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.


Distribution of unigenes annotated in different databases.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Distribution of unigenes annotated in different databases.

Mentions: Using several complementary approaches, we annotated the unigenes in diverse protein databases including the NCBI Nr protein database, UniProt/Swiss-Prot, KEGG, COGs of proteins (COG), and GO. Based on an E-value lower than 10-5, the best match was chosen (Table 2). First, utilizing the BLAST (Basic Local Alignment Search Tool) algorithm, a sequence similarity search was operated against the above databases. In total, 96,595 unigenes were significantly been matched in the Nr database and 71,002 unigenes were annotated in the Swiss-Prot database. Moreover, 68,250 unigenes matched in KEGG annotation, 49,460 unigenes matched in COG annotation, and 68,151 unigenes matched in GO annotation. However, 24,681 unigenes did not match in the databases evaluated. The distribution and overlaps of unigenes from different databases are displayed in Figure 3. In total, 37,763 unigenes matched in all of the databases.


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)

Distribution of unigenes annotated in different databases.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Distribution of unigenes annotated in different databases.
Mentions: Using several complementary approaches, we annotated the unigenes in diverse protein databases including the NCBI Nr protein database, UniProt/Swiss-Prot, KEGG, COGs of proteins (COG), and GO. Based on an E-value lower than 10-5, the best match was chosen (Table 2). First, utilizing the BLAST (Basic Local Alignment Search Tool) algorithm, a sequence similarity search was operated against the above databases. In total, 96,595 unigenes were significantly been matched in the Nr database and 71,002 unigenes were annotated in the Swiss-Prot database. Moreover, 68,250 unigenes matched in KEGG annotation, 49,460 unigenes matched in COG annotation, and 68,151 unigenes matched in GO annotation. However, 24,681 unigenes did not match in the databases evaluated. The distribution and overlaps of unigenes from different databases are displayed in Figure 3. In total, 37,763 unigenes matched in all of the databases.

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.