Limits...
Identification of Multiple Stress Responsive Genes by Sequencing a Normalized cDNA Library from Sea-Land Cotton (Gossypium barbadense L.).

Zhou B, Zhang L, Ullah A, Jin X, Yang X, Zhang X - PLoS ONE (2016)

Bottom Line: The blastx results demonstrated 2,746 unigenes showing significant similarity to known genes, 74 uniESTs displaying significant similarity to genes of predicted proteins, and 315 uniESTs remain uncharacterized.Annotation results showed that a huge number of genes respond to stress in our study, such as MYB-related, C2H2, FAR1, bHLH, bZIP, MADS, and mTERF.These results will improve our knowledge of stress tolerance in cotton.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China.

ABSTRACT

Background: Plants often face multiple stresses including drought, extreme temperature, salinity, nutrition deficiency and biotic stresses during growth and development. All the stresses result in a series of physiological and metabolic reactions and then generate reversible inhibition of metabolism and growth and can cause seriously irreversible damage, even death. At each stage of cotton growth, environmental stress conditions pose devastating threats to plant growth and development, especially yield and quality. Due to the complex stress conditions and unclear molecular mechanisms of stress response, there is an urgent need to explore the mechanisms of cotton response against abiotic stresses.

Methodology and principal findings: A normalized cDNA library was constructed using Gossypium barbadense Hai-7124 treated with different stress conditions (heat, cold, salt, drought, potassium and phosphorus deficit and Verticillium dahliae infection). Random sequencing of this library generated 6,047 high-quality expressed sequence tags (ESTs). The ESTs were clustered and assembled into 3,135 uniESTs, composed of 2,497 contigs and 638 singletons. The blastx results demonstrated 2,746 unigenes showing significant similarity to known genes, 74 uniESTs displaying significant similarity to genes of predicted proteins, and 315 uniESTs remain uncharacterized. Functional classification unveiled the abundance of uniESTs in binding, catalytic activity, and structural molecule activity. Annotations of the uniESTs by the plant transcription factor database (PlantTFDB) and Plant Stress Protein Database (PSPDB) disclosed that transcription factors and stress-related genes were enriched in the current library. The expression of some transcription factors and specific stress-related genes were verified by RT-PCR under various stress conditions.

Conclusions/significance: Annotation results showed that a huge number of genes respond to stress in our study, such as MYB-related, C2H2, FAR1, bHLH, bZIP, MADS, and mTERF. These results will improve our knowledge of stress tolerance in cotton. In addition, they are also helpful in discovering candidate genes related to stress tolerance. The publicly available ESTs from G. barbadense are a valuable genomic resource that will facilitate further molecular study and breeding of stress-tolerant cotton.

Show MeSH

Related in: MedlinePlus

Functional classifications of 2,678 uniESTs that were assigned GO terms.Tortadiagrams represented the second-level GO terms for three categories: cellular component (A), molecular function (B) and biological process (C). The histogram represents the GO term ‘Response to stimulus’ at level 4 (D).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4816313&req=5

pone.0152927.g004: Functional classifications of 2,678 uniESTs that were assigned GO terms.Tortadiagrams represented the second-level GO terms for three categories: cellular component (A), molecular function (B) and biological process (C). The histogram represents the GO term ‘Response to stimulus’ at level 4 (D).

Mentions: The GO categories MF, BP, and CC fell predominantly into two to four subcategories at the second level (Fig 4A–4D). Among the top 3 GO terms enriched in the CC class (second-level GO terms), terms of cell, organelle, and membrane were accumulated more compared to the other terms (Fig 4A); more category classifications (third-level GO terms) are shown in S2A Fig. In the MF class (second-level GO terms, as shown in the Fig 4B), mostly the GO terms were classified into two groups, i.e. binding (GO:0005488, 40.5%) and catalytic activity (GO:0003824, 39.4%). In the binding category, organic cyclic compound binding (GO:0097159, 14.3%), heterocyclic compound binding (GO: 1901363, 14.3%), ion binding (GO:0043167, 13.7%), and small molecule binding (GO:0036094, 8.8%) ranked the most enriched terms at third level. The highly enriched GO terms in catalytic activity covered transferase activity (GO:0016740, 6.8%), hydrolase activity (GO:0016787, 6.6%) and oxidoreductase activity (GO:0016491, 6.2%) (S2B Fig). For the biological process class, four categories with the GO terms cellular process (GO:0009987, 19.9%), metabolic process (GO:0008152, 19.7%), single-organism process (GO:0044699, 16.4%) and response to stimulus (GO:0050896, 10.1%) were dominantly enriched, which accounted for 66.1% of the assigned uniESTs (Fig 4C); more category classifications at the third level for the category biological process are shown in S2C Fig. The level 4 response to stimulus category mainly consists of ‘response to inorganic substance’, ‘response to oxygen-containing compound’, ‘defense response’, ‘response to osmotic stress’, ‘response to other organism’, ‘response to temperature stimulus’ and others (Fig 4D), which included most stress responses from among our previous treatments.


Identification of Multiple Stress Responsive Genes by Sequencing a Normalized cDNA Library from Sea-Land Cotton (Gossypium barbadense L.).

Zhou B, Zhang L, Ullah A, Jin X, Yang X, Zhang X - PLoS ONE (2016)

Functional classifications of 2,678 uniESTs that were assigned GO terms.Tortadiagrams represented the second-level GO terms for three categories: cellular component (A), molecular function (B) and biological process (C). The histogram represents the GO term ‘Response to stimulus’ at level 4 (D).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4816313&req=5

pone.0152927.g004: Functional classifications of 2,678 uniESTs that were assigned GO terms.Tortadiagrams represented the second-level GO terms for three categories: cellular component (A), molecular function (B) and biological process (C). The histogram represents the GO term ‘Response to stimulus’ at level 4 (D).
Mentions: The GO categories MF, BP, and CC fell predominantly into two to four subcategories at the second level (Fig 4A–4D). Among the top 3 GO terms enriched in the CC class (second-level GO terms), terms of cell, organelle, and membrane were accumulated more compared to the other terms (Fig 4A); more category classifications (third-level GO terms) are shown in S2A Fig. In the MF class (second-level GO terms, as shown in the Fig 4B), mostly the GO terms were classified into two groups, i.e. binding (GO:0005488, 40.5%) and catalytic activity (GO:0003824, 39.4%). In the binding category, organic cyclic compound binding (GO:0097159, 14.3%), heterocyclic compound binding (GO: 1901363, 14.3%), ion binding (GO:0043167, 13.7%), and small molecule binding (GO:0036094, 8.8%) ranked the most enriched terms at third level. The highly enriched GO terms in catalytic activity covered transferase activity (GO:0016740, 6.8%), hydrolase activity (GO:0016787, 6.6%) and oxidoreductase activity (GO:0016491, 6.2%) (S2B Fig). For the biological process class, four categories with the GO terms cellular process (GO:0009987, 19.9%), metabolic process (GO:0008152, 19.7%), single-organism process (GO:0044699, 16.4%) and response to stimulus (GO:0050896, 10.1%) were dominantly enriched, which accounted for 66.1% of the assigned uniESTs (Fig 4C); more category classifications at the third level for the category biological process are shown in S2C Fig. The level 4 response to stimulus category mainly consists of ‘response to inorganic substance’, ‘response to oxygen-containing compound’, ‘defense response’, ‘response to osmotic stress’, ‘response to other organism’, ‘response to temperature stimulus’ and others (Fig 4D), which included most stress responses from among our previous treatments.

Bottom Line: The blastx results demonstrated 2,746 unigenes showing significant similarity to known genes, 74 uniESTs displaying significant similarity to genes of predicted proteins, and 315 uniESTs remain uncharacterized.Annotation results showed that a huge number of genes respond to stress in our study, such as MYB-related, C2H2, FAR1, bHLH, bZIP, MADS, and mTERF.These results will improve our knowledge of stress tolerance in cotton.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China.

ABSTRACT

Background: Plants often face multiple stresses including drought, extreme temperature, salinity, nutrition deficiency and biotic stresses during growth and development. All the stresses result in a series of physiological and metabolic reactions and then generate reversible inhibition of metabolism and growth and can cause seriously irreversible damage, even death. At each stage of cotton growth, environmental stress conditions pose devastating threats to plant growth and development, especially yield and quality. Due to the complex stress conditions and unclear molecular mechanisms of stress response, there is an urgent need to explore the mechanisms of cotton response against abiotic stresses.

Methodology and principal findings: A normalized cDNA library was constructed using Gossypium barbadense Hai-7124 treated with different stress conditions (heat, cold, salt, drought, potassium and phosphorus deficit and Verticillium dahliae infection). Random sequencing of this library generated 6,047 high-quality expressed sequence tags (ESTs). The ESTs were clustered and assembled into 3,135 uniESTs, composed of 2,497 contigs and 638 singletons. The blastx results demonstrated 2,746 unigenes showing significant similarity to known genes, 74 uniESTs displaying significant similarity to genes of predicted proteins, and 315 uniESTs remain uncharacterized. Functional classification unveiled the abundance of uniESTs in binding, catalytic activity, and structural molecule activity. Annotations of the uniESTs by the plant transcription factor database (PlantTFDB) and Plant Stress Protein Database (PSPDB) disclosed that transcription factors and stress-related genes were enriched in the current library. The expression of some transcription factors and specific stress-related genes were verified by RT-PCR under various stress conditions.

Conclusions/significance: Annotation results showed that a huge number of genes respond to stress in our study, such as MYB-related, C2H2, FAR1, bHLH, bZIP, MADS, and mTERF. These results will improve our knowledge of stress tolerance in cotton. In addition, they are also helpful in discovering candidate genes related to stress tolerance. The publicly available ESTs from G. barbadense are a valuable genomic resource that will facilitate further molecular study and breeding of stress-tolerant cotton.

Show MeSH
Related in: MedlinePlus