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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.


Length distribution of unigenes in switchgrass. The horizontal coordinates are unigene lengths and the vertical coordinates are numbers of unigenes.
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Figure 2: Length distribution of unigenes in switchgrass. The horizontal coordinates are unigene lengths and the vertical coordinates are numbers of unigenes.

Mentions: Utilizing the Trinity de novo assembly program (Grabherr et al., 2011), 133,828 unigenes were detected. The total length for unigenes was 165,666,331 nt, with an average length of 1,238 nt and N50 of 1,890 nt. In total 38,027 transcripts (28.41%) had a length of 1–2 kb, 16,443 transcripts (12.29%) had a length of 2–3 kb, and 9,248 transcripts (6.91%) were longer than 3 kb. Approximately half of the unigenes (63,918) were >1 kb (Figure 2). These results indicate that high-quality transcriptome data were captured in this study. These datasets will provide a beneficial contribution to the transcriptome of switchgrass (Wang et al., 2012; Wilson et al., 2013; Xie et al., 2014).


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)

Length distribution of unigenes in switchgrass. The horizontal coordinates are unigene lengths and the vertical coordinates are numbers of unigenes.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Length distribution of unigenes in switchgrass. The horizontal coordinates are unigene lengths and the vertical coordinates are numbers of unigenes.
Mentions: Utilizing the Trinity de novo assembly program (Grabherr et al., 2011), 133,828 unigenes were detected. The total length for unigenes was 165,666,331 nt, with an average length of 1,238 nt and N50 of 1,890 nt. In total 38,027 transcripts (28.41%) had a length of 1–2 kb, 16,443 transcripts (12.29%) had a length of 2–3 kb, and 9,248 transcripts (6.91%) were longer than 3 kb. Approximately half of the unigenes (63,918) were >1 kb (Figure 2). These results indicate that high-quality transcriptome data were captured in this study. These datasets will provide a beneficial contribution to the transcriptome of switchgrass (Wang et al., 2012; Wilson et al., 2013; Xie et al., 2014).

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.