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Pantoea spp.
Published in Yong-Guan Zhu, Huaming Guo, Prosun Bhattacharya, Jochen Bundschuh, Arslan Ahmad, Ravi Naidu, Environmental Arsenic in a Changing World, 2019
All of the orthologous pairs between Pantoea test genomes were identified by Pan Genome Analysis Pipeline(PGAP). The common dataset of shared genes among test strains was defined as their core genome. The total set of genes with test genomes was defined as the pan genome. The set of genes in each strain not shared with other strains was defined as the unique genes.
A pilot study of exome sequencing in a diverse New Zealand cohort with undiagnosed disorders and cancer
Published in Journal of the Royal Society of New Zealand, 2018
Colina McKeown, Samantha Connors, Rachel Stapleton, Tim Morgan, Ian Hayes, Katherine Neas, Joanne Dixon, Kate Gibson, David M. Markie, Peter Tsai, Cherie Blenkiron, Sandra Fitzgerald, Paula Shields, Patrick Yap, Ben Lawrence, Cristin Print, Stephen P. Robertson
It seems likely that precision oncology will require more than simple WES. For example, solid tumours are frequently heterogeneous, requiring DTS to identify sub-clonal mutations (Patel & Tsui 2015; Morris et al. 2016). Mutational signatures are also emerging as an important indicator of tumour biology and patient 13 may have benefited from additional whole genome sequencing to identify these signatures (Morris et al. 2016). Knowing whether the BRCA1- and EP300-mutant tumour of this patient had the pan-genome DNA repair defect associated with BRCA pathway failure would give more certainty to clinical decisions about the use of platinum drugs or poly ADP ribose polymerase (PARP) inhibitors (Alexandrov et al. 2013). Sequencing of circulating tumour DNA facilitates quantification of tumour heterogeneity and detection of mutations in small, surgically inaccessible or radiologically invisible tumours (Patel & Tsui 2015). Finally, RNA expression analysis could identify potential BRCA1 haploinsufficiency and the effects of extensive LoH on oncogenic pathways (Sedic et al. 2015; Durrbaum & Storchova 2016).
Taxonomic, metabolic traits and species description of aromatic compound degrading Indian soil bacterium Pseudomonas bharatica CSV86T
Published in Journal of Environmental Science and Health, Part A, 2023
Balaram Mohapatra, Prashant S. Phale
Pan-genomic analysis was performed to decipher the genomic diversity (distinct core and accessory gene complements) of CSV86T and its relative species members. The pan-genome analysis involving 35 Pseudomonas genomes (CSV86T and phylogenetic relatives) revealed a total of 23,548 pan genes, out of which 981 represented the core gene complements (18.9% of an average genome). The pan-genome size of Pseudomonas increased exponentially with the number of genomes added into the dataset, and the pan-genome curve displayed an asymptotic trend demonstrating that 35 genomes were near sufficient to describe the complete genetic catalogue of Pseudomonas (Figure 6a). The new genes added per each genome showed a moderately increasing trend, (average of 355 genes added until 35th genome added) suggested that further addition of Pseudomonas genomes would result moderate changes in the total gene inventory, indicating its open pan genomic structure.[37,38] COG functional annotation of core genes showed predominance of cellular growth-motility, metabolism of glycan, cofactors and vitamins, drug resistance, and transcription-translation processes (Figure 6b). While, the COG annotation of accessory genes showed prevalence (1.2–1.5 fold increase of gene allocation w.r.t core genes) of inorganic ion transport, secondary metabolism, energy conversion, lipid metabolism, signal transduction, and secretion-transport (Figure 6b). It has been reported that for organisms (ubiquitous taxa) residing in soil, freshwater, and other redox-active habitats, increased gene allocations toward such functions is indicative of continual genomic flux and wide niche adaptive potential.[39,40] Thus, it is evident that Pseudomonas members are in continual genomic flux and possess the ability to adapt wide environmental niches.[41] Interestingly, with respect to strain CSV86T, the unique genes (from the total accessory gene pool) were allocated to SEED sub-systems belonging to metabolism of aromatics, terpenoid, polyketide, lipids, secondary metabolites synthesis-metabolism, energy and signal transduction, membrane transport (particularly for Fe, Co, Zn, and multidrug efflux), unknown (hypothetical) and mobile functions (Figure 6b). These genes showed its highest identity (78-92% at nucleotide level) to gamma- and beta-proteobacteria members. These observations are in good agreement with the greater diversity of aromatic metabolic pathways (Figure 4, Table 4), abundance of horizontally transferred genes (12.89%, highest amongst its relatives, Table 1) and other eco-physiological traits in CSV86T, pertinent for its better niche colonization and adaptation in redox-active/dynamic environment.[9,28,31]