Transcriptome profiles of Quercus rubra responding to increased O3 stress.

Abstract:

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.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

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

doi

10.1186/s12864-020-6549-5

subject

Has Abstract

pub_date

2020-02-14 00:00:00

pages

160

issue

1

issn

1471-2164

pii

10.1186/s12864-020-6549-5

journal_volume

21

pub_type

杂志文章
  • 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

    doi:10.1186/1471-2164-8-264

    authors: Ferrari F,Bortoluzzi S,Coppe A,Basso D,Bicciato S,Zini R,Gemelli C,Danieli GA,Ferrari S

    更新日期:2007-08-03 00:00:00

  • 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...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1173

    authors: Bobek J,Strakova E,Zikova A,Vohradsky J

    更新日期:2014-12-23 00:00:00

  • 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

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-26

    authors: Mace ES,Xia L,Jordan DR,Halloran K,Parh DK,Huttner E,Wenzl P,Kilian A

    更新日期:2008-01-22 00:00:00

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

    abstract:BACKGROUND:Bombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the m...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1287-9

    authors: Fang SM,Hu BL,Zhou QZ,Yu QY,Zhang Z

    更新日期:2015-02-06 00:00:00

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

    abstract:BACKGROUND:Galileo is one of three members of the P superfamily of DNA transposons. It was originally discovered in Drosophila buzzatii, in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between Galileo copies. Subsequently, Galileo was identified in six of 12 ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-792

    authors: Gonçalves JW,Valiati VH,Delprat A,Valente VL,Ruiz A

    更新日期:2014-09-13 00:00:00

  • 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

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-905

    authors: Wong RY,McLeod MM,Godwin J

    更新日期:2014-10-17 00:00:00

  • 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

    doi:10.1186/1471-2164-13-262

    authors: Bright AT,Tewhey R,Abeles S,Chuquiyauri R,Llanos-Cuentas A,Ferreira MU,Schork NJ,Vinetz JM,Winzeler EA

    更新日期:2012-06-21 00:00:00

  • 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.

    abstract:BACKGROUND:Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or Illumina short-read low-coverage ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-07292-5

    authors: Baeza JA

    更新日期:2020-12-09 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 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...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1216-y

    authors: Wang Z,Tang J,Hu R,Wu P,Hou XL,Song XM,Xiong AS

    更新日期:2015-01-23 00:00:00

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

    abstract:BACKGROUND:Previously, we could show that L-lactate affects cultured bovine granulosa cells (GC) in a specific manner driving the cells into an early pre-ovulatory phenotype. Here we studied genome wide effects in L-lactate-treated GC to further elucidate the underlying mechanisms that are responsible for the L-lactate...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5657-6

    authors: Baufeld A,Koczan D,Vanselow J

    更新日期:2019-04-05 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

  • G-spots cause incorrect expression measurement in Affymetrix microarrays.

    abstract:BACKGROUND:High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene's probe set will provide a consistent message signifying the gene's p...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-613

    authors: Upton GJ,Langdon WB,Harrison AP

    更新日期:2008-12-18 00:00:00

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

    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

    authors: Alam MT,Merlo ME,STREAM Consortium.,Hodgson DA,Wellington EM,Takano E,Breitling R

    更新日期:2010-03-26 00:00:00

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

    abstract:BACKGROUND:Filarial nematodes cause debilitating human diseases. While treatable, recent evidence suggests drug resistance is developing, necessitating the development of novel targets and new treatment options. Although transcriptomic and proteomic studies around the nematode life cycle have greatly enhanced our knowl...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2083-2

    authors: Luck AN,Anderson KG,McClung CM,VerBerkmoes NC,Foster JM,Michalski ML,Slatko BE

    更新日期:2015-11-11 00:00:00

  • Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species.

    abstract:BACKGROUND:Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is adapted to subtropical/temperate areas and is considered a source of high-quality cellulose; E. gr...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-201

    authors: Salazar MM,Nascimento LC,Camargo EL,Gonçalves DC,Lepikson Neto J,Marques WL,Teixeira PJ,Mieczkowski P,Mondego JM,Carazzolle MF,Deckmann AC,Pereira GA

    更新日期:2013-03-22 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

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

    abstract:BACKGROUND:Identifying the genotypes underlying human disease phenotypes is a fundamental step in human genetics and medicine. High-throughput genomic technologies provide thousands of genetic variants per individual. The causal genes of a specific phenotype are usually expected to be functionally close to each other. ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-256

    authors: Itan Y,Mazel M,Mazel B,Abhyankar A,Nitschke P,Quintana-Murci L,Boisson-Dupuis S,Boisson B,Abel L,Zhang SY,Casanova JL

    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.

    abstract:BACKGROUND:Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transcriptome (RNA-Seq) and metabolome analysis (UPLC-MS/MS) to identify structural and regulatory genes a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-07133-5

    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

    doi:10.1186/1471-2164-15-1096

    authors: Scully ED,Geib SM,Carlson JE,Tien M,McKenna D,Hoover K

    更新日期:2014-12-12 00:00:00

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

    abstract:BACKGROUND:Streptococcus uberis, a Gram positive bacterial pathogen responsible for a significant proportion of bovine mastitis in commercial dairy herds, colonises multiple body sites of the cow including the gut, genital tract and mammary gland. Comparative analysis of the complete genome sequence of S. uberis strain...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-54

    authors: Ward PN,Holden MT,Leigh JA,Lennard N,Bignell A,Barron A,Clark L,Quail MA,Woodward J,Barrell BG,Egan SA,Field TR,Maskell D,Kehoe M,Dowson CG,Chanter N,Whatmore AM,Bentley SD,Parkhill J

    更新日期:2009-01-28 00:00:00

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

    abstract:BACKGROUND:Three-dimensional (3D) multicellular spheroids of mesenchymal stem cells (MSCs) are generally regarded to have beneficial properties over MSCs in monolayer. Recent literatures have documented that MSCs can self-assemble into 3D spheroids with a greater capacity for differentiation into various cell types whe...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-10

    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

    doi:10.1186/1471-2164-13-654

    authors: Catalán A,Hutter S,Parsch J

    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.

    abstract:BACKGROUND:Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate-specific antigen era. Long intergenic noncoding RNAs (lincRNAs) play essential roles in many physiological processes and ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-16-S7-S3

    authors: Cui W,Qian Y,Zhou X,Lin Y,Jiang J,Chen J,Zhao Z,Shen B

    更新日期:2015-01-01 00:00:00

  • "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

    doi:10.1186/1471-2164-11-403

    authors: Gayán J,González-Pérez A,Ruiz A

    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

    doi:10.1186/1471-2164-7-255

    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

    更新日期:2006-10-11 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

    doi:10.1186/s12864-018-4576-2

    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

    doi:10.1186/1471-2164-11-S1-S13

    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

    doi:10.1186/s12864-016-3465-9

    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

    doi:10.1186/1471-2164-14-454

    authors: Ramírez CA,Requena JM,Puerta CJ

    更新日期:2013-07-06 00:00:00