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












  • Genomic expression during human myelopoiesis.

    abstract:BACKGROUND:Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where multipotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This stu...

    journal_title:BMC genomics

    pub_type: 杂志文章


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  • Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor.

    abstract:BACKGROUND:Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize second...

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  • DArT markers: diversity analyses and mapping in Sorghum bicolor.

    abstract:BACKGROUND:The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obt...

    journal_title:BMC genomics

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  • Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms.

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  • Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome.

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  • Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio).

    abstract:BACKGROUND:Male and female vertebrates typically differ in a range of characteristics, from morphology to physiology to behavior, which are influenced by factors such as the social environment and the internal hormonal and genetic milieu. However, sex differences in gene expression profiles in the brains of vertebrates...

    journal_title:BMC genomics

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  • Whole genome sequencing analysis of Plasmodium vivax using whole genome capture.

    abstract:BACKGROUND:Malaria caused by Plasmodium vivax is an experimentally neglected severe disease with a substantial burden on human health. Because of technical limitations, little is known about the biology of this important human pathogen. Whole genome analysis methods on patient-derived material are thus likely to have a...

    journal_title:BMC genomics

    pub_type: 杂志文章


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  • Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus.

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    journal_title:BMC genomics

    pub_type: 杂志文章


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  • 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.

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    journal_title:BMC genomics

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  • Genome-wide analysis of the R2R3-MYB transcription factor genes in Chinese cabbage (Brassica rapa ssp. pekinensis) reveals their stress and hormone responsive patterns.

    abstract:BACKGROUND:The MYB superfamily is one of the most abundant transcription factor (TF) families in plants. MYB proteins include highly conserved N-terminal MYB repeats (1R, R2R3, 3R, and atypical) and various C-terminal sequences that confer extensive functions. However, the functions of most MYB genes are unknown, and h...

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  • L-lactate induces specific genome wide alterations of gene expression in cultured bovine granulosa cells.

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  • Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor.

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  • Tissue-specific transcriptomics and proteomics of a filarial nematode and its Wolbachia endosymbiont.

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    pub_type: 杂志文章


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

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    journal_title:BMC genomics

    pub_type: 杂志文章


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  • HGCS: an online tool for prioritizing disease-causing gene variants by biological distance.

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    journal_title:BMC genomics

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    更新日期:2014-04-03 00:00:00

  • Combined Transcriptome and Metabolome analysis of Pitaya fruit unveiled the mechanisms underlying Peel and pulp color formation.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhou Z,Gao H,Ming J,Ding Z,Lin X,Zhan R

    更新日期:2020-10-22 00:00:00

  • Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles.

    abstract:BACKGROUND:Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecolo...

    journal_title:BMC genomics

    pub_type: 杂志文章


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  • Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis.

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    journal_title:BMC genomics

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  • Substrate-dependent gene regulation of self-assembled human MSC spheroids on chitosan membranes.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yeh HY,Liu BH,Sieber M,Hsu SH

    更新日期:2014-01-05 00:00:00

  • Population and sex differences in Drosophila melanogaster brain gene expression.

    abstract:BACKGROUND:Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-...

    journal_title:BMC genomics

    pub_type: 杂志文章


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    更新日期:2012-11-21 00:00:00

  • Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data.

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    journal_title:BMC genomics

    pub_type: 杂志文章


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  • "Does replication groups scoring reduce false positive rate in SNP interaction discovery? Response".

    abstract:BACKGROUND:The genomewide evaluation of genetic epistasis is a computationally demanding task, and a current challenge in Genetics. HFCC (Hypothesis-Free Clinical Cloning) is one of the methods that have been suggested for genomewide epistasis analysis. In order to perform an exhaustive search of epistasis, HFCC has im...

    journal_title:BMC genomics

    pub_type: 评论,杂志文章


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    更新日期:2010-06-24 00:00:00

  • Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags.

    abstract:BACKGROUND:Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a recognized pathogen for humans, little is known about how its transcriptional pattern is related...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang L,Ma L,Leng W,Liu T,Yu L,Yang J,Yang L,Zhang W,Zhang Q,Dong J,Xue Y,Zhu Y,Xu X,Wan Z,Ding G,Yu F,Tu K,Li Y,Li R,Shen Y,Jin Q

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  • 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

  • Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction.

    abstract:BACKGROUND:Tandem mass spectrometry (MS/MS) has become a standard method for identification of proteins extracted from biological samples but the huge number and the noise contamination of MS/MS spectra obstruct swift and reliable computer-aided interpretation. Typically, a minor fraction of the spectra per sample (mos...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Mujezinovic N,Schneider G,Wildpaner M,Mechtler K,Eisenhaber F

    更新日期:2010-02-10 00:00:00

  • Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.

    abstract:BACKGROUND:Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insight...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Brockmöller T,Ling Z,Li D,Gaquerel E,Baldwin IT,Xu S

    更新日期:2017-01-13 00:00:00

  • Alpha tubulin genes from Leishmania braziliensis: genomic organization, gene structure and insights on their expression.

    abstract:BACKGROUND:Alpha tubulin is a fundamental component of the cytoskeleton which is responsible for cell shape and is involved in cell division, ciliary and flagellar motility and intracellular transport. Alpha tubulin gene expression varies according to the morphological changes suffered by Leishmania in its life cycle. ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ramírez CA,Requena JM,Puerta CJ

    更新日期:2013-07-06 00:00:00