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De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.).

Fu N, Wang Q, Shen HL - PLoS ONE (2013)

Bottom Line: Large numbers of simple sequence repeats (SSRs) were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions.Our results provide a valuable resource for celery research.The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.

View Article: PubMed Central - PubMed

Affiliation: College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.

ABSTRACT

Background: Celery is an increasing popular vegetable species, but limited transcriptome and genomic data hinder the research to it. In addition, a lack of celery molecular markers limits the process of molecular genetic breeding. High-throughput transcriptome sequencing is an efficient method to generate a large transcriptome sequence dataset for gene discovery, molecular marker development and marker-assisted selection breeding.

Principal findings: Celery transcriptomes from four tissues were sequenced using Illumina paired-end sequencing technology. De novo assembling was performed to generate a collection of 42,280 unigenes (average length of 502.6 bp) that represent the first transcriptome of the species. 78.43% and 48.93% of the unigenes had significant similarity with proteins in the National Center for Biotechnology Information (NCBI) non-redundant protein database (Nr) and Swiss-Prot database respectively, and 10,473 (24.77%) unigenes were assigned to Clusters of Orthologous Groups (COG). 21,126 (49.97%) unigenes harboring Interpro domains were annotated, in which 15,409 (36.45%) were assigned to Gene Ontology(GO) categories. Additionally, 7,478 unigenes were mapped onto 228 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Large numbers of simple sequence repeats (SSRs) were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions.

Conclusions: This study demonstrates the feasibility of generating a large scale of sequence information by Illumina paired-end sequencing and efficient assembling. Our results provide a valuable resource for celery research. The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.

Show MeSH
Pathway assignment based on KEGG.(A) Classification based on metabolism categories; (B) Categories classified by KEGG.
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pone-0057686-g006: Pathway assignment based on KEGG.(A) Classification based on metabolism categories; (B) Categories classified by KEGG.

Mentions: Unigenes were compared with KEGG using BLASTx with an E-value of less than 1e−10 and the corresponding pathways were established. Out of the 42,280 unigenes, 30,704 (72.62%) were annotated and 9,982 (32.51%) were assigned to KEGG pathways. Among the 9,982 unigenes, 4,921 were assigned to the metabolic pathways, composing the largest group of the five categories classified by KEGG (Figure 6B). The KEGG metabolic pathways (Figure 6A) mainly contained carbohydrate metabolism, energy metabolism, amino acid metabolism, lipid metabolism and glycan biosynthesis and nucleotide metabolism. In addition to the unigenes assigned to the metabolism pathways, 4,128 unigenes were sorted to the genetic information processing involving folding, sorting, degradation, replication and repair, transcription and translation. Additionally, there were 1,265 and 1,149 unigenes classified to cellular processes and environmental information processing respectively.


De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.).

Fu N, Wang Q, Shen HL - PLoS ONE (2013)

Pathway assignment based on KEGG.(A) Classification based on metabolism categories; (B) Categories classified by KEGG.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585167&req=5

pone-0057686-g006: Pathway assignment based on KEGG.(A) Classification based on metabolism categories; (B) Categories classified by KEGG.
Mentions: Unigenes were compared with KEGG using BLASTx with an E-value of less than 1e−10 and the corresponding pathways were established. Out of the 42,280 unigenes, 30,704 (72.62%) were annotated and 9,982 (32.51%) were assigned to KEGG pathways. Among the 9,982 unigenes, 4,921 were assigned to the metabolic pathways, composing the largest group of the five categories classified by KEGG (Figure 6B). The KEGG metabolic pathways (Figure 6A) mainly contained carbohydrate metabolism, energy metabolism, amino acid metabolism, lipid metabolism and glycan biosynthesis and nucleotide metabolism. In addition to the unigenes assigned to the metabolism pathways, 4,128 unigenes were sorted to the genetic information processing involving folding, sorting, degradation, replication and repair, transcription and translation. Additionally, there were 1,265 and 1,149 unigenes classified to cellular processes and environmental information processing respectively.

Bottom Line: Large numbers of simple sequence repeats (SSRs) were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions.Our results provide a valuable resource for celery research.The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.

View Article: PubMed Central - PubMed

Affiliation: College of Agriculture and Biotechnology, China Agricultural University, Beijing, China.

ABSTRACT

Background: Celery is an increasing popular vegetable species, but limited transcriptome and genomic data hinder the research to it. In addition, a lack of celery molecular markers limits the process of molecular genetic breeding. High-throughput transcriptome sequencing is an efficient method to generate a large transcriptome sequence dataset for gene discovery, molecular marker development and marker-assisted selection breeding.

Principal findings: Celery transcriptomes from four tissues were sequenced using Illumina paired-end sequencing technology. De novo assembling was performed to generate a collection of 42,280 unigenes (average length of 502.6 bp) that represent the first transcriptome of the species. 78.43% and 48.93% of the unigenes had significant similarity with proteins in the National Center for Biotechnology Information (NCBI) non-redundant protein database (Nr) and Swiss-Prot database respectively, and 10,473 (24.77%) unigenes were assigned to Clusters of Orthologous Groups (COG). 21,126 (49.97%) unigenes harboring Interpro domains were annotated, in which 15,409 (36.45%) were assigned to Gene Ontology(GO) categories. Additionally, 7,478 unigenes were mapped onto 228 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Large numbers of simple sequence repeats (SSRs) were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions.

Conclusions: This study demonstrates the feasibility of generating a large scale of sequence information by Illumina paired-end sequencing and efficient assembling. Our results provide a valuable resource for celery research. The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.

Show MeSH