Abstract:
BACKGROUND:BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. RESULTS:This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. CONCLUSIONS:Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Feltus FA,Saski CA,Mockaitis K,Haiminen N,Parida L,Smith Z,Ford J,Staton ME,Ficklin SP,Blackmon BP,Cheng CH,Schnell RJ,Kuhn DN,Motamayor JCdoi
10.1186/1471-2164-12-379subject
Has Abstractpub_date
2011-07-27 00:00:00pages
379issn
1471-2164pii
1471-2164-12-379journal_volume
12pub_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:Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not been identified. A transcriptomic approach was used to search for such genes in the intestine of eur...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1134
更新日期:2014-12-18 00:00:00
abstract:BACKGROUND:Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid) and this bipartite genome structure is characteristic for most R. solanacearum strains. To determine whether the megaplasmid was acquired...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-4-10
更新日期:2003-03-17 00:00:00
abstract:BACKGROUND:The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constrain...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-202
更新日期:2010-03-26 00:00:00
abstract:BACKGROUND:An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-254
更新日期:2012-06-19 00:00:00
abstract:BACKGROUND:The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to defi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5099-6
更新日期:2018-10-03 00:00:00
abstract:BACKGROUND:Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. I...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1272-3
更新日期:2015-02-25 00:00:00
abstract:BACKGROUND:Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallani...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4237-x
更新日期:2017-11-02 00:00:00
abstract:BACKGROUND:Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental prog...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1491-7
更新日期:2015-04-13 00:00:00
abstract:BACKGROUND:Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insigh...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3885-1
更新日期:2017-06-28 00:00:00
abstract:BACKGROUND:Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and perfo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3215-z
更新日期:2016-11-04 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:Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-chara...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2960-3
更新日期:2016-08-11 00:00:00
abstract:BACKGROUND:Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1636-8
更新日期:2015-07-17 00:00:00
abstract:BACKGROUND:Extra-cellular components, such as serum and exosome, have drawn great attention as a readily accessible source of biomarkers for mammalian health. However, the contribution of different blood components to the signature of respective microRNAs (miRNAs) remains unknown, especially in cattle. In this study we...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2962-1
更新日期:2016-08-12 00:00:00
abstract:BACKGROUND:Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in rec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-201
更新日期:2012-05-23 00:00:00
abstract:BACKGROUND:Uranium (U) is a naturally occurring radionuclide that has been found in the aquatic environment due to anthropogenic activities. Exposure to U may pose risk to aquatic organisms due to its radiological and chemical toxicity. The present study aimed to characterize the chemical toxicity of U in Atlantic salm...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-694
更新日期:2014-08-20 00:00:00
abstract:BACKGROUND:Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21) is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB) disease in many cereals. Understanding the interaction between mycoviruses and plant pathogenic fungi is necessa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-173
更新日期:2012-05-06 00:00:00
abstract:BACKGROUND:Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2884-y
更新日期:2016-08-09 00:00:00
abstract:BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4656-3
更新日期:2018-04-16 00:00:00
abstract:BACKGROUND:Gaucher disease is caused by defective glucocerebrosidase activity and the consequent accumulation of glucosylceramide. The pathogenic pathways resulting from lipid laden macrophages (Gaucher cells) in visceral organs and their abnormal functions are obscure. RESULTS:To elucidate this pathogenic pathway, de...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-20
更新日期:2011-01-11 00:00:00
abstract:BACKGROUND:The hepatitis E virus (HEV) is the causative pathogen of hepatitis E, a global public health concern. HEV comprises 8 genotypes with a wide host range and geographic distribution. This study aims to determine the genetic factors influencing the molecular adaptive changes of HEV open reading frames (ORFs) and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6100-8
更新日期:2019-10-29 00:00:00
abstract:BACKGROUND:Domestic broiler chickens rapidly accumulate adipose tissue due to intensive genetic selection for rapid growth and are naturally hyperglycemic and insulin resistant, making them an attractive addition to the suite of rodent models used for studies of obesity and type 2 diabetes in humans. Furthermore, chick...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-441
更新日期:2012-08-31 00:00:00
abstract:BACKGROUND:A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-203
更新日期:2012-05-25 00:00:00
abstract:BACKGROUND:A-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5364-8
更新日期:2018-12-27 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. ME...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3114-3
更新日期:2016-10-04 00:00:00
abstract:BACKGROUND:Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4861-0
更新日期:2018-06-20 00:00:00
abstract:BACKGROUND:Although an adverse early-life environment has been linked to an increased risk of developing the metabolic syndrome, the molecular mechanisms underlying altered disease susceptibility as well as their relevance to humans are largely unknown. Importantly, emerging evidence suggests that these effects operate...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-509
更新日期:2011-10-16 00:00:00
abstract:BACKGROUND:Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3699-1
更新日期:2017-05-02 00:00:00
abstract:BACKGROUND:Armigeres subalbatus is a natural vector of the filarial worm Brugia pahangi, but it rapidly and proficiently kills Brugia malayi microfilariae by melanotic encapsulation. Because B. malayi and B. pahangi are morphologically and biologically similar, the Armigeres-Brugia system serves as a valuable model for...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-463
更新日期:2007-12-18 00:00:00