Ontology highlight
ABSTRACT:
PROVIDER: PRJNA483508 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7624610_1.fastq.gz | Fastqsanger.gz | |||
| SRR7624610_2.fastq.gz | Fastqsanger.gz | |||
| SRR7624611_1.fastq.gz | Fastqsanger.gz | |||
| SRR7624611_2.fastq.gz | Fastqsanger.gz | |||
| SRR7624612_1.fastq.gz | Fastqsanger.gz |
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Project description:Tung oil, the major product of tung tree (Vernicia fordii) seeds, is one of the highest quality oils for industrial applications and has been considered to the production of biodiesel. Because of the poor agronomical traits of this crop, efforts have been made to breed tung tree for higher fruit yield and for modification of oil properties to be used as biodiesel, or to engineer higher yielding plants to produce tung oil. However, these efforts have been hampered by the lack of molecular information since there is no available genome and the identified and characterized transcripts of tung are scarce. Furthermore, there are still many knowledge gaps regarding tung oil biosynthesis. To provide a comprehensive and accurate foundation for molecular studies of tung tree, herein we present the reference transcriptome dataset of tung mature seeds. A set of 43,081,927 ESTs were assembled into 47,585 unigenes. The homology search using blastx against the GenBank non-redundant protein database and the Swiss-Prot database resulted in the annotation of 96 % and 81% of the unigenes, respectively. We also systematically arranged the series of transcripts potentially associated with oil biosynthesis and breakdown and examined the expression profile of a subset of those genes in samples from different stages of seed development, providing a valuable source of genes and transcriptional information related to these pathways. This study represents the first large-scale transcriptome annotation of tung tree seeds and will be useful to breed tung for oil properties and other agronomical traits.
2017-04-09 | GSE56652 | GEO
Project description:Background: Vernicia fordii (Tung oil tree) is a popular tree for biodiesel production in China. Unfortunately, the devastating Fusarium wilt disease caused great losses in production. Its sister species (Vernicia montana) was shown resistant to this pathogen. Vernicia fordii and Vernicia montana are main Vernicia species. V. fordii owns superior oil and agronomic traits, but susceptible to tung wilt disease, while V. nontana is resistant the wilt. However, the plants response mechanism remains largely unknown. Method: To define the divergence of gene expression modules between the resistant and susceptible Vernicia species responding to tung wilt pathogen, we generated comparative transcriptome atlases of two species during the process of infection with the pathogen F. oxysporum by RNA Sequencing in three biological replicates. Results: We describe the de novo assembly of the transcriptome of V. fordii and V. montana, comprising 258,430 and 245,240 non-redundant transcripts with N50 of 1,776 and 2,452 respectively. About 44,310 pair of putatively one-to-one orthologous genes between V. fordii and V. montana transcriptoms were identified. Overall, a high proportion of orthologous genes shared remarkably similar expression mode between Vernicia species. K means clustering indicated 2 cluster appear opposite expression mode. The highly connected gene expression analysis were conducted among genes with significantly differential expression mode, and the result indicated D6PK and LRR-RLK CLAVATA2 were top hub genes and hub genes glycosyltransferase (Gts), GLABRA2, PERK15 and EREBP-like factor were significantly associated with pathologic grades in resistant V. montana. Moreover, the result showed the resistant is a crucial signaling network, where MAPK signaling pathway, Plant-pathogen interaction, Circadian rhythm, Calcium signaling pathway and apoptosis fulfill distinct function. Additionally, dozens of unigenes were validated by quantitative real-time PCR (qRT-PCR). The study provided insight into the resistance gene expression modules. Conclusion: We first conducted a system analyses of the dynamics of gene expression both in susceptible and resistant Vernicia species with pathogen F. oxysporum infection. The results will serve as the important foundation to further deeply validation the resistance mechanism and breeding of the woody biodiesel plants V. fordii and V. montana.
2017-02-08 | GSE80228 | GEO
Project description:Tung tree (Vernicia fordii) provides the sole source of tung oil widely used in industry. Transcriptome or Gene expression
| PRJNA242689 | ENA
Project description:Transcriptome of tung tree sees with emphasis on genes from lipid metabolism
| PRJNA244238 | ENA
Project description:We conducted micro-array analysis to quantify the global transcriptome variations in floral organs of a male and female tree allowing for identification of sex-linked transcripts. We used RNA samples from male floral buds in August and female floral buds in September. Bud scale were removed. While the sampling time differed, the developmental stage of the floral organs was similar between the male and female. Five independent samples of floral bud tissues with bud scales removes were collected from the upper crown of a sexually mature male tree and female tree. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array.
2011-12-29 | E-GEOD-29336 | biostudies-arrayexpress
Project description:We conducted micro-array analysis to quantify the global transcriptome variations in floral buds through the course of the year allowing for identification of changing developmental signals. We used RNA samples from floral buds, with bud scale removed, in the upper crown of a sexually mature Populus deltoides tree 2 hours after sunrise. Three independent samples of floral bud tissues with bud scales removes were collected from the upper crown of a single sexually mature male tree. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array.
2011-12-29 | E-GEOD-29335 | biostudies-arrayexpress