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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
Clusters of orthologous groups (COG) classification.In total, 10,473 sequences were grouped into 24 COG classifications.
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pone-0057686-g005: Clusters of orthologous groups (COG) classification.In total, 10,473 sequences were grouped into 24 COG classifications.

Mentions: All unigenes were subjected to a search against the COG database for functional prediction and classification. 9,332 sequences were assigned to COG classifications (Figure 5). Among the 24 COG categories, the cluster for general function prediction only (17.38%) was the largest group, followed by posttranslational modification, protein turnover and chaperones (9.14%), translation, ribosomal structure and biogenesis (8.82%) and carbohydrate transport and metabolism (8.36%).


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)

Clusters of orthologous groups (COG) classification.In total, 10,473 sequences were grouped into 24 COG classifications.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0057686-g005: Clusters of orthologous groups (COG) classification.In total, 10,473 sequences were grouped into 24 COG classifications.
Mentions: All unigenes were subjected to a search against the COG database for functional prediction and classification. 9,332 sequences were assigned to COG classifications (Figure 5). Among the 24 COG categories, the cluster for general function prediction only (17.38%) was the largest group, followed by posttranslational modification, protein turnover and chaperones (9.14%), translation, ribosomal structure and biogenesis (8.82%) and carbohydrate transport and metabolism (8.36%).

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