Abstract:
BACKGROUND:Gene identification and sequence determination are critical requirements for many biological, genomic, and bioinformatic studies. With the advent of next generation sequencing (NGS) technologies, such determinations are predominantly accomplished in silico for organisms for which the genome is known or for which there exists substantial gene sequence information. Without detailed genomic/gene information, in silico sequence determination is not straightforward, and full coding sequence determination typically involves time- and labor-intensive PCR-based amplification and cloning methods. RESULTS:An improved method was developed with which to determine full length gene coding sequences in silico using de novo assembly of RNA-Seq data. The scheme improves upon initial contigs through contig-to-gene identification by BLAST nearest-neighbor comparison, and through single-contig refinement by iterative-binning and -assembly of reads. Application of the iterative method produced the gene identification and full coding sequence for 9 of 12 genes and improved the sequence of 3 of the 12 genes targeted by benzimidazole, macrocyclic lactone, and nicotinic agonist classes of anthelminthic drugs in the swine nodular parasite Oesophagostomum dentatum. The approach improved upon the initial optimized assembly with Velvet that only identified full coding sequences for 2 genes. CONCLUSIONS:Our reiterative methodology represents a simplified pipeline with which to determine longer gene sequences in silico from next generation sequence data for any nematode for which detailed genetic/gene information is lacking. The method significantly improved upon an initial Velvet assembly of RNA-Seq data that yielded only 2 full length sequences. The identified coding sequences for the 11 target genes enables further future examinations including: (i) the use of recombinant target protein in functional assays seeking a better understanding of the mechanism of drug resistance, and (ii) seeking comparative genomic and transcriptomic assessments between parasite isolates that exhibit varied drug sensitivities.
journal_name
BMC Genetjournal_title
BMC geneticsauthors
Romine NM,Martin RJ,Beetham JKdoi
10.1186/1471-2156-14-55subject
Has Abstractpub_date
2013-06-18 00:00:00pages
55issn
1471-2156pii
1471-2156-14-55journal_volume
14pub_type
杂志文章相关文献
BMC GENETICS文献大全abstract:BACKGROUND:Pulmonary arterial hypertension (PAH) is a rare vascular disorder characterized by a capillary wedge pressure ≤ 15 mmHg and a mean pulmonary arterial pressure ≥ 25 mmHg at rest. PAH can be idiopathic, heritable or associated with other conditions. The aim of this study was to analyze the Endoglin (ENG) gene ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0384-3
更新日期:2016-06-04 00:00:00
abstract:BACKGROUND:Spotted wilt caused by tomato spotted wilt virus (TSWV) is one of the major peanut (Arachis hypogaea L.) diseases in the southeastern United States. Occurrence, severity, and symptoms of spotted wilt disease are highly variable from season to season, making it difficult to efficiently evaluate breeding popul...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0435-9
更新日期:2016-09-06 00:00:00
abstract:BACKGROUND:The Sapsaree is a breed of dog (Canis familiaris) native to Korea, which became perilously close to extinction in the mid-1980s. However, with systematic genetic conservation and restoration efforts, this breed was rescued from extinction and population sizes have been gradually increasing over the past few ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-019-0757-5
更新日期:2019-08-05 00:00:00
abstract:BACKGROUND:In humans, muscle-specific nicotinergic acetylcholine receptor (AChR) is a transmembrane protein with five different subunits, coded by CHRNA1, CHRNB, CHRND and CHRNG/CHRNE. The gamma subunit of AChR encoded by CHRNG is expressed during early foetal development, whereas in the adult, the γ subunit is replace...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0382-5
更新日期:2016-05-31 00:00:00
abstract:BACKGROUND:Non-invasive sampling has opened avenues for the genetic study of elusive species, which has contributed significantly to their conservation. Where field based identity of non-invasive sample is ambiguous (e.g. carnivore scats), it is essential to establish identity of the species through molecular approache...
journal_title:BMC genetics
pub_type: 杂志文章,评审
doi:10.1186/s12863-016-0344-y
更新日期:2016-02-09 00:00:00
abstract:BACKGROUND:Use of anti-hyperlipidemic medications compromises genetic analysis because of altered lipid profiles. We propose an empirical method to adjust lipid levels for medication effects so that the adjusted lipid values substitute the unmedicated lipid values in the genetic analysis. RESULTS:Published clinical tr...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-8-60
更新日期:2007-09-10 00:00:00
abstract:BACKGROUND:Several lines of evidence including allozyme analysis, restriction digest patterns and sequencing of mtDNA as well as mini- and micro-satellite allele frequencies indicate that Atlantic salmon (Salmo salar) from North America and Europe are genetically distinct. These observations are supported by karyotype ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-105
更新日期:2010-11-23 00:00:00
abstract:BACKGROUND:There is increasing evidence that the ability to adapt to seawater in teleost fish is modulated by genetic factors. Most studies have involved the comparison of species or strains and little is known about the genetic architecture of the trait. To address this question, we searched for QTL affecting osmoregu...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-12-46
更新日期:2011-05-14 00:00:00
abstract:BACKGROUND:Pest eradication using the Sterile Insect Technique (SIT) involves high-density releases of sterilized males that mate with wild females and ultimately suppress the population. Sterilized females are not required for SIT and their removal or separation from males prior to release remains challenging. In orde...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-00934-3
更新日期:2020-12-18 00:00:00
abstract:BACKGROUND:India is home to many ethnically and linguistically diverse populations. It is hypothesized that history of invasions by people from Persia and Central Asia, who are referred as Aryans in Hindu Holy Scriptures, had a defining role in shaping the Indian population canvas. A shift in spoken languages from Drav...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-86
更新日期:2014-07-22 00:00:00
abstract:BACKGROUND:The Gpnmb gene encodes a transmembrane protein whose function(s) remain largely unknown. Here, we assess if a mutant allele of Gpnmb confers susceptibility to glaucoma by altering immune functions. DBA/2J mice have a mutant Gpnmb gene and they develop a form of glaucoma preceded by a pigment dispersing iris ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-30
更新日期:2008-04-10 00:00:00
abstract:BACKGROUND:Arabian horses are commonly believed to be one of the oldest and the most popular horse breeds in the world, characterized by favourable stamina traits and exercise phenotypes. During intensive training, the rates of lactate production and utilization are critical to avoid muscle fatigue and a decrease in ex...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-019-0774-4
更新日期:2019-09-11 00:00:00
abstract:BACKGROUND:Monogenic diabetes is a genetic disease often caused by mutations in genes involved in beta-cell function. Correct sub-categorization of the disease is a prerequisite for appropriate treatment and genetic counseling. Target-region capture sequencing is a combination of genomic region enrichment and next gene...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-13
更新日期:2014-01-29 00:00:00
abstract:BACKGROUND:Peach [Prunus persica (L.) Batsch] is one of the most economically important fruit crops that, due to its genetic and biological characteristics (small genome size, taxonomic proximity to other important species and short juvenile period), has become a model plant in genomic studies of fruit trees. Our aim w...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-69
更新日期:2010-07-20 00:00:00
abstract:BACKGROUND:Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 3...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-7-10
更新日期:2006-02-16 00:00:00
abstract:BACKGROUND:The Glued gene of Drosophila melanogaster encodes the homologue of the vertebrate p150Glued subunit of dynactin. The Glued1 mutation compromises the dynein-dynactin retrograde motor complex and causes disruptions to the adult eye and the CNS, including sensory neurons and the formation of the giant fiber sys...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-10-77
更新日期:2009-11-30 00:00:00
abstract::Alcohol dependence is a serious public health problem. We studied data from families participating in the Collaborative Study on the Genetics of Alcoholism (COGA) and made available to participants in the Genetic Analysis Workshop 14 (GAW14) in order to search for genes predisposing to alcohol dependence. Using factor...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S15
更新日期:2005-12-30 00:00:00
abstract:BACKGROUND:Koala (Koa) is a dominant mutation in mice causing bushy muzzle and pinna, and is associated with a chromosomal inversion on the distal half of chromosome 15. To identify the gene responsible for the Koa phenotypes, we investigated phenotypes of Koa homozygous mice and determined the breakpoints of the inver...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-10-60
更新日期:2009-09-22 00:00:00
abstract:BACKGROUND:Congenital heart defects (CHD) is the most common cause of death from a congenital structure abnormality in newborns and is often associated with fetal loss. There are many types of CHD. Human genetic studies have identified genes that are responsible for the inheritance of a particular type of CHD and for s...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-14-44
更新日期:2013-05-24 00:00:00
abstract:BACKGROUND:The establishment of the bisexual fertile fish hybrid lineage including the allodiploid and allotetraploid hybrids, from interspecific hybridization of red crucian carp (Carassius auratus red var. 2n = 100, 2n = AA) (♀) × common carp (Cyprinus carpio L. 2n = 100, 2n = BB) (♂), provided a good platform to inv...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0295-8
更新日期:2015-12-03 00:00:00
abstract:BACKGROUND:Hip dysplasia remains one of the most serious hereditary diseases occurring in dogs despite long-standing evaluation schemes designed to aid selection for healthy joints. Many researchers have recommended the use of estimated breeding values (EBV) to improve the rate of genetic progress from selection agains...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-14-16
更新日期:2013-03-02 00:00:00
abstract:BACKGROUND:Numerous studies have attempted to relate genetic polymorphisms within the N-acetyltransferase 2 gene (NAT2) to interindividual differences in response to drugs or in disease susceptibility. However, genotyping of individuals single-nucleotide polymorphisms (SNPs) alone may not always provide enough informat...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-30
更新日期:2005-06-02 00:00:00
abstract:BACKGROUND:Marek's disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes t...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-00884-w
更新日期:2020-07-16 00:00:00
abstract:BACKGROUND:Cockerham genetic models are commonly used in quantitative trait loci (QTL) analysis with a special feature of partitioning genotypic variances into various genetic variance components, while the F(infinity) genetic models are widely used in genetic association studies. Over years, there have been some confu...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-10-52
更新日期:2009-09-04 00:00:00
abstract:BACKGROUND:Discerning the traits evolving under neutral conditions from those traits evolving rapidly because of various selection pressures is a great challenge. We propose a new method, composite selection signals (CSS), which unifies the multiple pieces of selection evidence from the rank distribution of its diverse...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-34
更新日期:2014-03-17 00:00:00
abstract:BACKGROUND:Genome-wide association studies (GWAS) are a widely used study design for detecting genetic causes of complex diseases. Current studies provide good coverage of common causal SNPs, but not rare ones. A popular method to detect rare causal variants is haplotype testing. A disadvantage of this approach is that...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-80
更新日期:2010-09-09 00:00:00
abstract:BACKGROUND:Structured association mapping is proving to be a powerful strategy to find genetic polymorphisms associated with disease. However, these algorithms are often distributed as command line implementations that require expertise and effort to customize and put into practice. Because of the difficulty required t...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-13-24
更新日期:2012-04-03 00:00:00
abstract:BACKGROUND:Genomic information can be used to predict not only continuous but also categorical (e.g. binomial) traits. Several traits of interest in human medicine and agriculture present a discrete distribution of phenotypes (e.g. disease status). Root vigor in sugar beet (B. vulgaris) is an example of binomial trait ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-87
更新日期:2014-07-22 00:00:00
abstract:BACKGROUND:Marbling score (MS) is the major quantitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the micromolar calcium-activated neutral protease gene (micro-calpain, CAPN1) and carcass traits in Korean cattle (also known as Hanwoo)...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-33
更新日期:2008-04-19 00:00:00
abstract::The purpose of these analyses was to determine if incorporating or adjusting for covariates in genetic analyses helped or hindered in genetic analyses, specifically heritability and linkage analyses. To study this question, two types of covariate models were used in the simulated Genetic Analysis Workshop 14 dataset i...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S49
更新日期:2005-12-30 00:00:00