scholarly journals Dcode.org anthology of comparative genomic tools

2005 ◽  
Vol 33 (Web Server) ◽  
pp. W56-W64 ◽  
Author(s):  
G. G. Loots ◽  
I. Ovcharenko
Keyword(s):  
Comparative Genomic ◽  
Genomic Tools

scholarly journals Recent Advances in Medicago truncatula Genomics

2008 ◽  
Vol 2008 ◽  
pp. 1-11 ◽  
Author(s):  
Jean-Michel Ané ◽  
Hongyan Zhu ◽  
Julia Frugoli
Keyword(s):  
Medicago Truncatula ◽  
Human Population ◽  
Lotus Japonicus ◽  
Model Systems ◽  
Biological Information ◽  
Comparative Genomic ◽  
Legume Nodulation ◽  
Symbiotic Interactions ◽  
Genomic Tools ◽  
Consistent Increase

Legume rotation has allowed a consistent increase in crop yield and consequently in human population since the antiquity. Legumes will also be instrumental in our ability to maintain the sustainability of our agriculture while facing the challenges of increasing food and biofuel demand. Medicago truncatula and Lotus japonicus have emerged during the last decade as two major model systems for legume biology. Initially developed to dissect plant-microbe symbiotic interactions and especially legume nodulation, these two models are now widely used in a variety of biological fields from plant physiology and development to population genetics and structural genomics. This review highlights the genetic and genomic tools available to the M. truncatula community. Comparative genomic approaches to transfer biological information between model systems and legume crops are also discussed.

scholarly journals panModule: detecting conserved modules in the variable regions of a pangenome graph

2021 ◽  
Author(s):  
Adelme Bazin ◽  
Claudine Medigue ◽  
David Vallenet ◽  
Alexandra Calteau
Keyword(s):  
Original Method ◽  
Comparative Genomic ◽  
Phylogenetic Groups ◽  
Variable Regions ◽  
Microbial Genomes ◽  
As Species ◽  
Genomic Tools ◽  
Strain Adaptation ◽  
Synteny Blocks ◽  
Genomic Regions

The recent years have seen the rise of pangenomes as comparative genomic tools to better understand the evolution of gene content among microbial genomes in close phylogenetic groups such as species. While the core or persistent genome is often well-known as it includes essential or ubiquitous genes, the variable genome is usually less characterized and includes many genes with unknown functions even among the most studied organisms. It gathers important genes for strain adaptation that are acquired by horizontal gene transfer. Here, we introduce panModule, an original method to identify conserved modules in pangenome graphs built from thousands of microbial genomes. These modules correspond to synteny blocks composed of consecutive genes that are conserved in a subset of the compared strains. Identifying conserved modules can provide insights on genes involved in the same functional processes, and as such is a very helpful tool to facilitate the understanding of genomic regions with complex evolutionary histories. The panModule method was benchmarked on a curated dataset of conserved modules in Escherichia coli genomes. Its use was illustrated through a study of a high pathogenicity island in Klebsiella pneumoniae that allowed a better understanding of this region. panModule is freely available and accessible through the PPanGGOLiN software suite (https://github.com/labgem/PPanGGOLiN).

scholarly journals Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production

2021 ◽  
Vol 9 (5) ◽  
pp. 1042
Author(s):  
Dingrong Kang ◽  
Saeed Shoaie ◽  
Samuel Jacquiod ◽  
Søren J. Sørensen ◽  
Rodrigo Ledesma-Amaro
Keyword(s):  
Secondary Metabolite ◽  
Genome Mining ◽  
Tca Cycle ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Bioactive Natural Products ◽  
A Genome ◽  
Genomic Tools ◽  
Keratinous Materials

A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.

566: Comparative Genomic Hybridization of Chemotherapy Survived Wilms' Tumor Cells

2004 ◽  
Vol 171 (4S) ◽  
pp. 150-151
Author(s):  
Thorsten Schlomm ◽  
Bastian Gunawan ◽  
Hans J. Schulten ◽  
Norbert Graf ◽  
Ivo Leuschner ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Comparative Genomic Hybridization ◽  
Wilms Tumor ◽  
Comparative Genomic ◽  
Genomic Hybridization
Sign in / Sign up

Export Citation Format

Share Document