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De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

ABSTRACT: Purpose: The goals of this study are to compare the gene expression profiling for drought treated and control plants by using NGS. Methods: The four RNA samples were pooled to one, using equivalent quantities of each sample for transctiptome sequencing. Meanwhile, the four RNA samples were used to construct the library for DGE sequencing. Results: Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length=728 bp).In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified.

ORGANISM(S): Haloxylon ammodendron

PROVIDER: GSE63970 | GEO | 2014/12/20

SECONDARY ACCESSION(S): PRJNA269636

REPOSITORIES: GEO

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De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

Project description:Purpose: The goals of this study are to compare the gene expression profiling for drought treated and control plants by using NGS. Methods: The four RNA samples were pooled to one, using equivalent quantities of each sample for transctiptome sequencing. Meanwhile, the four RNA samples were used to construct the library for DGE sequencing. Results: Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length=728 bp).In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. H. ammodendron seedlings grew for one month, and then one set of seedlings were treated with a one-week (7d) stress, and the second set of seedlings was used as a control and received no treatment. Each treatment was with two replicates.

2014-12-20 | E-GEOD-63970 | biostudies-arrayexpress

Transcriptome analysis of drought treated Caragana korshinskii and control

Project description:To discover the molecular events that occur during exposure to drought, two digital gene expression (DGE) libraries were constructed by sequencing RNA extracted from two pools of control and drought-treated plants using Illumina technology.

2019-06-14 | GSE132673 | GEO

Whole-genome transcriptomic analysis in Sorghum bicolor variety M35-1

Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in grain sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

2023-12-31 | GSE178603 | GEO

Whole-genome transcriptomic analysis from stem internodes in Sorghum bicolor variety ICSV12012

Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

2023-12-31 | GSE178993 | GEO

Whole-genome transcriptomic analysis in Sorghum bicolor variety CSV24SS

Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

2023-12-31 | GSE155194 | GEO

Host transcriptome response to Lumpy Skin Disease (LSD) infection depends on the challenging virus strain

Project description:Ten cattle have been challenged with two Lumpy Skin Disease Virus (LSDV). They were sampled for whole blood immediately before (pre) and three and seven days after (post) infection challenge with two virus strains (H vs. O). The whole RNA-sequencing was done, and 150bp paired reads were assembled as the transcriptome. It was then computationally analyzed to find the differentially expressed genes (DGE) that enrich the gene ontology (GO) terms and KEGG pathways. Depending on the challenged LSDV strain, they influence the host response differently.

2023-06-15 | E-MTAB-12965 | biostudies-arrayexpress

Genome-wide transcriptome analysis of rice in response to controlled drought stress at vegetative

Project description:In this study, genome-wide transcriptome profiling was used to understand molecular genetic mechanism of drought tolerance in rice. Illumina High-Seq 2000 platform was used for sequencing RNA from leaf tissue of rice plants exposed to controlled drought stress and well-watered conditions. The differentially expressed genes were used to identify biological process and cis-regulatory elements enriched under drought stress compared to well-watered conditions. Oryza sativa ssp. japonica cv. Nipponbare plants were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.

2015-01-16 | E-GEOD-65022 | biostudies-arrayexpress

Transcriptome analysis of Osbhlh148 mutant plants under controlled drought stress and well-watered conditions at vegetative stage

Project description:The members of bHLH transcription factor superfamily are known to play key role in plant development and abiotic stress response. Loss-of-function of OsbHLH148 gene resulted in increased sensitivity of rice plants to drought stress. To identify the targets of OsbHLH148 and dissect the drought stress response pathway regulated by it, we performed transcriptome profiling of Osbhlh148 mutant plants under drought stress as well as well-watered conditions by RNA-sequencing. OsbHLH148 loss-of-function rice plants (Oryza sativa ssp. japonica cv. Nipponbare) were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.

2015-01-16 | E-GEOD-65024 | biostudies-arrayexpress

Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage

Project description:Heat shock factors (Hsfs) are known to regulate heat and drought stress response by controlling the expression of heat shock proteins and oxidative stress responsive genes. Loss-of-function of OsHSFA2e gene resulted in increased sensitivity of rice plants to drought and heat stress. To identify the targets of OsHSFA2e and dissect the stress response pathway regulated by it, we performed transcriptome profiling of Oshsfa2e mutant plants under drought stress as well as well-watered conditions by RNA-sequencing. OsHSFA2e loss-of-function rice plants (Oryza sativa ssp. japonica cv. Nipponbare) were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.

2015-01-16 | E-GEOD-65025 | biostudies-arrayexpress

Identification of drought resistance related factors in Quercus liaotungensis leaf via transcriptome sequencing

Project description:Purpose: The goal of this study is to screen the candidate genes involved in drought avoidance of Q. liaotungensis Methods:The Q. liaotungensis leaves were generated by deep sequencing, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The transcriptome were de novo assembly. Results:A total of 54153182 raw reads were obtained from Illumina sequencing platform, and 53021436 clean reads were generated after filtering out the low quality reads. The clean reads were assembled into 41207 transcripts with median length 704 and GC content 42.17%, and 25593 unigenes with median length 687 and GC content 42.31%, based on Trinity assembly platform Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. liaotungensis to obtain the transcriptome. De novo assembly was then applied followed by gene annotation and functional classification. The SSRs and SNPs were also obtained using assembled transcripts as reference sequences. The results of this study lay the foundation for further research on genetic diversity of Quercus.

2019-01-29 | GSE125798 | GEO

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