De novo assembly in defense against pests in Pinus massoniana
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ABSTRACT:
ORGANISM(S): Pinus massoniana
PROVIDER: GSE72294 | GEO | 2015/08/24
SECONDARY ACCESSION(S): PRJNA293676
REPOSITORIES: GEO
Similar Datasets
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
Project description:De novo assembly in defense against pests in Pinus massoniana
| PRJNA293676 | ENA
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
Project description:Pines are the most important tree species to the international forestry industry, covering 42 % of the global industrial forest plantation area. One of the most pressing threats to cultivation of some pine species is the pitch canker fungus, Fusarium circinatum, which can have devastating effects in both the field and nursery. Investigation of the Pinus-F. circinatum host-pathogen interaction is crucial for development of effective disease management strategies. As with many non-model organisms, investigation of host-pathogen interactions in pine species is hampered by limited genomic resources. This was partially alleviated through release of the 22 Gbp Pinus taeda v1.01 genome sequence ( http://pinegenome.org/pinerefseq/ ) in 2014. Despite the fact that the fragmented state of the genome may hamper comprehensive transcriptome analysis, it is possible to leverage the inherent redundancy resulting from deep RNA sequencing with Illumina short reads to assemble transcripts in the absence of a completed reference sequence. These data can then be integrated with available genomic data to produce a comprehensive transcriptome resource. The aim of this study was to provide a foundation for gene expression analysis of disease response mechanisms in Pinus patula through transcriptome assembly.Eighteen de novo and two reference based assemblies were produced for P. patula shoot tissue. For this purpose three transcriptome assemblers, Trinity, Velvet/OASES and SOAPdenovo-Trans, were used to maximise diversity and completeness of assembled transcripts. Redundancy in the assembly was reduced using the EvidentialGene pipeline. The resulting 52 Mb P. patula v1.0 shoot transcriptome consists of 52 112 unigenes, 60 % of which could be functionally annotated.The assembled transcriptome will serve as a major genomic resource for future investigation of P. patula and represents the largest gene catalogue produced to date for this species. Furthermore, this assembly can help detect gene-based genetic markers for P. patula and the comparative assembly workflow could be applied to generate similar resources for other non-model species.
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Project description:The transcriptome of PpNAC1 RNAi Pinus pinaster plantlets (60 days) were analyzed.
2018-01-22 | GSE89341 | GEO
Project description:Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
| S-EPMC6778806 | biostudies-literature
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
Project description:Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora.
| S-EPMC4691086 | biostudies-literature
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
Project description:Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus
| PRJEB18435 | ENA