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De novo assembly and transcriptome analysis of two contrary tillering mutants to learn the mechanisms of tillers outgrowth in switchgrass (Panicum virgatum L.).

Xu K, Sun F, Chai G, Wang Y, Shi L, Liu S, Xi Y - Front Plant Sci (2015)

Bottom Line: Alteration of tillering ability resulted from different tiller buds outgrowth in the two mutants.In the de novo assembly results, 133,828 unigenes were detected with an average length of 1,238 bp, and 5,290 unigenes were differentially expressed between the two mutants, including 3,225 up-regulated genes and 2,065 down-regulated genes.This is the first study to explore the tillering transcriptome in two types of tillering mutants by de novo sequencing.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University Yangling, China ; Institute of Cotton Research of CAAS Anyang, China.

ABSTRACT
Tillering is an important trait in monocotyledon plants. The switchgrass (Panicum virgatum), studied usually as a source of biomass for energy production, can produce hundreds of tillers in its lifetime. Studying the tillering of switchgrass also provides information for other monocot crops. High-tillering and low-tillering mutants were produced by ethyl methanesulfonate mutagenesis. Alteration of tillering ability resulted from different tiller buds outgrowth in the two mutants. We sequenced the tiller buds transcriptomes of high-tillering and low-tillering plants using next-generation sequencing technology, and generated 34 G data in total. In the de novo assembly results, 133,828 unigenes were detected with an average length of 1,238 bp, and 5,290 unigenes were differentially expressed between the two mutants, including 3,225 up-regulated genes and 2,065 down-regulated genes. Differentially expressed gene analysis with functional annotations was performed to identify candidate genes involved in tiller bud outgrowth processes using Gene Ontology classification, Cluster of Orthologous Groups of proteins, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This is the first study to explore the tillering transcriptome in two types of tillering mutants by de novo sequencing.

No MeSH data available.


Gene Ontology (GO) functional classification of DEGs and total unigenes in switchgrass tillering mutants.
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Figure 6: Gene Ontology (GO) functional classification of DEGs and total unigenes in switchgrass tillering mutants.

Mentions: Using the GO annotation, 2,260 DEGs were assigned to 50 subcategories. Among them, 1,752 DEGs were involved in biological processes, 1,781 DEGs were related to cellular components, and 1,875 DEGs were grouped under molecular functions. Within the biological process category, the most represented DEGs classified as “metabolic process,” “cellular process,” and “single-organism process.” Within the cellular component category, the most represented DEGs were classified as “cell,” “cell part,” and “organelle.” Within the molecular function category, the largest proportion of DEGs was classified as “binding,” “catalytic activity” and “transporter activity” (Figure 6). Compared to the GO classification of DEGs and all unigenes, the proportion of unigenes from DEGs involved in “electron carrier activity,” “antioxidant activity,” and “enzyme regulator activity” was larger than that of all unigenes, indicating that these DEGs may be involved in tillering.


De novo assembly and transcriptome analysis of two contrary tillering mutants to learn the mechanisms of tillers outgrowth in switchgrass (Panicum virgatum L.).

Xu K, Sun F, Chai G, Wang Y, Shi L, Liu S, Xi Y - Front Plant Sci (2015)

Gene Ontology (GO) functional classification of DEGs and total unigenes in switchgrass tillering mutants.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4584987&req=5

Figure 6: Gene Ontology (GO) functional classification of DEGs and total unigenes in switchgrass tillering mutants.
Mentions: Using the GO annotation, 2,260 DEGs were assigned to 50 subcategories. Among them, 1,752 DEGs were involved in biological processes, 1,781 DEGs were related to cellular components, and 1,875 DEGs were grouped under molecular functions. Within the biological process category, the most represented DEGs classified as “metabolic process,” “cellular process,” and “single-organism process.” Within the cellular component category, the most represented DEGs were classified as “cell,” “cell part,” and “organelle.” Within the molecular function category, the largest proportion of DEGs was classified as “binding,” “catalytic activity” and “transporter activity” (Figure 6). Compared to the GO classification of DEGs and all unigenes, the proportion of unigenes from DEGs involved in “electron carrier activity,” “antioxidant activity,” and “enzyme regulator activity” was larger than that of all unigenes, indicating that these DEGs may be involved in tillering.

Bottom Line: Alteration of tillering ability resulted from different tiller buds outgrowth in the two mutants.In the de novo assembly results, 133,828 unigenes were detected with an average length of 1,238 bp, and 5,290 unigenes were differentially expressed between the two mutants, including 3,225 up-regulated genes and 2,065 down-regulated genes.This is the first study to explore the tillering transcriptome in two types of tillering mutants by de novo sequencing.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University Yangling, China ; Institute of Cotton Research of CAAS Anyang, China.

ABSTRACT
Tillering is an important trait in monocotyledon plants. The switchgrass (Panicum virgatum), studied usually as a source of biomass for energy production, can produce hundreds of tillers in its lifetime. Studying the tillering of switchgrass also provides information for other monocot crops. High-tillering and low-tillering mutants were produced by ethyl methanesulfonate mutagenesis. Alteration of tillering ability resulted from different tiller buds outgrowth in the two mutants. We sequenced the tiller buds transcriptomes of high-tillering and low-tillering plants using next-generation sequencing technology, and generated 34 G data in total. In the de novo assembly results, 133,828 unigenes were detected with an average length of 1,238 bp, and 5,290 unigenes were differentially expressed between the two mutants, including 3,225 up-regulated genes and 2,065 down-regulated genes. Differentially expressed gene analysis with functional annotations was performed to identify candidate genes involved in tiller bud outgrowth processes using Gene Ontology classification, Cluster of Orthologous Groups of proteins, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This is the first study to explore the tillering transcriptome in two types of tillering mutants by de novo sequencing.

No MeSH data available.