Identification of hydroxy fatty acid and triacylglycerol metabolism-related genes in lesquerella through seed transcriptome analysis.

Abstract:

BACKGROUND:Castor oil is the only commercial source of hydroxy fatty acid that has industrial value. The production of castor oil is hampered by the presence of the toxin ricin in its seed. Lesquerella seed also accumulates hydroxy fatty acid and is free of ricin, and thus it is being developed as a new crop for hydroxy fatty acid production. A high-throughput, large-scale sequencing of transcripts from developing lesquerella seeds was carried out by 454 pyrosequencing to generate a database for quality improvement of seed oil and other agronomic traits. Deep mining and characterization of acyl-lipid genes were conducted to uncover candidate genes for further studies of mechanisms underlying hydroxy fatty acid and seed oil synthesis. RESULTS:A total of 651 megabases of raw sequences from an mRNA sample of developing seeds was acquired. Bioinformatic analysis of these sequences revealed 59,914 transcripts representing 26,995 unique genes that include nearly all known seed expressed genes. Based on sequence similarity with known plant proteins, about 74% (19,861) genes matched with annotated coding genes. Among them, 95% (18,868) showed highest sequence homology with Arabidopsis genes, which will allow translation of genomics and genetics findings from Arabidopsis to lesquerella. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome assembly and identified 615 lesquerella genes involved in all known pathways of acyl-lipid metabolism. Further deep mining the transcriptome assembly led to identification of almost all lesquerella genes involved in fatty acid and triacylglycerol synthesis. Moreover, we characterized the spatial and temporal expression profiles of 15 key genes using the quantitative PCR assay. CONCLUSIONS:We have built a lesquerella seed transcriptome that provides a valuable reference in addition to the castor database for discovering genes involved in the synthesis of triacylglycerols enriched with hydroxy fatty acids. The information obtained from data mining and gene expression profiling will provide a resource not only for the study of hydroxy fatty acid metabolism, but also for the biotechnological production of hydroxy fatty acids in existing oilseed crops.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Kim HU,Chen GQ

doi

10.1186/s12864-015-1413-8

subject

Has Abstract

pub_date

2015-03-24 00:00:00

pages

230

issn

1471-2164

pii

10.1186/s12864-015-1413-8

journal_volume

16

pub_type

杂志文章
  • Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis.

    abstract:BACKGROUND:Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-326

    authors: Llorens F,Hummel M,Pastor X,Ferrer A,Pluvinet R,Vivancos A,Castillo E,Iraola S,Mosquera AM,González E,Lozano J,Ingham M,Dohm JC,Noguera M,Kofler R,del Río JA,Bayés M,Himmelbauer H,Sumoy L

    更新日期:2011-06-23 00:00:00

  • Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes.

    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

    authors: Morton RA,Morton BR

    更新日期:2007-10-12 00:00:00

  • Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum.

    abstract:BACKGROUND:It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene m...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-587

    authors: López-Barragán MJ,Lemieux J,Quiñones M,Williamson KC,Molina-Cruz A,Cui K,Barillas-Mury C,Zhao K,Su XZ

    更新日期:2011-11-30 00:00:00

  • Effects of dietary physical or nutritional factors on morphology of rumen papillae and transcriptome changes in lactating dairy cows based on three different forage-based diets.

    abstract:BACKGROUND:Rumen epithelial tissue plays an important role in nutrient absorption and rumen health. However, whether forage quality and particle size impact the rumen epithelial morphology is unclear. The current study was conducted to elucidate the effects of forage quality and forage particle size on rumen epithelial...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3726-2

    authors: Wang B,Wang D,Wu X,Cai J,Liu M,Huang X,Wu J,Liu J,Guan L

    更新日期:2017-05-06 00:00:00

  • Target genes of myostatin loss-of-function in muscles of late bovine fetuses.

    abstract:BACKGROUND:Myostatin, a muscle-specific member of the Transforming Growth Factor beta family, negatively regulates muscle development. Double-muscled (DM) cattle have a loss-of-function mutation in their myostatin gene responsible for the hypermuscular phenotype. Thus, these animals are a good model for understanding t...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-63

    authors: Cassar-Malek I,Passelaigue F,Bernard C,Léger J,Hocquette JF

    更新日期:2007-03-01 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

    doi:10.1186/1471-2164-13-135

    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

  • Comparative genomics of downy mildews reveals potential adaptations to biotrophy.

    abstract:BACKGROUND:Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the pa...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5214-8

    authors: Fletcher K,Klosterman SJ,Derevnina L,Martin F,Bertier LD,Koike S,Reyes-Chin-Wo S,Mou B,Michelmore R

    更新日期:2018-11-29 00:00:00

  • Next generation sequencing and comparative analyses of Xenopus mitogenomes.

    abstract:BACKGROUND:Mitochondrial genomes comprise a small but critical component of the total DNA in eukaryotic organisms. They encode several key proteins for the cell's major energy producing apparatus, the mitochondrial respiratory chain. Additionally, their nucleotide and amino acid sequences are of great utility as marker...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-496

    authors: Lloyd RE,Foster PG,Guille M,Littlewood DT

    更新日期:2012-09-19 00:00:00

  • InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia.

    abstract::In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the I...

    journal_title:BMC genomics

    pub_type:

    doi:10.1186/1471-2164-12-S3-S1

    authors: Schönbach C,Tan TW,Kelso J,Rost B,Nathan S,Ranganathan S

    更新日期:2011-11-30 00:00:00

  • Accuracy of genomic selection for alfalfa biomass yield in different reference populations.

    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

    authors: Annicchiarico P,Nazzicari N,Li X,Wei Y,Pecetti L,Brummer EC

    更新日期:2015-12-01 00:00:00

  • Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation.

    abstract:BACKGROUND:Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or stuck fermentations. Selection and development of new Saccharomyces cerevisiae strains well adapted a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1755-2

    authors: López-Malo M,García-Rios E,Melgar B,Sanchez MR,Dunham MJ,Guillamón JM

    更新日期:2015-07-22 00:00:00

  • Insights into the Musa genome: syntenic relationships to rice and between Musa species.

    abstract:BACKGROUND:Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-58

    authors: Lescot M,Piffanelli P,Ciampi AY,Ruiz M,Blanc G,Leebens-Mack J,da Silva FR,Santos CM,D'Hont A,Garsmeur O,Vilarinhos AD,Kanamori H,Matsumoto T,Ronning CM,Cheung F,Haas BJ,Althoff R,Arbogast T,Hine E,Pappas GJ Jr,Sas

    更新日期:2008-01-30 00:00:00

  • SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance.

    abstract:BACKGROUND:Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two major sources of SCN resistance with Peking requiring both Rhg1 and Rhg4 alleles and PI 88788 only...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1531-3

    authors: Shi Z,Liu S,Noe J,Arelli P,Meksem K,Li Z

    更新日期:2015-04-18 00:00:00

  • Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease.

    abstract:BACKGROUND:The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1154

    authors: Krishna A,Biryukov M,Trefois C,Antony PM,Hussong R,Lin J,Heinäniemi M,Glusman G,Köglsberger S,Boyd O,van den Berg BH,Linke D,Huang D,Wang K,Hood L,Tholey A,Schneider R,Galas DJ,Balling R,May P

    更新日期:2014-12-20 00:00:00

  • Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.

    abstract:BACKGROUND:RNA-seq has shown huge potential for phylogenomic inferences in non-model organisms. However, error, incompleteness, and redundant assembled transcripts for each gene in de novo assembly of short reads cause noise in analyses and a large amount of missing data in the aligned matrix. To address these problems...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-328

    authors: Yang Y,Smith SA

    更新日期:2013-05-14 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

    doi:10.1186/s12864-016-3457-9

    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

  • Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.

    abstract:BACKGROUND:The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-120

    authors: McGuire AM,Weiner B,Park ST,Wapinski I,Raman S,Dolganov G,Peterson M,Riley R,Zucker J,Abeel T,White J,Sisk P,Stolte C,Koehrsen M,Yamamoto RT,Iacobelli-Martinez M,Kidd MJ,Maer AM,Schoolnik GK,Regev A,Galagan J

    更新日期:2012-03-28 00:00:00

  • A transcriptome-based protein network that identifies new therapeutic targets in colorectal cancer.

    abstract:BACKGROUND:Colon cancer occurrence is increasing worldwide, making it the third most frequent cancer. Although many therapeutic options are available and quite efficient at the early stages, survival is strongly decreased when the disease has spread to other organs. The identification of molecular markers of colon canc...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4139-y

    authors: Durand S,Trillet K,Uguen A,Saint-Pierre A,Le Jossic-Corcos C,Corcos L

    更新日期:2017-09-30 00:00:00

  • Chronic wounds alter the proteome profile in skin mucus of farmed gilthead seabream.

    abstract:BACKGROUND:Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers as external clinical signs. However, there is no information about the changes produced by the wounds...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4349-3

    authors: Cordero H,Brinchmann MF,Cuesta A,Esteban MA

    更新日期:2017-12-02 00:00:00

  • Comparative analysis of surface-exposed virulence factors of Acinetobacter baumannii.

    abstract:BACKGROUND:Acinetobacter baumannii is a significant hospital pathogen, particularly due to the dissemination of highly multidrug resistant isolates. Genome data have revealed that A. baumannii is highly genetically diverse, which correlates with major variations seen at the phenotypic level. Thus far, comparative genom...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1020

    authors: Eijkelkamp BA,Stroeher UH,Hassan KA,Paulsen IT,Brown MH

    更新日期:2014-11-25 00:00:00

  • Nonlinear transcriptomic response to dietary fat intake in the small intestine of C57BL/6J mice.

    abstract:BACKGROUND:A high caloric diet, in conjunction with low levels of physical activity, promotes obesity. Many studies are available regarding the relation between dietary saturated fats and the etiology of obesity, but most focus on liver, muscle and white adipose tissue. Furthermore, the majority of transcriptomic studi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-2424-9

    authors: Nyima T,Müller M,Hooiveld GJ,Morine MJ,Scotti M

    更新日期:2016-02-09 00:00:00

  • Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells.

    abstract:BACKGROUND:Various cancer cells, including those of colorectal cancer (CRC), release microvesicles (exosomes) into surrounding tissues and peripheral circulation. These microvesicles can mediate communication between cells and affect various tumor-related processes in their target cells. RESULTS:We present potential r...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-556

    authors: Hong BS,Cho JH,Kim H,Choi EJ,Rho S,Kim J,Kim JH,Choi DS,Kim YK,Hwang D,Gho YS

    更新日期:2009-11-25 00:00:00

  • mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development.

    abstract:BACKGROUND:Rich in genetic information and cost-effective to genotype, the Insertion-Deletion (InDel) molecular marker system is an important tool for studies in genetics, genomics and for marker-assisted breeding. Advent of next-generation sequencing (NGS) revolutionized the speed and throughput of sequence data gener...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-2614-5

    authors: Lv Y,Liu Y,Zhao H

    更新日期:2016-04-14 00:00:00

  • Phytochemical and comparative transcriptome analyses reveal different regulatory mechanisms in the terpenoid biosynthesis pathways between Matricaria recutita L. and Chamaemelum nobile L.

    abstract:BACKGROUND:Matricaria recutita (German chamomile) and Chamaemelum nobile (Roman chamomile) belong to the botanical family Asteraceae. These two herbs are not only morphologically distinguishable, but their secondary metabolites - especially the essential oils present in flowers are also different, especially the terpen...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6579-z

    authors: Tai Y,Hou X,Liu C,Sun J,Guo C,Su L,Jiang W,Ling C,Wang C,Wang H,Pan G,Si X,Yuan Y

    更新日期:2020-02-18 00:00:00

  • New enumeration algorithm for protein structure comparison and classification.

    abstract:BACKGROUND:Protein structure comparison and classification is an effective method for exploring protein structure-function relations. This problem is computationally challenging. Many different computational approaches for protein structure comparison apply the secondary structure elements (SSEs) representation of prot...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-S2-S1

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

    更新日期:2013-01-01 00:00:00

  • angaGEDUCI: Anopheles gambiae gene expression database with integrated comparative algorithms for identifying conserved DNA motifs in promoter sequences.

    abstract:BACKGROUND:The completed sequence of the Anopheles gambiae genome has enabled genome-wide analyses of gene expression and regulation in this principal vector of human malaria. These investigations have created a demand for efficient methods of cataloguing and analyzing the large quantities of data that have been produc...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-116

    authors: Dissanayake SN,Marinotti O,Ribeiro JM,James AA

    更新日期:2006-05-17 00:00:00

  • Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi.

    abstract:BACKGROUND:Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. RESULTS:In this study, we identified a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3502-3

    authors: Liu YC,Chen WL,Kung WH,Huang HD

    更新日期:2017-03-14 00:00:00

  • Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols.

    abstract:BACKGROUND:RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kits. To date there has been no analysis of the effect of these choices on identifying differentially e...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3797-0

    authors: Corley SM,MacKenzie KL,Beverdam A,Roddam LF,Wilkins MR

    更新日期:2017-05-23 00:00:00

  • Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.

    abstract:BACKGROUND:With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal r...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-150

    authors: Dharmawardhana P,Brunner AM,Strauss SH

    更新日期:2010-03-04 00:00:00

  • Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea.

    abstract:BACKGROUND:Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.In order to evaluate the potential of these technologies in pea, we selected a ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-468

    authors: Deulvot C,Charrel H,Marty A,Jacquin F,Donnadieu C,Lejeune-Hénaut I,Burstin J,Aubert G

    更新日期:2010-08-11 00:00:00