Limits...
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.


Concordant Differentially expressed genes (DEGs) of ht and lt from two generations. (A) DEGs of H-1 and H-2, and L-1 and L-2 are indicated in blue; those of H-3 and H-4, and L-3 and L-4 are indicated in pink. The overlap region indicates the number of common DEGs in the two groups. (B) The number of concordant up-regulated and down-regulated DEGs excluding unigenes with contrary variation trend in the two groups.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4584987&req=5

Figure 5: Concordant Differentially expressed genes (DEGs) of ht and lt from two generations. (A) DEGs of H-1 and H-2, and L-1 and L-2 are indicated in blue; those of H-3 and H-4, and L-3 and L-4 are indicated in pink. The overlap region indicates the number of common DEGs in the two groups. (B) The number of concordant up-regulated and down-regulated DEGs excluding unigenes with contrary variation trend in the two groups.

Mentions: Tillering with monocots is a well-known agronomic trait that involves a complicated development process. Although many genes and their mechanisms of regulating tillering have been extensively studied in plants, the mechanisms underlying tillering remain to be elucidated. In this study, DEGs were identified from H1 and H2 and L1 and L2 at the same generation (FDR < 0.001, Log2ratio > 1). Other DEG data were from H3 and H4, and L3 and L4 of another generation. Thus, 5,410 DEGs from the two experimental groups were detected (Figure 5A). In total, 5,290 DEGs, including 3,225 up-regulated DEGs and 2,065 down-regulated DEGs, were selected for subsequent study, excluding the unigenes with a contrary variation trend in the two groups (Figure 5B). For 2,526 (47.75%) unigenes, including 1,279 up-regulated and 1,247 down-regulated genes, the log2 (L/H) was 1–3, and differential expression was thus not observed in these two mutants. In contrast, in 839 unigenes (104 up-regulated and 735 down-regulated), the log2 (L/H) exceeded 10, and these genes were thus significantly up-regulated or down-regulated in the two mutants (Table 3). These differentially expressed unigenes underlie the difference in tillering ability in the two mutants.


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)

Concordant Differentially expressed genes (DEGs) of ht and lt from two generations. (A) DEGs of H-1 and H-2, and L-1 and L-2 are indicated in blue; those of H-3 and H-4, and L-3 and L-4 are indicated in pink. The overlap region indicates the number of common DEGs in the two groups. (B) The number of concordant up-regulated and down-regulated DEGs excluding unigenes with contrary variation trend in the two groups.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Concordant Differentially expressed genes (DEGs) of ht and lt from two generations. (A) DEGs of H-1 and H-2, and L-1 and L-2 are indicated in blue; those of H-3 and H-4, and L-3 and L-4 are indicated in pink. The overlap region indicates the number of common DEGs in the two groups. (B) The number of concordant up-regulated and down-regulated DEGs excluding unigenes with contrary variation trend in the two groups.
Mentions: Tillering with monocots is a well-known agronomic trait that involves a complicated development process. Although many genes and their mechanisms of regulating tillering have been extensively studied in plants, the mechanisms underlying tillering remain to be elucidated. In this study, DEGs were identified from H1 and H2 and L1 and L2 at the same generation (FDR < 0.001, Log2ratio > 1). Other DEG data were from H3 and H4, and L3 and L4 of another generation. Thus, 5,410 DEGs from the two experimental groups were detected (Figure 5A). In total, 5,290 DEGs, including 3,225 up-regulated DEGs and 2,065 down-regulated DEGs, were selected for subsequent study, excluding the unigenes with a contrary variation trend in the two groups (Figure 5B). For 2,526 (47.75%) unigenes, including 1,279 up-regulated and 1,247 down-regulated genes, the log2 (L/H) was 1–3, and differential expression was thus not observed in these two mutants. In contrast, in 839 unigenes (104 up-regulated and 735 down-regulated), the log2 (L/H) exceeded 10, and these genes were thus significantly up-regulated or down-regulated in the two mutants (Table 3). These differentially expressed unigenes underlie the difference in tillering ability in the two mutants.

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.