Abstract:
BACKGROUND:Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis-associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major new subtype in the United States. In this study, we sequenced the genomes of two field specimens from each of the two subtypes and conducted a comparative genomic analysis of the obtained sequences with those from the only fully sequenced Cryptosporidium parvum genome. RESULTS:Altogether, 8.59-9.05 Mb of Cryptosporidium sequences in 45-767 assembled contigs were obtained from the four specimens, representing 94.36-99.47% coverage of the expected genome. These genomes had complete synteny in gene organization and 96.86-97.0% and 99.72-99.83% nucleotide sequence similarities to the published genomes of C. parvum and C. hominis, respectively. Several major insertions and deletions were seen between C. hominis and C. parvum genomes, involving mostly members of multicopy gene families near telomeres. The four C. hominis genomes were highly similar to each other and divergent from the reference IaA25R3 genome in some highly polymorphic regions. Major sequence differences among the four specimens sequenced in this study were in the 5' and 3' ends of chromosome 6 and the gp60 region, largely the result of genetic recombination. CONCLUSIONS:The sequence similarity among specimens of the two dominant outbreak subtypes and genetic recombination in chromosome 6, especially around the putative virulence determinant gp60 region, suggest that genetic recombination plays a potential role in the emergence of hyper-transmissible C. hominis subtypes. The high sequence conservation between C. parvum and C. hominis genomes and significant differences in copy numbers of MEDLE family secreted proteins and insulinase-like proteases indicate that telomeric gene duplications could potentially contribute to host expansion in C. parvum.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Guo Y,Tang K,Rowe LA,Li N,Roellig DM,Knipe K,Frace M,Yang C,Feng Y,Xiao Ldoi
10.1186/s12864-015-1517-1subject
Has Abstractpub_date
2015-04-18 00:00:00pages
320issn
1471-2164pii
10.1186/s12864-015-1517-1journal_volume
16pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Many bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. Mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. Such a pattern could also arise from selection coupled ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-369
更新日期:2007-10-12 00:00:00
abstract:BACKGROUND:The orange pigmentation of the agar cultures of many Fusarium species is due to the production of carotenoids, terpenoid pigments whose synthesis is stimulated by light. The genes of the carotenoid pathway and their regulation have been investigated in detail in Fusarium fujikuroi. In this and other Fusarium...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5430-x
更新日期:2019-01-21 00:00:00
abstract:BACKGROUND:Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-637
更新日期:2008-12-31 00:00:00
abstract:BACKGROUND:The Brassicaceae family is an exemplary model for studying plant polyploidy. The Brassicaceae knowledge-base includes the well-annotated Arabidopsis thaliana reference sequence; well-established evidence for three rounds of whole genome duplication (WGD); and the conservation of genomic structure, with 24 co...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-606
更新日期:2014-07-18 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:Streptococcus infantarius subsp. infantarius (Sii) belongs to the Streptococcus bovis/Streptococcus equinus complex associated with several human and animal infections. Sii is a predominant bacterium in spontaneously fermented milk products in Africa. The genome sequence of Sii strain CJ18 was compared with ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-200
更新日期:2013-03-22 00:00:00
abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular sys...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3907-z
更新日期:2017-07-19 00:00:00
abstract:BACKGROUND:Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes. RESULTS:We have analyzed aspects of the information content of Homo sapiens, Mus musculus, Drosophila melanogast...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-509
更新日期:2008-10-30 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:BACKGROUND:Pre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops. RESULTS:We identified orthologous...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3880-6
更新日期:2017-06-29 00:00:00
abstract:BACKGROUND:Identification of acute or recent hepatitis C virus (HCV) infections is important for detecting outbreaks and devising timely public health interventions for interruption of transmission. Epidemiological investigations and chemistry-based laboratory tests are 2 main approaches that are available for identifi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4269-2
更新日期:2017-12-06 00:00:00
abstract:BACKGROUND:As is true for many other antibiotic-resistant Gram-negative pathogens, members of the Burkholderia cepacia complex (BCC) are currently being assessed for their susceptibility to phage therapy as an antimicrobial treatment. The objective of this study was to perform genomic and limited functional characteriz...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-574
更新日期:2013-08-27 00:00:00
abstract:UNLABELLED:AB BACKGROUND: MicroRNAs (miRNAs) are small, non-coding 21-25 nt RNA molecules that play an important role in regulating gene expression. Little is known about the expression profiles and functions of miRNAs in skin and their role in pigmentation. Alpacas have more than 22 natural coat colors, more than any ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-555
更新日期:2012-10-16 00:00:00
abstract:BACKGROUND:Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error. It has a negative impact on performance of downstream analysis. Technically, most existing approaches suffer from this prevalent problem. Imputation is one of the frequently used metho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S9-S1
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-475
更新日期:2012-09-13 00:00:00
abstract:BACKGROUND:The freshwater snail Lymnaea stagnalis (L. stagnalis) has served as a successful model for studies in the field of Neuroscience. However, a serious drawback in the molecular analysis of the nervous system of L. stagnalis has been the lack of large-scale genomic or neuronal transcriptome information, thereby ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-451
更新日期:2009-09-23 00:00:00
abstract:BACKGROUND:The beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease), the role of multisite sequence va...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-252
更新日期:2010-04-19 00:00:00
abstract:BACKGROUND:Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserv...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-463
更新日期:2008-10-08 00:00:00
abstract:BACKGROUND:Genomic inversion is one type of structural variations (SVs) and is known to play an important biological role. An established problem in sequence data analysis is calling inversions from high-throughput sequence data. It is more difficult to detect inversions because they are surrounded by duplication or ot...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6585-1
更新日期:2020-03-05 00:00:00
abstract:BACKGROUND:The astounding regenerative abilities of planarian flatworms prompt steadily growing interest in examining their molecular foundation. Planarian regeneration was found to require hundreds of genes and is hence a complex process. Thus, RNA interference followed by transcriptome-wide gene expression analysis b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6292-y
更新日期:2019-11-29 00:00:00
abstract:BACKGROUND:In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4697-7
更新日期:2018-05-02 00:00:00
abstract:BACKGROUND:Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS:Existing algorithms are largely optimized for speed and coverage; in con...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-461
更新日期:2010-08-05 00:00:00
abstract:BACKGROUND:Though glioblastoma multiforme (GBM) is the most frequently occurring brain malignancy in adults, clinical treatment still faces challenges due to poor prognoses and tumor relapses. Recently, microRNAs (miRNAs) have been extensively used with the aim of developing accurate molecular therapies, because of the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3321-y
更新日期:2016-12-22 00:00:00
abstract:BACKGROUND:Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immun...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5362-x
更新日期:2019-01-05 00:00:00
abstract:BACKGROUND:Gene duplication underlies a significant proportion of gene functional diversity and genome complexity in both eukaryotes and prokaryotes. Although several reports in the literature described the duplication of specific genes in E. coli, a detailed analysis of the extent of gene duplications in this microorg...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5683-4
更新日期:2019-04-24 00:00:00
abstract:BACKGROUND:Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4768-9
更新日期:2018-05-18 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3238-5
更新日期:2016-11-08 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:Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1557-6
更新日期:2015-05-28 00:00:00
abstract:BACKGROUND:Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predicting ability also for germplasm/reference populations other than those for which it was defined. Pre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2212-y
更新日期:2015-12-01 00:00:00