Search results for " Genome sequencing"
showing 10 items of 161 documents
Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems
2021
A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293T, CECT 9390T and CECT 9393T were isolated from sites in Barcelona, Spain, in the framework of a project aimed at generating the first MALDI-TOF database specific for bacteria present in water for human consumption. Their partial 16S rRNA sequences showed that their closest relatives among the type strains of Chryseobacterium exhibited 98 % similarity or less, supporting their taxonomic novelty. At the same time, comparison between them…
Simple Sequence Repeat Marker Development and Mapping Targeted to Previously Unmapped Regions of the Strawberry Genome Sequence
2011
The genome sequence of the woodland strawberry (Fragaria vesca L.) is an important resource providing a reference for comparative genomics studies and future sequenced rosaceous species and has great utility as a model for the development of markers for mapping in the cultivated strawberry Fragaria ×ananassa Duchesne ex Rozier. A set of 152 microsatellite simple sequence repeat (SSR) primer pairs was developed and mapped, along with 42 previously published but unmapped SSRs, permitting the precise assignment of 28.2 Mbp of previously unanchored genome sequence scaffolds (13% of the F. vesca genome sequence). The original ordering of F. vesca sequence scaffolds was performed without a physic…
Distance measures for biological sequences: Some recent approaches
2008
AbstractSequence comparison has become a very essential tool in modern molecular biology. In fact, in biomolecular sequences high similarity usually implies significant functional or structural similarity. Traditional approaches use techniques that are based on sequence alignment able to measure character level differences. However, the recent developments of whole genome sequencing technology give rise to need of similarity measures able to capture the rearrangements involving large segments contained in the sequences. This paper is devoted to illustrate different methods recently introduced for the alignment-free comparison of biological sequences. Goal of the paper is both to highlight t…
2019
We report a complete genome sequence of a Finnish isolate of the fish pathogen Flavobacterium columnare . Using PacBio RS II sequencing technology, the complete circular genome of F. columnare strain B185 with 3,261,404 bp was obtained.
A genomic epidemiology investigation of yaws re-emergence and bacterial drug resistance selection
2020
Abstract Background In a longitudinal study assessing the WHO strategy for yaws eradication using mass azithromycin treatment, we observed resurgence of yaws cases with dominance of a single JG8 sequence type and emergence of azithromycin-resistant Treponema pallidum. Here, we analyse genomic changes in the bacterial population using samples collected during the study. Methods We performed whole bacterial genome sequencing directly on DNA extracted from 37 lesion swabs collected from patients on Lihir Island, Papua New Guinea, between 2013 and 2016. We produced phylogenies and correlated these with temporo-spatial information to investigate the source of new cases and the emergence of five …
Complete Genome Sequence of the Enterobacter cancerogenus Bacteriophage Enc34
2012
ABSTRACT Enterobacter cancerogenus is widely distributed in nature and is generally recovered from environmental or vegetal sources. In some cases, it has also been associated with human infections. In this study, the complete genomic sequence of virulent E. cancerogenus bacteriophage Enc34 was determined. The Enc34 genome is 60,364 bp in length and contains 80 open reading frames. To our knowledge, this is the first report of a bacteriophage infecting E. cancerogenus .
Echinostomes: genomics and proteomics
2008
Echinostomes are excellent models to study host-parasite interactions in intestinal helminthiases. In this chapter, data available from genomic and proteomic studies are analyzed in detail to indicate advantages and pitfalls in the research using these organisms. The lack of a genome sequence project and the low number of sequences deposited in the databases not only affect the genomic studies but also debilitate proteomic findings since in most cases, although good spectrometric data can be obtained, the available database often fail to identify the protein from the peptides obtained.
The evolutionary history of HSA7/16 synteny in vertebrates: a critical interpretation of comparative cytogenetic and genome sequence data
2013
The current work is an in silico study of data from previous publications and genome browsers, on the origin of the human synteny HSA7a/16p. The molecular composition of the chromosomal segments identified as HSA7a/16 and 7b (free or differently associated) is not yet clear. This means that a syntenic association 7/16, which can be detected by an in situ hybridization (FISH) method in different taxa, may not necessarily correspond to those of the same association in different lineages. In silico research, together with comparative cytogenetics, have been applied in order to define the composition of the 7/16 syntenic association. These results allow a confident reconstruction of the synteni…
Lightweight LCP construction for next-generation sequencing datasets
2012
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection would facilitate the rapid computation of maximal exact matches, shortest unique substrings and shortest absent words. CPU-efficient algorithms for computing the LCP of a string have been described in the literature, but require the presence in RAM of large data structures. This prevents such methods from being feasible for NGS datasets. In this paper we propose the first lightweight method that simultaneously computes, via sequential scans, the LCP and B…
Draft Genome Sequence of Actibacterium mucosum KCTC 23349, a Marine Alphaproteobacterium with Complex Ionic Requirements Isolated from Mediterranean …
2014
ABSTRACT Strain R46 (CECT 7668; KCTC 23349), a nomenclatural type of Actibacterium mucosum , was isolated from surface seawater collected at Malvarrosa Beach (Valencia, Spain) in July 2008. The draft genome sequence of strain R46 (approximately 3.72 Mbp) contains 22 scaffolds and 3,619 protein-encoding genes, with a G+C content of 60.8 mol%.