Abstract:
BACKGROUND:Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in its genome promote rearrangements that impact its phenotype. One of the main virulence factors of this bacterium, its type three secretion system (TTSS), is affected by these rearrangements. In Aeromonas salmonicida subsp. salmonicida most of the TTSS genes are encoded in a single locus on a large plasmid called pAsa5, and may be lost when the bacterium is cultivated at a higher temperature (25 °C), producing non-virulent mutants. In a previous study, pAsa5-rearranged strains that lacked the TTSS locus on pAsa5 were produced using parental strains, including 01-B526. Some of the generated deletions were explained by homologous recombination between ISs found on pAsa5, whereas the others remained unresolved. To investigate those rearrangements, short- and long-read high-throughput sequencing technologies were used on the A. salmonicida subsp. salmonicida 01-B526 whole genome. RESULTS:Whole genome sequencing of the 01-B526 strain revealed that its pAsa5 has an additional IS copy, an ISAS5, compared to the reference strain (A449) sequence, which allowed for a previously unknown rearrangement to occur. It also appeared that 01-B526 bears a second large plasmid, named pAsa9, which shares 40 kbp of highly similar sequences with pAsa5. Following these discoveries, previously unexplained deletions were elucidated by genotyping. Furthermore, in one of the derived strains a fusion of pAsa5 and pAsa9, involving the newly discovered ISAS5 copy, was observed. CONCLUSION:The loss of TTSS and hence virulence is explained by one consistent mechanism: IS-driven homologous recombination. The similarities between pAsa9 and pAsa5 also provide another example of genetic diversity driven by ISs.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Tanaka KH,Vincent AT,Emond-Rheault JG,Adamczuk M,Frenette M,Charette SJdoi
10.1186/s12864-017-3921-1subject
Has Abstractpub_date
2017-07-12 00:00:00pages
528issue
1issn
1471-2164pii
10.1186/s12864-017-3921-1journal_volume
18pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Malaria caused by Plasmodium vivax is an experimentally neglected severe disease with a substantial burden on human health. Because of technical limitations, little is known about the biology of this important human pathogen. Whole genome analysis methods on patient-derived material are thus likely to have a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-262
更新日期:2012-06-21 00:00:00
abstract:BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2474-z
更新日期:2016-02-29 00:00:00
abstract:BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-271
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:The mitochondrial genomes of higher plants vary remarkably in size, structure and sequence content, as demonstrated by the accumulation and activity of repetitive DNA sequences. Incompatibility between mitochondrial genome and nuclear genome leads to non-functional male reproductive organs and results in cyt...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5122-y
更新日期:2018-10-26 00:00:00
abstract:BACKGROUND:Glutamine is a major amino donor for the synthesis of amino acids, nucleotides, and other nitrogen-containing compounds in all organisms. In addition to its role in nutrition and metabolism, glutamine can also function as a signaling molecule in bacteria, yeast, and humans. By contrast, the functions of glut...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1892-7
更新日期:2015-09-25 00:00:00
abstract:BACKGROUND:Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the mainte...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-740
更新日期:2013-10-29 00:00:00
abstract:UNLABELLED:Transcription-induced chimerism, a mechanism involving the transcription and intergenic splicing of two consecutive genes, has recently been estimated to account for approximately 5% of the human transcriptome. Despite this prevalence, the regulation and function of these fused transcripts remains largely un...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-348
更新日期:2007-10-01 00:00:00
abstract:BACKGROUND:Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of word embedding. RESULTS:From a pure data-driven fashion, we trained a 200-dimension vector represe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5370-x
更新日期:2019-02-04 00:00:00
abstract:BACKGROUND:The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-544
更新日期:2012-10-10 00:00:00
abstract:BACKGROUND:Osteoporosis is a common and debilitating bone disease that is characterised by a low bone mineral density (BMD), a highly heritable trait. Genome-wide association studies (GWAS) have proven to be very successful in identifying common genetic variants associated with BMD adjusted for age, gender and weight, ...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/s12864-016-2481-0
更新日期:2016-02-25 00:00:00
abstract:BACKGROUND:Human T cell leukemia virus type 1 (HTLV-1) Tax is a potent activator of viral and cellular gene expression that interacts with a number of cellular proteins. Many reports show that Tax is capable of regulating cell cycle progression and apoptosis both positively and negatively. However, it still remains to ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-275
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3990-1
更新日期:2017-08-16 00:00:00
abstract:BACKGROUND:Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in man...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-188
更新日期:2012-05-15 00:00:00
abstract:BACKGROUND:Understanding the processes that drive the evolution of snake venom is a topic of great research interest in molecular and evolutionary toxinology. Recent studies suggest that ontogenetic changes in venom composition are genetically controlled rather than environmentally induced. However, the molecular mecha...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-234
更新日期:2013-04-10 00:00:00
abstract:BACKGROUND:Large-scale comparison of metazoan genomes has revealed that a significant fraction of genes of the last common ancestor of Bilateria (Urbilateria) is lost in each animal lineage. This event could be one of the underlying mechanisms involved in generating metazoan diversity. However, the present functions of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-17
更新日期:2009-01-12 00:00:00
abstract:BACKGROUND:By assaying hundreds of thousands of single nucleotide polymorphisms, genome wide association studies (GWAS) allow for a powerful, unbiased review of the entire genome to localize common genetic variants that influence health and disease. Although it is widely recognized that some correction for multiple tes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-516
更新日期:2008-10-31 00:00:00
abstract:BACKGROUND:Understanding the genome sequence-specific positioning of nucleosomes is essential to understand various cellular processes, such as transcriptional regulation and replication. As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still uncl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-309
更新日期:2010-05-17 00:00:00
abstract:BACKGROUND:The obligate intracellular parasite Toxoplasma gondii establishes a life-long chronic infection within any warm-blooded host. After ingestion of an encysted parasite, T. gondii disseminates throughout the body as a rapidly replicating form during acute infection. Over time and after stimulation of the host i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-806
更新日期:2014-09-20 00:00:00
abstract:BACKGROUND:The ability to identify regions of the genome inherited with a dominant trait in one or more families has become increasingly valuable with the wide availability of high throughput sequencing technology. While a number of methods exist for mapping of homozygous variants segregating with recessive traits in c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1360-4
更新日期:2015-03-10 00:00:00
abstract:BACKGROUND:The MHC and KIR loci are clinically relevant regions of the genome. Typing the sequence of these loci has a wide range of applications including organ transplantation, drug discovery, pharmacogenomics and furthering fundamental research in immune genetics. Rapid advances in biochemical and next-generation se...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1949-7
更新日期:2015-11-05 00:00:00
abstract:BACKGROUND:The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-178
更新日期:2013-03-15 00:00:00
abstract:BACKGROUND:Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strateg...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-459
更新日期:2014-06-10 00:00:00
abstract:BACKGROUND:Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina Methylation...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07168-8
更新日期:2020-10-27 00:00:00
abstract::The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the billions of base-pairs of Archosaur sequence that have become available in the last few years. This editorial de...
journal_title:BMC genomics
pub_type:
doi:10.1186/1471-2164-10-S2-I1
更新日期:2009-07-14 00:00:00
abstract:BACKGROUND:Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function. However, protein-coding genes comprise < 2% of the se...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6497-0
更新日期:2020-01-31 00:00:00
abstract:BACKGROUND:The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri ('Dangshansuli', an Asian pear) and Pyrus communis ('Bartlett', a European pear) genomes, but the patterns of ge...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07226-1
更新日期:2020-11-19 00:00:00
abstract:BACKGROUND:Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5467-x
更新日期:2019-04-04 00:00:00
abstract:BACKGROUND:Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07340-0
更新日期:2021-01-09 00:00:00
abstract:BACKGROUND:Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5863-2
更新日期:2019-07-16 00:00:00
abstract:BACKGROUND:Celiac disease (CD) is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the presence of specific T-cell epitopes (9-mer peptides; CD epitopes) that mediate the stimulation of HL...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-277
更新日期:2012-06-22 00:00:00