By Alessio Mengoni, Marco Galardini, Marco Fondi
Bacterial genomics is a mature examine interdisciplinary box, that is approached by way of ecologists, geneticists, bacteriologists, molecular biologists and evolutionary biologists operating in scientific, business and easy technology. because of the massive diffusion of bacterial genome research, Bacterial Pangenomics: equipment and Protocols is ready to give you the latest methodologies in regards to the research of bacterial pangenomes by way of masking the 3 significant components: the experimental equipment for impending bacterial pangenomics, the bio informatic pipelines for research and annotation of series information and at last the equipment for inferring sensible and evolutionary beneficial properties from the pangenome. Written within the profitable Methods in Molecular Biology sequence layout, chapters contain introductions to their respective themes, lists of the mandatory fabrics and reagents, step by step, conveniently reproducible protocols and notes on troubleshooting and keeping off identified pitfalls.
Authoritative and simply available, Bacterial Pangenomics: tools and Protocols will function a box advisor for either certified bacterial genomics investigators who are looking to replace their technical wisdom, for much less skilled researchers who are looking to begin operating with bacterial genomics and pangenomics, in addition to serving as a guide and supplemental textbook for graduate scholars of genomics and bioinformatics.
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Extra resources for Bacterial Pangenomics: Methods and Protocols
Single or paired end reads). Also this sequencing pipeline can be useful for de novo and re-sequencing projects [7, 8]. In the study of Ancora et al. , this pipeline has been used for sequencing genomic DNA from Brucella ceti ST26 strain, isolated from Italian striped dolphins (Stenella coeruleoalba). The genome of Brucella is composed of two circular chromosomes without any plasmids. In this pipeline, as first step the genomic DNA is purified and quantified by Qubit® dsDNA HS Assay Kit (Invitrogen™, Life Technologies).
White arrow heads represent FRT recombination sites. Black arrows indicate the location of PCR primers. X indicates the site of homologous recombination. Km kanamycin, Gm gentamicin, Suc sucrose This unmarked mutagenesis technique is useful for the excision of target gene clusters that can exceed 100 kb. The procedure involves the integration (via homologous recombination) of plasmids on both flanks of the target gene cluster. The two plasmids contain different antibiotic resistance markers (Gm and Km).
Studies on evolution of antibiotic resistance in vivo) . Other approaches such as the targeted sequencing of the 16S rRNA gene is one of the genetic tools to produce diversity profiling in natural samples by using a shotgun NGS Pipelines 33 NGS approach. This targeted gene application finds a wide range of applications, including the characterization of bacterial populations belonging to human gut-, airflow-, skin-microbiota [1–4, 10], and to other biological systems like bioremediation environment of contaminated water .
Bacterial Pangenomics: Methods and Protocols by Alessio Mengoni, Marco Galardini, Marco Fondi