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De novo assembly in defense against pests in Pinus massoniana

ABSTRACT: We sequenced mRNA from the insect-resistant and poor insect resistance Pinus massoniana to discover metabolic pathways and genes that are involved in defense against pests.

ORGANISM(S): Pinus massoniana

PROVIDER: GSE72294 | GEO | 2015/08/24

SECONDARY ACCESSION(S): PRJNA293676

REPOSITORIES: GEO

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De novo assembly in defense against pests in Pinus massoniana

Project description:We sequenced mRNA from the insect-resistant and poor insect resistance Pinus massoniana to discover metabolic pathways and genes that are involved in defense against pests. Examination of mRNA levels in strain insect-resistant and poor insect resistance Pinus massoniana

2015-08-24 | E-GEOD-72294 | biostudies-arrayexpress

Pinus massoniana

Project description:De novo assembly in defense against pests in Pinus massoniana

| PRJNA293676 | ENA

Transcriptome-wide analysis of xylogenesis during growing season in Pinus canariensis

Project description:Wood in conifers is mainly composed of tracheids. Some taxa, such as Pinus, present tracheids also in the rays, but are axial tracheids which constitute the vast majority of secondary xylem. Nevertheless, radial and axial parenchyma surrounding constitutive and traumatic resin ducts is known to serve as crucial reserve storage. These reserves are mobilized in response to traumatism, insect and pathogen attacks and defoliation, allowing the synthesis of resin, healing and, in few taxa, even resprouting. However, due to the low proportion of parenchymatic cells in secondary xylem relevant genes involved in their differentiation may have been missed in studies of transcriptomics of conifer wood formation. In this study we have used Pinus canariensis as a model species, given its comparatively high proportion of axial parenchyma. We have prepared two normalized libraries from its cambial zone, covering early- and late-wood differentiation. We have de novo assembled a transcriptome, and have analyzed the transcriptional profiles during the growing season, getting a more complete picture of wood formation in conifers. SUBMITTER_CITATION: Chano, V., López de Heredia, U., Collada, C., et al. (2017). Transcriptomic analysis of juvenile wood formation during the growing season in Pinus canariensis. Holzforschung, 0(0), pp. -. Retrieved 8 Aug. 2017, from doi:10.1515/hf-2017-0014

2016-09-01 | GSE82217 | GEO

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome.

Project description: Not available

| S-EPMC4676862 | biostudies-literature

Expression profiling of PpNAC1 RNAi Pinus pinaster plantlets

Project description:The transcriptome of PpNAC1 RNAi Pinus pinaster plantlets (60 days) were analyzed.

2018-01-22 | GSE89341 | GEO

Utilization of Tissue Ploidy Level Variation in <i>de Novo</i> Transcriptome Assembly of <i>Pinus sylvestris</i>.

Project description: Not available

| S-EPMC6778806 | biostudies-literature

Heterologous hybridization to an oligonucleotide microarray monitors differential gene expression in Pinus radiata exposed to long-term Ethephon exposure

Project description:Comparison of transcriptomes from bark, developing xylem and xylem of P. radiata saplings exposed to 0 or 1mg of Ethephon in lanolin for 1 or 8 weeks We developed an oligonucleotide microarray using sequences (mostly from Pinus taeda) from public sequence databases. These sequences were reconstituted into a non-redundant database by CAP3 assembly and used as templates for automated design of 60-mer oligonucleotide probes through eArray, Agilent’s online facility. The microarray slides, manufactured by Agilent, were used to monitor gene expression in an Ethephon-induction experiment. Ethephon was dispersed in lanolin paste and applied in a 3 cm band near the base of the stem of 2-year old Pinus radiata saplings. RNA was extracted from bark, cambial region, also known as “developing xylem”, and xylem tissues exposed for 1 or 8 weeks to Ethephon. The transcriptomes from these extracts were compared by hybridization onto the All-Pinus microarray slides. Statistically significant differentially expressed genes identified by limma (Linear Models for Microarray Data) were subsequently analysed by singular enrichment analysis through the Database for Annotation, Visualization and Integrated Discovery (DAVID) portal. Results revealed that bark, cambial region and xylem generate mostly mutually exclusive cohorts of genes and Gene Ontology (GO) classes. Ethephon induction led to the upregulation of xylem genes related to the metabolism of phenylpropanoids and flavonoids and to defence responses, specifically, fungal/insect attack and oxidative stress. Independent validation of the microarray data for five genes was obtained by quantitative RT-PCR. The results are also interpreted in reference to gross and microscopic morphological changes. These results confirm the utility of the All-Pinus microarray for transcriptomic research in P. radiata.

2012-11-15 | GSE42300 | GEO

De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora).

Project description: Not available

| S-EPMC4691086 | biostudies-literature

RNA-sequencing reveals differentially expressed rice genes functionally associated with defense against brown planthopper in NILs pyramiding BPH14 and BPH15

Project description:Brown planthopper (BPH) is one of the most destructive pests in rice production. The pyramiding application of BPH-resistance genes BPH14 and BPH15 can effectively improve rice resistance to BPH, however, the molecular mechanisms underlying BPH14/BPH15 pyramiding lines are poorly understood. Here, a mRNA expression profiling analysis was performed on the near isogenic lines (NILs) containing the BPH14, BPH15 or BPH14/BPH15 and their recurrent parent (RP) Wushansimiao. A total of 14492 differentially expressed mRNAs (DEGs) were identified from 12 mRNA profiles of resistant NILs and RP at different feeding stages. In the transcriptome analysis, 531 DEGs appeared to be common among the resistant NILs compared to RP before and after BPH feeding, which were enriched in defense response, phosphorylation and salt stress response. In addition, 258 DEGs shared only in resistant NILs were obtained among the different feeding stages, which were enriched in oxidative stress response, karrikin response and chloroplast organization. 21 DEGs were further selected as candidates for BPH resistance. OsPOX8.1, a potential candidate DEG related to BPH resistance, increased reactive oxygen species levels in rice protoplast. Our results provide valuable information to further explore the defense mechanism of insect-resistant gene pyramiding lines and develop robust strategies for insect control.

2023-07-03 | GSE232449 | GEO

Pinus mtDNA Assembly

Project description:Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus

| PRJEB18435 | ENA