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De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress.
Gene. 2013 Aug 01; 525(1):26-34.GENE

Abstract

Salinity stress is one of the most serious factors that impede the growth and development of various crops. Wild Gossypium species, which are remarkably tolerant to salt water immersion, are valuable resources for understanding salt tolerance mechanisms of Gossypium and improving salinity resistance in upland cotton. To generate a broad survey of genes with altered expression during various stages of salt stress, a mixed RNA sample was prepared from the roots and leaves of Gossypium aridum plants subjected to salt stress. The transcripts were sequenced using the Illumina sequencing platform. After cleaning and quality checks, approximately 41.5 million clean reads were obtained. Finally, these reads were eventually assembled into 98,989 unigenes with a mean size of 452 bp. All unigenes were compared to known cluster of orthologous groups (COG) sequences to predict and classify the possible functions of these genes, which were classified into at least 25 molecular families. Variations in gene expression were then examined after exposing the plants to 200 mM NaCl for 3, 12, 72 or 144 h. Sequencing depths of approximately six million raw tags were achieved for each of the five stages of salt stress. There were 2634 (1513 up-regulated/1121 down-regulated), 2449 (1586 up-regulated/863 down-regulated), 2271 (946 up-regulated/1325 down-regulated) and 3352 (933 up-regulated/2419 down-regulated) genes that were differentially expressed after exposure to NaCl for 3, 12, 72 and 144 h, respectively. Digital gene expression analysis indicated that pathways involved in "transport", "response to hormone stimulus" and "signaling" play important roles during salt stress, while genes involved in "protein kinase activity" and "transporter activity" undergo major changes in expression during early and later stages of salt stress, respectively.

Authors+Show Affiliations

Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, PR China.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23651590

Citation

Xu, Peng, et al. "De Novo Transcriptome Sequencing and Comparative Analysis of Differentially Expressed Genes in Gossypium Aridum Under Salt Stress." Gene, vol. 525, no. 1, 2013, pp. 26-34.
Xu P, Liu Z, Fan X, et al. De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress. Gene. 2013;525(1):26-34.
Xu, P., Liu, Z., Fan, X., Gao, J., Zhang, X., Zhang, X., & Shen, X. (2013). De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress. Gene, 525(1), 26-34. https://doi.org/10.1016/j.gene.2013.04.066
Xu P, et al. De Novo Transcriptome Sequencing and Comparative Analysis of Differentially Expressed Genes in Gossypium Aridum Under Salt Stress. Gene. 2013 Aug 1;525(1):26-34. PubMed PMID: 23651590.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress. AU - Xu,Peng, AU - Liu,Zhangwei, AU - Fan,Xinqi, AU - Gao,Jin, AU - Zhang,Xia, AU - Zhang,Xianggui, AU - Shen,Xinlian, Y1 - 2013/05/04/ PY - 2012/12/14/received PY - 2013/04/14/revised PY - 2013/04/22/accepted PY - 2013/5/9/entrez PY - 2013/5/9/pubmed PY - 2013/11/14/medline SP - 26 EP - 34 JF - Gene JO - Gene VL - 525 IS - 1 N2 - Salinity stress is one of the most serious factors that impede the growth and development of various crops. Wild Gossypium species, which are remarkably tolerant to salt water immersion, are valuable resources for understanding salt tolerance mechanisms of Gossypium and improving salinity resistance in upland cotton. To generate a broad survey of genes with altered expression during various stages of salt stress, a mixed RNA sample was prepared from the roots and leaves of Gossypium aridum plants subjected to salt stress. The transcripts were sequenced using the Illumina sequencing platform. After cleaning and quality checks, approximately 41.5 million clean reads were obtained. Finally, these reads were eventually assembled into 98,989 unigenes with a mean size of 452 bp. All unigenes were compared to known cluster of orthologous groups (COG) sequences to predict and classify the possible functions of these genes, which were classified into at least 25 molecular families. Variations in gene expression were then examined after exposing the plants to 200 mM NaCl for 3, 12, 72 or 144 h. Sequencing depths of approximately six million raw tags were achieved for each of the five stages of salt stress. There were 2634 (1513 up-regulated/1121 down-regulated), 2449 (1586 up-regulated/863 down-regulated), 2271 (946 up-regulated/1325 down-regulated) and 3352 (933 up-regulated/2419 down-regulated) genes that were differentially expressed after exposure to NaCl for 3, 12, 72 and 144 h, respectively. Digital gene expression analysis indicated that pathways involved in "transport", "response to hormone stimulus" and "signaling" play important roles during salt stress, while genes involved in "protein kinase activity" and "transporter activity" undergo major changes in expression during early and later stages of salt stress, respectively. SN - 1879-0038 UR - https://www.unboundmedicine.com/medline/citation/23651590/De_novo_transcriptome_sequencing_and_comparative_analysis_of_differentially_expressed_genes_in_Gossypium_aridum_under_salt_stress_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0378-1119(13)00563-5 DB - PRIME DP - Unbound Medicine ER -