regulation of P. brassicae metabolism during infection and in response to diverse constraints.

scholarly journals Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design

Genomics ◽  
2019 ◽  
Vol 111 (6) ◽  
pp. 1629-1640 ◽  
Author(s):  
Stéphanie Daval ◽  
Arnaud Belcour ◽  
Kévin Gazengel ◽  
Ludovic Legrand ◽  
Jérôme Gouzy ◽  
...  
Keyword(s):  
Metabolic Pathway ◽  
Computational Analysis ◽  
Plasmodiophora Brassicae ◽  
Database Design ◽  
Pathway Database ◽  
Mitochondrial Sequence

scholarly journals Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing

2014 ◽  
Vol 67 (2) ◽  
pp. 7247-7260 ◽  
Author(s):  
Pablo Andrés Gutiérrez Sánchez ◽  
Juan Fernando Alzate ◽  
Mauricio Marín Montoya
Keyword(s):  
Dna Sequences ◽  
454 Pyrosequencing ◽  
Plant Pathogens ◽  
Plasmodiophora Brassicae ◽  
Bioinformatic Analysis ◽  
Spongospora Subterranea ◽  
Sequencing Technologies ◽  
Intron Structure ◽  
Basic Biology

Spongospora subterranea, the causal agent of Potato powdery scab, is an important soil-borne obligate protozoan commonly found in Andean soils. This is a serious problem that causes cosmetic damage on the skin of tubers and induces root gall formation, diminishing the yield and commercial value of the potato. Genetic studies on S. subterranea are difficult due to its obligate parasitism, which explains the lack of available knowledge on its basic biology. S. subterranea is a member of the Plasmodiophorida order, a protist taxa that includes other important plant pathogens such as Plasmodiophora brassicae and Spongospora nasturtii. Little is known about the genomes of Plasmodiophorida; however, with the use of Next-Generation Sequencing technologies combined with appropriate bioinformatic techniques, it is possible to obtain genomic sequences from obligate pathogens such as S. subterranea. To gain a better understanding of the biology of this pathogen and Plasmodiophorida in general, DNA sequences from a cystosori-enriched sample of S. subterranea were obtained using 454 pyrosequencing technology. As a first step in understanding the nutritional requirements of S. subterranea as well as its infective and resistance structures, we present a bioinformatic analysis of 24 contigs related to genes involved in the glycolysis, starch, celullose and chitin metabolism. Intron structure and codon usage is also discussed. The genes analyzed in this study are a good source of information for studies aimed at characterizing these enzymes in vitro, as well as the generation of new methods for the molecular detection of S. subterranea in either soils or infected plants.

scholarly journals The in vivo ISGylome links ISG15 to metabolic pathways and autophagy upon Listeria monocytogenes infection

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yifeng Zhang ◽  
Fabien Thery ◽  
Nicholas C. Wu ◽  
Emma K. Luhmann ◽  
Olivier Dussurget ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Metabolic Pathways ◽  
Quantitative Proteomics ◽  
Computational Analysis ◽  
Murine Models ◽  
Direct Modification ◽  
Catalytic Sites ◽  
Listeria Monocytogenes Infection

AbstractISG15 is an interferon-stimulated, ubiquitin-like protein, with anti-viral and anti-bacterial activity. Here, we map the endogenous in vivo ISGylome in the liver following Listeria monocytogenes infection by combining murine models of reduced or enhanced ISGylation with quantitative proteomics. Our method identifies 930 ISG15 sites in 434 proteins and also detects changes in the host ubiquitylome. The ISGylated targets are enriched in proteins which alter cellular metabolic processes, including upstream modulators of the catabolic and antibacterial pathway of autophagy. Computational analysis of substrate structures reveals that a number of ISG15 modifications occur at catalytic sites or dimerization interfaces of enzymes. Finally, we demonstrate that animals and cells with enhanced ISGylation have increased basal and infection-induced autophagy through the modification of mTOR, WIPI2, AMBRA1, and RAB7. Taken together, these findings ascribe a role of ISGylation to temporally reprogram organismal metabolism following infection through direct modification of a subset of enzymes in the liver.

scholarly journals In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Calum J. Walsh ◽  
Caitriona M. Guinane ◽  
Colin Hill ◽  
R. Paul Ross ◽  
Paul W. O’Toole ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
In Silico ◽  
Reference Genome ◽  
Human Microbiome ◽  
Gene Clusters ◽  
Genome Database ◽  
In Silico Identification ◽  
Reference Genome Database ◽  
Bacteriocin Gene

scholarly journals Improving the usability and comprehensiveness of microbial databases

2018 ◽  
Author(s):  
Caitlin Loeffler ◽  
Aaron Karlsberg ◽  
Lana S. Martin ◽  
Eleazar Eskin ◽  
David Koslicki ◽  
...  
Keyword(s):  
Translational Research ◽  
Basic Science ◽  
Reference Genome ◽  
Reference Database ◽  
Data Preparation ◽  
Genome Database ◽  
Reference Databases ◽  
Reference Genome Database

AbstractMetagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibility, hindering their quality and comprehensiveness, and calling for the establishment of recommendations for reference genome database assembly. Here, we analyze existing fungal and bacterial databases and discuss guidelines for the development of a master reference database that promises to improve the quality and quantity of omics research.

scholarly journals Bovine Genome Database: new annotation tools for a new reference genome

2019 ◽  
Author(s):  
Md Shamimuzzaman ◽  
Justin J Le Tourneau ◽  
Deepak R Unni ◽  
Colin M Diesh ◽  
Deborah A Triant ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Genome Annotation ◽  
Reference Genome ◽  
Gene Annotation ◽  
Bovine Genome ◽  
Data Retrieval ◽  
Genome Database ◽  
Ruminant Species ◽  
Search Tool ◽  
Efficient Data

Abstract The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.

scholarly journals Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome

2020 ◽  
Vol 51 (5) ◽  
pp. 675-682
Author(s):  
D. A. Triant ◽  
J. J. Le Tourneau ◽  
C. M. Diesh ◽  
D. R. Unni ◽  
M. Shamimuzzaman ◽  
...  
Keyword(s):  
Reference Genome ◽  
Bovine Genome ◽  
Genome Database ◽  
Online Tools

scholarly journals High-throughput evaluation of synthetic metabolic pathways

TECHNOLOGY ◽  
2016 ◽  
Vol 04 (01) ◽  
pp. 9-14
Author(s):  
Justin R. Klesmith ◽  
Timothy A. Whitehead
Keyword(s):  
Metabolic Engineering ◽  
High Throughput ◽  
Metabolic Pathway ◽  
Metabolic Pathways ◽  
High Throughput Screening ◽  
Computational Analysis ◽  
Living Cells ◽  
Specific Productivity ◽  
Process Conditions ◽  
Review Current

A central challenge in the field of metabolic engineering is the efficient identification of a metabolic pathway genotype that maximizes specific productivity over a robust range of process conditions. Here we review current methods for optimizing specific productivity of metabolic pathways in living cells. New tools for library generation, computational analysis of pathway sequence-flux space, and high-throughput screening and selection techniques are discussed.

scholarly journals Scalable metagenomic taxonomy classification using a reference genome database

2013 ◽  
Vol 29 (18) ◽  
pp. 2253-2260 ◽  
Author(s):  
Sasha K. Ames ◽  
David A. Hysom ◽  
Shea N. Gardner ◽  
G. Scott Lloyd ◽  
Maya B. Gokhale ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genome Database ◽  
Reference Genome Database
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