Whole Genome Sequence Comparisons in Taxonomy

Taxogenomic and Comparative Genomic Analysis of the Genus Saccharomonospora Focused on the Identification of Biosynthetic Clusters PKS and NRPS

“…Spatial distribution of locally collinear blocks between two or more genomes (synteny) analysis can provide some clues about the evolutionary processes that lead to diversity, chromosomal dynamics, and rearrangement rates between species ( Bhutkar et al, 2006 ). An approach to gain insight into the evolutionary distance between two species is to inspect the synteny of the genome sequences ( Borriss et al, 2011 ). Here, we have applied the synteny study to elucidate suspicious clusters in the phylogenomic tree, particularly, the one formed by the two subspecies of S. iraqiensis and S. halophila 8 T , using the cluster including S. piscinae KCTC 19743 T , Saccharomonospora sp.…”

Whole-Genome Analyses

“…It also needs to be stressed that additional valuable taxonomic information can be gleaned from whole-genome sequences (even from partial ones with reasonable random coverage), including the G + C content of the DNA, and sequences of genetic markers. Moreover, other analyses can be used to define the core genome, singleton genes , genomic islands and the pan genome, thereby providing other estimates of genomic relatedness (Ben Zakour, Beatson, van den Broek, Thoday, & Fitzgerald, 2012;Borriss et al, 2011;Chan, Halachev, Loman, Constantinidou, & Pallen, 2012;Flowers et al, 2013;Frank, Klockow, Richter, Glöckner, & Harder, 2013;Romano et al, 2013;Scortichini, Marcelletti, Ferrante, & Firrao, 2013;Sentausa & Fournier, 2013;Tamura et al, 2012;Yi, Chun, & Cha, 2014;Zhang, Tian, Sui, Chen, & Chen, 2012). Finally, whole-genome sequences generated by taxonomists provide valuable data for biotechnology and bioprospecting, not least for data mining.…”

“…The advantages and details associated with each NGS system, including costs, components, error rates and applications, have been the subject of several excellent reviews (Liu et al, 2012;Loman et al, 2012;Quail et al, 2012). The impact of such developments on microbial genome assembly, annotation and analysis of data of taxonomic value has also been addressed (Borriss et al, 2011;Dark, 2013;Mavromatis et al, 2012). Benchtop instruments include 454 GS FLX Titanium/GS Junior (Roche), Genome Analyzer/HiSeq 2000/MiSeq (Illumina), SOLiD/Ion Torrent PGM (Life Technologies) and RS (Pacific Biosciences).…”

“…Moreover, the coverage per strain will of course be lower because the reads are shared, while the likely uneven distribution of reads may mean that not all samples reach the desired sequencing depth of coverage, thereby causing delays and additional costs. To avoid this, it is recommended to aim for a 25-fold coverage as this is usually enough to assemble correctly 95-99% of a good-quality sequence (Borriss et al, 2011); for most prokaryotes (genome sizes 2-8 Mb) this means 50-200 Mb length. The current tendency for prokaryotic genomic sequencing and assembly is to use a long-read, high-error platform (such as Pacific Biosciences and Oxford Nanopore Technologies) to get the scaffold of the sequence and then a short-read, low-error platform (such as Illumina or SOLiD) which can provide an extraordinarily high coverage of reads that are mapped onto the scaffold to provide a highly reliable genomic sequence.…”

Taxonomic Identification of Different Species of the Genus Aeromonas by Whole-Genome Sequencing and Use of Their Species-Specific β-Lactamases as Phylogenetic Markers

“…The phylogenetic study that led to the creation of this taxon was based on the genes gyr B and rpo D, which were later complemented by rec A , dna J and gyr A in a MLPA [ 18 ]. The latest method used to identify different Aeromonas strains in clinical settings is whole-genome sequencing (WGS), which has emerged as a promising and highly discriminative tool, not only for epidemiology, but also in taxonomy [ 21 ].…”