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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.


Cluster of Orthologous Group (COG) classification of DEGs and total unigenes in switchgrass tillering mutants.
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Figure 7: Cluster of Orthologous Group (COG) classification of DEGs and total unigenes in switchgrass tillering mutants.

Mentions: All of the DEGs were submitted to the COG database to search for functional prediction and classification, and 1,913 unigenes were assigned to 25 COG functional categories. Among these categories, the cluster of “function unknown” was the largest group, followed by “general function prediction”; “translation, ribosomal structure, and biogenesis”; “replication, recombination, and repair”; “transcription”; and “cell cycle control, cell division, and chromosome partitioning.” The smallest groups were “chromatin structure and dynamics,” “RNA processing and modification,” and “extracellular structures” (Figure 7). The percentage of unigenes involved in “coenzyme transport and metabolism”; “secondary metabolites biosynthesis, transport, and catabolism”; and “carbohydrate transport and metabolism” was higher in DEGs than in all unigenes considered together, indicating that these three functional categories are important for tiller development.


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)

Cluster of Orthologous Group (COG) 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 7: Cluster of Orthologous Group (COG) classification of DEGs and total unigenes in switchgrass tillering mutants.
Mentions: All of the DEGs were submitted to the COG database to search for functional prediction and classification, and 1,913 unigenes were assigned to 25 COG functional categories. Among these categories, the cluster of “function unknown” was the largest group, followed by “general function prediction”; “translation, ribosomal structure, and biogenesis”; “replication, recombination, and repair”; “transcription”; and “cell cycle control, cell division, and chromosome partitioning.” The smallest groups were “chromatin structure and dynamics,” “RNA processing and modification,” and “extracellular structures” (Figure 7). The percentage of unigenes involved in “coenzyme transport and metabolism”; “secondary metabolites biosynthesis, transport, and catabolism”; and “carbohydrate transport and metabolism” was higher in DEGs than in all unigenes considered together, indicating that these three functional categories are important for tiller development.

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.