New Approaches to Prokaryotic Systematics: Volume 41

ISBN-13: 9780128001769 / Angielski / Twarda / 2014 / 348 str.

Michael Goodfellow; Iain Sutcliffe; Jongsik Chun

Opis

Volume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic systematics. This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries.

• Detailed protocols on cutting edge methods
• Prepared by leading international experts in the relevant fields

Spis treści

1. The Need for Change: Embracing the Genome
William B. Whitman
2. An Introduction to Phylogenetics and The Tree of Life1
Tom A. Williams and Sarah E. Heap
3. The All-Species Living Tree Project
Pablo Yarza and Raul Munoz
4. 16S rRNA Gene-based Identification of Bacteria and Archaea using the EzTaxon Server
Mincheol Kim and Jongsik Chun
5. Revolutionising Prokaryotic Systematics Through Next-Generation Sequencing
Vartul Sangal, Leena Nieminen, Nicholas P. Tucker and Paul A. Hoskisson
6. Whole Genome Analyses: Average Nucleotide Identity
David R. Arahal
7. Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways
Simon R. Harris and Chinyere K. Okoro
8. Identification of Conserved Indels that are useful for Classification and Evolutionary Studies
Radhey S. Gupta
9. Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees
Olga K.Kamneva and Naomi L. Ward
10. Multi-locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation
Alison J. Cody, Julia S. Bennett and Martin C.J. Maiden
11. Multilocus Sequence Analysis: Bringing Bacterial Systematics to the Next Level
Xiaoying Rong and Ying Huang
12. Bacterial Typing and Identification by Genomic Analysis of 16s-23s rRNA Intergenic Spacer (ITS) Sequences
Volker Gürtler, Gangavarapu Subrahmanyam, Malathi Shakar, Biswajit Maiti and Indrani Karunasagar
13. MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria
Peter Schumann and Thomas Maier
14. Continuing Importance of the "Phenotype” in the Genomic Era
Peter Kämpfer