Abstract:
BACKGROUND:Association mapping approaches are dependent upon discovery and validation of single nucleotide polymorphisms (SNPs). To further association studies in Anopheles gambiae we conducted a major resequencing programme, primarily targeting regions within or close to candidate genes for insecticide resistance. RESULTS:Using two pools of mosquito template DNA we sequenced over 300 kbp across 660 distinct amplicons of the An. gambiae genome. Comparison of SNPs identified from pooled templates with those from individual sequences revealed a very low false positive rate. False negative rates were much higher and mostly resulted from SNPs with a low minor allele frequency. Pooled-template sequencing also provided good estimates of SNP allele frequencies. Allele frequency estimation success, along with false positive and negative call rates, improved significantly when using a qualitative measure of SNP call quality. We identified a total of 7062 polymorphic features comprising 6995 SNPs and 67 indels, with, on average, a SNP every 34 bp; a high rate of polymorphism that is comparable to other studies of mosquitoes. SNPs were significantly more frequent in members of the cytochrome p450 mono-oxygenases and carboxy/cholinesterase gene-families than in glutathione-S-transferases, other detoxification genes, and control genomic regions. Polymorphic sites showed a significantly clustered distribution, but the degree of SNP clustering (independent of SNP frequency) did not vary among gene families, suggesting that clustering of polymorphisms is a general property of the An. gambiae genome. CONCLUSION:The high frequency and clustering of SNPs has important ramifications for the design of high-throughput genotyping assays based on allele specific primer extension or probe hybridisation. We illustrate these issues in the context of the design of Illumina GoldenGate assays.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Wilding CS,Weetman D,Steen K,Donnelly MJdoi
10.1186/1471-2164-10-320subject
Has Abstractpub_date
2009-07-16 00:00:00pages
320issn
1471-2164pii
1471-2164-10-320journal_volume
10pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression and defence against exogenous and endogenous genetic elements (viruses and transposable elements). The vast majority of endogenous small RNAs produced by the siRNA and piRNA pathways originate from repet...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1436-1
更新日期:2015-04-10 00:00:00
abstract:BACKGROUND:The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1867-8
更新日期:2015-09-02 00:00:00
abstract:BACKGROUND:One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the "normal" vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5284-7
更新日期:2018-12-31 00:00:00
abstract:BACKGROUND:The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis). While classical microbial taxonomy proposed these organisms as distinct species, newer molecular phylogenies and comparative genome sequencing s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-430
更新日期:2011-08-24 00:00:00
abstract:BACKGROUND:In natural environments, bacteria must frequently cope with extremely scarce nutrients. Most studies focus on bacterial growth in nutrient replete conditions, while less is known about the stationary phase. Here, we are interested in global gene expression throughout all growth phases, including the adjustme...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5749-3
更新日期:2019-05-09 00:00:00
abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-252
更新日期:2006-10-09 00:00:00
abstract:BACKGROUND:Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induce...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-630
更新日期:2010-11-12 00:00:00
abstract:BACKGROUND:G protein-coupled receptors (GPCRs) are major players in cell communication, regulate a whole range of physiological functions during development and throughout adult life, are affected in numerous pathological situations, and constitute so far the largest class of drugable targets for human diseases. The co...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-241
更新日期:2011-05-16 00:00:00
abstract:BACKGROUND:Pharmacological and gene ablation studies have demonstrated the crucial role of the endocrine function of the heart as mediated by the polypeptide hormones ANF and BNP in the maintenance of cardiovascular homeostasis. The importance of these studies lies on the fact that hypertension and chronic congestive h...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-254
更新日期:2009-06-01 00:00:00
abstract:BACKGROUND:The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genome-wide association (GWAS) studies along with gene expression studies in soybean [Glycine max (L.) Me...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5449-z
更新日期:2019-01-21 00:00:00
abstract:BACKGROUND:Transporter proteins are one of an organism's primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. The functional annotation of most transporters is currently limited to general...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S1-S8
更新日期:2011-06-15 00:00:00
abstract:BACKGROUND:Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S3-S14
更新日期:2011-11-30 00:00:00
abstract:BACKGROUND:The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese jujube (Ziziphus jujuba Mill.) is the largest type of dried fruit tree in China in terms of production,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5789-8
更新日期:2019-06-07 00:00:00
abstract:BACKGROUND:Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06784-8
更新日期:2020-06-03 00:00:00
abstract:BACKGROUND:Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, plays a crucial role in protec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4394-y
更新日期:2018-01-06 00:00:00
abstract:BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5827-6
更新日期:2019-05-30 00:00:00
abstract:BACKGROUND:Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-351
更新日期:2009-08-03 00:00:00
abstract:BACKGROUND:Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-732
更新日期:2013-10-25 00:00:00
abstract:BACKGROUND:Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangem...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S15
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:Scaleless (sc/sc) chickens carry a single recessive mutation that causes a lack of almost all body feathers, as well as foot scales and spurs, due to a failure of skin patterning during embryogenesis. This spontaneous mutant line, first described in the 1950s, has been used extensively to explore the tissue ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-257
更新日期:2012-06-19 00:00:00
abstract:BACKGROUND:Xanthomonas citri pv. citri (Xcc) is a citrus canker causing Gram-negative bacteria. Currently, little is known about the biological and molecular responses of Xcc to low temperatures. RESULTS:Results depicted that low temperature significantly reduced growth and increased biofilm formation and unsaturated ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6193-0
更新日期:2019-11-06 00:00:00
abstract:BACKGROUND:Lung aging is characterized by a number of structural alterations including fibrosis, chronic inflammation and the alteration of inflammatory cell composition. Chronic exposure to cigarette smoke (CS) is known to induce similar alterations and may contribute to premature lung aging. Additionally, aging and C...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6712-z
更新日期:2020-04-09 00:00:00
abstract:BACKGROUND:Genome research in farm animals will expand our basic knowledge of the genetic control of complex traits, and the results will be applied in the livestock industry to improve meat quality and productivity, as well as to reduce the incidence of disease. A combination of quantitative trait locus mapping and mi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-36
更新日期:2006-02-27 00:00:00
abstract:BACKGROUND:The recent advance of high-throughput sequencing makes it feasible to study entire transcriptomes through the application of de novo sequence assembly algorithms. While a popular strategy is to first construct an intermediate de Bruijn graph structure to represent the transcriptome, an additional step is nee...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S5-S6
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sorting and prioritization of the output data. Previously described methodologies have used functional pat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-58
更新日期:2004-08-20 00:00:00
abstract:BACKGROUND:Deep sequencing is a powerful tool for assessing viral genetic diversity. Such experiments harness the high coverage afforded by next generation sequencing protocols by treating sequencing reads as a population sample. Distinguishing true single nucleotide variants (SNVs) from sequencing errors remains chall...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-501
更新日期:2013-07-24 00:00:00
abstract:BACKGROUND:The question of whether synonymous codon choice is affected by cellular tRNA abundance has been positively answered in many organisms. In some recent works, concerning the human genome, this relation has been studied, but no conclusive answers have been found. In the human genome, the variation in base compo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-67
更新日期:2006-04-03 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:High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integrat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-514
更新日期:2013-07-29 00:00:00
abstract:BACKGROUND:Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents explora...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1968-4
更新日期:2015-10-21 00:00:00