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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.


Species distribution of the result of non-redundant (NR) annotation.
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Figure 4: Species distribution of the result of non-redundant (NR) annotation.

Mentions: Annotation was also analyzed to estimate the gene proportions of other plants represented in the switchgrass transcriptome data. According to the Nr annotation database, 63,335 (65.6%) unigenes were most closely related to genes of Setaria italica, 9,852 (10.20%) unigenes were most closely related to genes of Sorghum bicolor, and 7,478 (7.74%) unigenes were most closely to genes of Zea mays (Figure 4). These results indicated that millet was the best match among the translated switchgrass contig sequences, followed by sorghum and maize. Therefore, although switchgrass is polyploid, its gene space is not different from that of other grass (Wang et al., 2012).


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)

Species distribution of the result of non-redundant (NR) annotation.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Species distribution of the result of non-redundant (NR) annotation.
Mentions: Annotation was also analyzed to estimate the gene proportions of other plants represented in the switchgrass transcriptome data. According to the Nr annotation database, 63,335 (65.6%) unigenes were most closely related to genes of Setaria italica, 9,852 (10.20%) unigenes were most closely related to genes of Sorghum bicolor, and 7,478 (7.74%) unigenes were most closely to genes of Zea mays (Figure 4). These results indicated that millet was the best match among the translated switchgrass contig sequences, followed by sorghum and maize. Therefore, although switchgrass is polyploid, its gene space is not different from that of other grass (Wang et al., 2012).

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.