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Genome-wide transcriptome analysis to identify genes involved in adventitious root formation of ramie (Boehmeria nivea L. Gaud) cutting

ABSTRACT: Genome-wide transcriptome analysis to identify genes involved in adventitious root formation of ramie (Boehmeria nivea L. Gaud) cutting

PROVIDER: PRJNA476939 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7405020_1.fastq.gz	Fastqsanger.gz
	SRR7405020_2.fastq.gz	Fastqsanger.gz
	SRR7405030_1.fastq.gz	Fastqsanger.gz
	SRR7405030_2.fastq.gz	Fastqsanger.gz
	SRR7405021_1.fastq.gz	Fastqsanger.gz

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Genome-wide transcriptome analysis to identify genes involved in adventitious root formation of ramie (Boehmeria nivea L. Gaud) cutting

Project description:Two ramie cultivars, Zhongzhu no 2(Z2) and Huazhu no 4 (H4), showed constructing adventitious root formation (ARF) rate. Comparative transcriptome analysis was performed to study gene expression profiles in Z2 and H4 ramie during adventitious root formation. Illumina sequencing yielded a total of 92,794,556,688 bases data, and about 301.47 M and 313.06 M raw reads for Z2 and H4 plants, respectively. After quality control, every library obtained over 43 million reads, which is enough for the quantitative analysis of gene expression. Using Trinity software, these clean reads were first assembled into 121,492 transcripts, finally into 66,881 unigenes with an average length of 1144.25 bp. About 148.74 M and 138.72 M clean reads of H4 and Z2 were mapped to reference genes via Bowtie, respectively. The ratio of mapped clean reads for eight libraries ranged from 74.47% to 75.38% (average: 74.8%). By comparing gene expression levels in Tm and CK ramie stems, we identified 772 DEGs in H4 plants during RPF, including 7220 up-regulated and 8154 down-regulated DEGs. We identified 1256 DEGs in Z2 plants during RPF, which included 779 up-regulated and 447 down-regulated DEGs. We also identified 1919 DEGs between Z2 and H4 plants. There were 1147 (731 up-regulate and 416 down-regulated) DEGs uniquely in Z2, and 603 (202 up-regulate and 461 down-regulated) DEGs uniquely in H4 plants. The two genotypes shared 109 DEGs, which indicates some common pathways during ARF.

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Project description:Identification of drought stress-responsive transcription factor in ramie (Boehmeria nivea L．Gaud)

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Identification of drought stress-responsive transcription factor in ramie (Boehmeria nivea L．Gaud)

Project description:Drought is a main environment stress which severely inhibits the stem growth of ramie and lead to a decrease of the fiber yield. The mechanisms of ramie responding to drought stress are poorly understood. Using Illumina sequencing, approximately 4.8 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from the drought-stressed ramie (DS), and about 4.7 M were sequenced in the cDNA library constructed from the control ramie under well water condition (CO). The tags generated from two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in two libraries revealed that 1101 and 505 genes were respectively up- and down- regulated under drought stress. Pathway enrichment analysis identified a set of significantly enriched pathways of DEGs. A series of candidate genes and pathways that may contribute to drought tolerance in ramie will be helpful for further improving ramie drought tolerance ability.

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