Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes.


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.


BMC Genomics


BMC genomics


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 JC




Has Abstract


2011-07-27 00:00:00










  • Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development.

    abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit crops, including those...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kang C,Liu Z

    更新日期:2015-10-19 00:00:00

  • Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds.

    abstract:BACKGROUND:A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic regions defined by genes gro...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Fang L,Sahana G,Ma P,Su G,Yu Y,Zhang S,Lund MS,Sørensen P

    更新日期:2017-08-10 00:00:00

  • Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence for gene duplications and extensive gene clustering.

    abstract:BACKGROUND:Phanerochaete chrysosporium, the model white rot basidiomycetous fungus, has the extraordinary ability to mineralize (to CO2) lignin and detoxify a variety of chemical pollutants. Its cytochrome P450 monooxygenases have recently been implied in several of these biotransformations. Our initial P450 cloning ef...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Doddapaneni H,Chakraborty R,Yadav JS

    更新日期:2005-06-14 00:00:00

  • Comparative genomics and concerted evolution of beta-tubulin paralogs in Leishmania spp.

    abstract:BACKGROUND:Tubulin isotypes and expression patterns are highly regulated in diverse organisms. The genome sequence of the protozoan parasite Leishmania major contains three distinct beta-tubulin loci. To investigate the diversity of beta-tubulin genes, we have compared the published genome sequence to draft genome sequ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jackson AP,Vaughan S,Gull K

    更新日期:2006-06-06 00:00:00

  • Correction to: De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia.

    abstract::Following the publication of this article [1], the authors reported that the original shading in columns 3 and 4 of Table 3, which indicated the presence or absence of viruses in each library, had been removed during typesetting. ...

    journal_title:BMC genomics

    pub_type: 杂志文章,已发布勘误


    authors: Belda E,Nanfack-Minkeu F,Eiglmeier K,Carissimo G,Holm I,Diallo M,Diallo D,Vantaux A,Kim S,Sharakhov IV,Vernick KD

    更新日期:2019-09-05 00:00:00

  • Network analysis uncovers putative genes affecting resistance to tick infestation in Braford cattle skin.

    abstract:BACKGROUND:Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated the genetic mechanisms underlying the variation of Braford resistance to tick infestation. Skin bio...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Moré DD,Cardoso FF,Mudadu MA,Malagó-Jr W,Gulias-Gomes CC,Sollero BP,Ibelli AMG,Coutinho LL,Regitano LCA

    更新日期:2019-12-19 00:00:00

  • Identification of microRNA-mRNA modules using microarray data.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA expression and are involved in numerous cellular processes. Consequently, miRNAs are an important component of gene regulatory networks and an improved understanding of miRNAs will further our knowledge of these networks. There is a many-to-many ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jayaswal V,Lutherborrow M,Ma DD,Yang YH

    更新日期:2011-03-06 00:00:00

  • Regulatory network changes between cell lines and their tissues of origin.

    abstract:BACKGROUND:Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lopes-Ramos CM,Paulson JN,Chen CY,Kuijjer ML,Fagny M,Platig J,Sonawane AR,DeMeo DL,Quackenbush J,Glass K

    更新日期:2017-09-12 00:00:00

  • Gene expression profiling in peanut using high density oligonucleotide microarrays.

    abstract:BACKGROUND:Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently has a significant number of ESTs been released into the public domain. Utilization of these ESTs for oligonucleotide microarrays provides a means to investigate large-scale transcript res...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Payton P,Kottapalli KR,Rowland D,Faircloth W,Guo B,Burow M,Puppala N,Gallo M

    更新日期:2009-06-12 00:00:00

  • The arrhythmogenic cardiomyopathy-specific coding and non-coding transcriptome in human cardiac stromal cells.

    abstract:BACKGROUND:Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recent...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rainer J,Meraviglia V,Blankenburg H,Piubelli C,Pramstaller PP,Paolin A,Cogliati E,Pompilio G,Sommariva E,Domingues FS,Rossini A

    更新日期:2018-06-25 00:00:00

  • Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era.

    abstract:BACKGROUND:The overwhelming amount of network data in functional genomics is making its visualization cluttered with jumbling nodes and edges. Such cluttered network visualization, which is known as "hair-balls", is significantly hindering data interpretation and analysis of researchers. Effective navigation approaches...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Praneenararat T,Takagi T,Iwasaki W

    更新日期:2012-01-01 00:00:00

  • Effects of Alu elements on global nucleosome positioning in the human genome.

    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


    authors: Tanaka Y,Yamashita R,Suzuki Y,Nakai K

    更新日期:2010-05-17 00:00:00

  • A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation.

    abstract:BACKGROUND:Miniature inverted repeat transposable element (MITE) is one type of transposable element (TE), which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only few MITEs were proved to be currently active and their physiological function remains largely unknown...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dong HT,Zhang L,Zheng KL,Yao HG,Chen J,Yu FC,Yu XX,Mao BZ,Zhao D,Yao J,Li DB

    更新日期:2012-04-13 00:00:00

  • Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome.

    abstract:BACKGROUND:Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease f...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Tremblay DC,Alexander G Jr,Moseley S,Chadwick BP

    更新日期:2010-11-15 00:00:00

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    abstract:BACKGROUND:Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yin C,Li M,Hu J,Lang K,Chen Q,Liu J,Guo D,He K,Dong Y,Luo J,Song Z,Walters JR,Zhang W,Li F,Chen X

    更新日期:2018-05-30 00:00:00

  • A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola.

    abstract:BACKGROUND:Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Buiate EAS,Xavier KV,Moore N,Torres MF,Farman ML,Schardl CL,Vaillancourt LJ

    更新日期:2017-01-10 00:00:00

  • Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate.

    abstract:BACKGROUND:The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug development and safety assessment. In contrast to the growing interest for the marmoset as an animal mode...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Datson NA,Morsink MC,Atanasova S,Armstrong VW,Zischler H,Schlumbohm C,Dutilh BE,Huynen MA,Waegele B,Ruepp A,de Kloet ER,Fuchs E

    更新日期:2007-06-25 00:00:00

  • Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data.

    abstract:BACKGROUND:Runs of Homozygosity (ROH) are genomic regions where identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits an...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ceballos FC,Hazelhurst S,Ramsay M

    更新日期:2018-01-30 00:00:00

  • Genomic analysis of nontypeable pneumococci causing invasive pneumococcal disease in South Africa, 2003-2013.

    abstract:BACKGROUND:The capsular polysaccharide is the principal virulence factor of Streptococcus pneumoniae and a target for current pneumococcal vaccines. However, some pathogenic pneumococci are serologically nontypeable [nontypeable pneumococci (NTPn)]. Due to their relative rarity, NTPn are poorly characterized, and, as s...

    journal_title:BMC genomics

    pub_type: 历史文章,杂志文章


    authors: Mohale T,Wolter N,Allam M,Ndlangisa K,Crowther-Gibson P,du Plessis M,von Gottberg A

    更新日期:2016-06-22 00:00:00

  • Methods for high-throughput MethylCap-Seq data analysis.

    abstract:BACKGROUND:Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measu...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rodriguez BA,Frankhouser D,Murphy M,Trimarchi M,Tam HH,Curfman J,Huang R,Chan MW,Lai HC,Parikh D,Ball B,Schwind S,Blum W,Marcucci G,Yan P,Bundschuh R

    更新日期:2012-01-01 00:00:00

  • Recurrent miscalling of missense variation from short-read genome sequence data.

    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


    authors: Field MA,Burgio G,Chuah A,Al Shekaili J,Hassan B,Al Sukaiti N,Foote SJ,Cook MC,Andrews TD

    更新日期:2019-07-16 00:00:00

  • The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus.

    abstract:BACKGROUND:Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic i...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Heitlinger E,Bridgett S,Montazam A,Taraschewski H,Blaxter M

    更新日期:2013-02-08 00:00:00

  • Differential gene expression and alternative splicing in insect immune specificity.

    abstract:BACKGROUND:Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris/trypanosome Crithidia bombi model system (two bumblebee colonies by two Crithidia strains), we have ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Riddell CE,Lobaton Garces JD,Adams S,Barribeau SM,Twell D,Mallon EB

    更新日期:2014-11-27 00:00:00

  • Wheat EST resources for functional genomics of abiotic stress.

    abstract:BACKGROUND:Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a la...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Houde M,Belcaid M,Ouellet F,Danyluk J,Monroy AF,Dryanova A,Gulick P,Bergeron A,Laroche A,Links MG,MacCarthy L,Crosby WL,Sarhan F

    更新日期:2006-06-13 00:00:00

  • A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes.

    abstract:BACKGROUND:Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Röske K,Foecking MF,Yooseph S,Glass JI,Calcutt MJ,Wise KS

    更新日期:2010-07-13 00:00:00

  • Survey of cryptic unstable transcripts in yeast.

    abstract:BACKGROUND:Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell or whether CUTs represent noise in the yeast transcriptome. We sought to ascertain the extent of c...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Vera JM,Dowell RD

    更新日期:2016-04-26 00:00:00

  • Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes.

    abstract:BACKGROUND:The Transcription Factor (TF) p63 is a master regulator of epidermal development and differentiation as evident from the remarkable skin phenotype of p63 mouse knockouts. Furthermore, ectopic expression of p63 alone is sufficient to convert simple epithelium into stratified epithelial tissues in vivo and p63...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sethi I,Sinha S,Buck MJ

    更新日期:2014-11-29 00:00:00

  • New enumeration algorithm for protein structure comparison and classification.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ashby C,Johnson D,Walker K,Kanj IA,Xia G,Huang X

    更新日期:2013-01-01 00:00:00

  • Transcriptional insights into key genes and pathways controlling muscle lipid metabolism in broiler chickens.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu L,Liu X,Cui H,Liu R,Zhao G,Wen J

    更新日期:2019-11-15 00:00:00

  • EPAS1 gene variants are associated with sprint/power athletic performance in two cohorts of European athletes.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Voisin S,Cieszczyk P,Pushkarev VP,Dyatlov DA,Vashlyayev BF,Shumaylov VA,Maciejewska-Karlowska A,Sawczuk M,Skuza L,Jastrzebski Z,Bishop DJ,Eynon N

    更新日期:2014-05-18 00:00:00