Transcriptome profiles of Quercus rubra responding to increased O3 stress.


BACKGROUND:Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3). Ozone is formed by the interaction of sunlight, molecular oxygen and by the reactions of chemicals commonly found in industrial and automobile emissions such as nitrogen oxides and volatile organic compounds. Although it is well known that productivity of Northern red oak (Quercus rubra) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O3, limited information is available on its responses to exogenous stimuli at the level of gene expression. RESULTS:RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, of which more than 42,000 sequences could be annotated through homology-based searches. A total of 4140 differential expressed genes (DEGs) were detected in response to O3 stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O3-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction. CONCLUSION:This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O3. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.


BMC Genomics


BMC genomics


Soltani N,Best T,Grace D,Nelms C,Shumaker K,Romero-Severson J,Moses D,Schuster S,Staton M,Carlson J,Gwinn K




Has Abstract


2020-02-14 00:00:00












  • Preferred and avoided codon pairs in three domains of life.

    abstract:BACKGROUND:Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserv...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Tats A,Tenson T,Remm M

    更新日期:2008-10-08 00:00:00

  • A gene sets approach for identifying prognostic gene signatures for outcome prediction.

    abstract:BACKGROUND:Gene expression profiling is a promising approach to better estimate patient prognosis; however, there are still unresolved problems, including little overlap among similarly developed gene sets and poor performance of a developed gene set in other datasets. RESULTS:We applied a gene sets approach to develo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kim SY,Kim YS

    更新日期:2008-04-16 00:00:00

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

    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, specif...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: 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

    更新日期:2011-07-27 00:00:00

  • Genome-wide analysis of the TPX2 family proteins in Eucalyptus grandis.

    abstract:BACKGROUND:The Xklp2 (TPX2) proteins belong to the microtubule-associated (MAP) family of proteins. All members of the family contain the conserved TPX2 motif, which can interact with microtubules, regulate microtubule dynamics or assist with different microtubule functions, for example, maintenance of cell morphology ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Du P,Kumar M,Yao Y,Xie Q,Wang J,Zhang B,Gan S,Wang Y,Wu AM

    更新日期:2016-11-24 00:00:00

  • Stress-mediated convergence of splicing landscapes in male and female rock doves.

    abstract:BACKGROUND:The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus c...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lang AS,Austin SH,Harris RM,Calisi RM,MacManes MD

    更新日期:2020-03-23 00:00:00

  • The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna.

    abstract:BACKGROUND:The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely re...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Schedina IM,Groth D,Schlupp I,Tiedemann R

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  • Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes.

    abstract:BACKGROUND:Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed defense mechanisms against TE invasion such as RIP (Repeat-Induced Point mutation), MIP (Methylation Induced Premeiotically) and Quelling (RNA interference). RIP inactivates repeated sequ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Amselem J,Lebrun MH,Quesneville H

    更新日期:2015-02-28 00:00:00

  • Highly sensitive amplicon-based transcript quantification by semiconductor sequencing.

    abstract:BACKGROUND:In clinical and basic research custom panels for transcript profiling are gaining importance because only project specific informative genes are interrogated. This approach reduces costs and complexity of data analysis and allows multiplexing of samples. Polymerase-chain-reaction (PCR) based TaqMan assays ha...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang JD,Schindler T,Küng E,Ebeling M,Certa U

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  • A transcript profiling approach reveals the zinc finger transcription factor ZNF191 is a pleiotropic factor.

    abstract:BACKGROUND:The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp191), which is the most highly conserved among the human-mouse SCAN family member orthologues pairs. ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li J,Chen X,Gong X,Liu Y,Feng H,Qiu L,Hu Z,Zhang J

    更新日期:2009-05-22 00:00:00

  • A high-density genetic map developed by specific-locus amplified fragment (SLAF) sequencing and identification of a locus controlling anthocyanin pigmentation in stalk of Zicaitai (Brassica rapa L. ssp. chinensis var. purpurea).

    abstract:BACKGROUND:Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li GH,Chen HC,Liu JL,Luo WL,Xie DS,Luo SB,Wu TQ,Akram W,Zhong YJ

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  • Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease.

    abstract:BACKGROUND:Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epig...

    journal_title:BMC genomics

    pub_type: 杂志文章


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  • DAWN: a resource for yielding insights into the diversity among wheat genomes.

    abstract:BACKGROUND:Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by the lack of a genome reference and the large computational requirements for analysing these data sets. RESULTS:DAWN (Diversity Among Wheat geNomes) integrates data from the T. aes...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Watson-Haigh NS,Suchecki R,Kalashyan E,Garcia M,Baumann U

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  • Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting.

    abstract:BACKGROUND:Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades. RESULTS:In the present study we have genotyped and sequenc...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Perdigão J,Silva H,Machado D,Macedo R,Maltez F,Silva C,Jordao L,Couto I,Mallard K,Coll F,Hill-Cawthorne GA,McNerney R,Pain A,Clark TG,Viveiros M,Portugal I

    更新日期:2014-11-18 00:00:00

  • Characterization of the bovine pregnancy-associated glycoprotein gene family--analysis of gene sequences, regulatory regions within the promoter and expression of selected genes.

    abstract:BACKGROUND:The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Telugu BP,Walker AM,Green JA

    更新日期:2009-04-24 00:00:00

  • Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows.

    abstract:BACKGROUND:The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ov...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sun X,Mei S,Tao H,Wang G,Su L,Jiang S,Deng C,Xiong Y,Li F

    更新日期:2011-02-16 00:00:00

  • SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population.

    abstract:BACKGROUND:Progress in genetics and breeding in pea still suffers from the limited availability of molecular resources. SNP markers that can be identified through affordable sequencing processes, without the need for prior genome reduction or a reference genome to assemble sequencing data would allow the discovery and ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Boutet G,Alves Carvalho S,Falque M,Peterlongo P,Lhuillier E,Bouchez O,Lavaud C,Pilet-Nayel ML,Rivière N,Baranger A

    更新日期:2016-02-18 00:00:00

  • Are personalities genetically determined? Inferences from subsocial spiders.

    abstract:BACKGROUND:Recent research has revealed that polymorphic behavioral strategies shape intra-and interspecific interactions and contribute to fitness in many animal species. A better understanding of the proximate mechanisms underlying these behavioral syndromes will enhance our grasp this phenomenon. Spiders in the genu...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Purcell J,Pruitt JN

    更新日期:2019-11-22 00:00:00

  • Identifying Mendelian disease genes with the variant effect scoring tool.

    abstract:BACKGROUND:Whole exome sequencing studies identify hundreds to thousands of rare protein coding variants of ambiguous significance for human health. Computational tools are needed to accelerate the identification of specific variants and genes that contribute to human disease. RESULTS:We have developed the Variant Eff...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Carter H,Douville C,Stenson PD,Cooper DN,Karchin R

    更新日期:2013-01-01 00:00:00

  • Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan.

    abstract:BACKGROUND:Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geog...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gamboa M,Watanabe K

    更新日期:2019-01-24 00:00:00

  • Improving ancient DNA read mapping against modern reference genomes.

    abstract:BACKGROUND:Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem D...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Schubert M,Ginolhac A,Lindgreen S,Thompson JF,Al-Rasheid KA,Willerslev E,Krogh A,Orlando L

    更新日期:2012-05-10 00:00:00

  • Predicting tissue specific transcription factor binding sites.

    abstract:BACKGROUND:Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contexts such as developmental stages and tissue types. Experimental methods to study in vivo binding, inc...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhong S,He X,Bar-Joseph Z

    更新日期:2013-11-15 00:00:00

  • The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance.

    abstract:BACKGROUND:The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplif...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Molin WT,Wright AA,Lawton-Rauh A,Saski CA

    更新日期:2017-01-17 00:00:00

  • De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions.

    abstract:BACKGROUND:The phytoflagellated protozoan, Euglena gracilis, has been proposed as an attractive feedstock for the accumulation of valuable compounds such as β-1,3-glucan, also known as paramylon, and wax esters. The production of wax esters proceeds under anaerobic conditions, designated as wax ester fermentation. In s...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yoshida Y,Tomiyama T,Maruta T,Tomita M,Ishikawa T,Arakawa K

    更新日期:2016-03-03 00:00:00

  • Expression of immune-response genes in lepidopteran host is suppressed by venom from an endoparasitoid, Pteromalus puparum.

    abstract:BACKGROUND:The relationships between parasitoids and their insect hosts have attracted attention at two levels. First, the basic biology of host-parasitoid interactions is of fundamental interest. Second, parasitoids are widely used as biological control agents in sustainable agricultural programs. Females of the grega...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Fang Q,Wang L,Zhu J,Li Y,Song Q,Stanley DW,Akhtar ZR,Ye G

    更新日期:2010-09-02 00:00:00

  • Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni.

    abstract:BACKGROUND:It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of t...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Laha T,Kewgrai N,Loukas A,Brindley PJ

    更新日期:2005-11-04 00:00:00

  • Genome sequence of an aflatoxigenic pathogen of Argentinian peanut, Aspergillus arachidicola.

    abstract:BACKGROUND:Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. This aflatoxigenic species is capable of secreting both B and G aflatoxins, similar to A. parasit...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Moore GG,Mack BM,Beltz SB,Puel O

    更新日期:2018-03-09 00:00:00

  • Transcriptome analysis of bolting in A. tequilana reveals roles for florigen, MADS, fructans and gibberellins.

    abstract:BACKGROUND:Reliable indicators for the onset of flowering are not available for most perennial monocarpic species, representing a drawback for crops such as bamboo, agave and banana. The ability to predict and control the transition to the reproductive stage in A. tequilana would represent an advantage for field manage...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Avila de Dios E,Delaye L,Simpson J

    更新日期:2019-06-10 00:00:00

  • Using genomic resources for linkage analysis in Peromyscus with an application for characterizing Dominant Spot.

    abstract:BACKGROUND:Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely related and can generate viable and fertile hybrid offspring. The ability to generate hybrid offspring...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Shang Z,Horovitz DJ,McKenzie RH,Keisler JL,Felder MR,Davis SW

    更新日期:2020-09-11 00:00:00

  • Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.

    abstract:BACKGROUND:Insertion sequences (ISs) are approximately 1 kbp long "jumping" genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I ("cut-and-paste") Mobile Genetic Elements. ISs are proposed to be involve...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Vigil-Stenman T,Larsson J,Nylander JA,Bergman B

    更新日期:2015-03-17 00:00:00

  • A fast-linear mixed model for genome-wide haplotype association analysis: application to agronomic traits in maize.

    abstract:BACKGROUND:Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analysis, both haplotype alleles and blocks are tested. Haplotype alleles can be inferred with the same st...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chen H,Hao Z,Zhao Y,Yang R

    更新日期:2020-02-11 00:00:00