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Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN - G3 (Bethesda) (2014)

Bottom Line: An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation.The deep RNA-Seq reassembled Brassica rapa transcriptome identified 44,239 protein-coding genes.Gaps in the current genome assembly of B. rapa are highlighted by our identification of 780 unmapped transcripts.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of California, Davis, California 95616.

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Pipeline illustrating the overall transcriptome assembly and annotation of Brassica rapa genotype R500.
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fig2: Pipeline illustrating the overall transcriptome assembly and annotation of Brassica rapa genotype R500.

Mentions: The pipeline for R500 transcriptome assembly and re-annotation of B. rapa genome involved three steps. First, transcriptome sequence libraries were assembled and novel transcripts were detected and annotated. Second, the current genome annotation of B. rapa was updated and annotated. Third, both the novel annotated transcripts and updated annotated transcripts were combined to generate a final improved transcriptome assembly and genome annotation of B. rapa (Figure 2). For assembling and re-annotation purposes, we used reads from one genotype only (R500) to avoid mis-assemblies that could be caused by the approximately 330,000 SNPs existing between the two genotypes. In addition, we only used a subset of total reads for R500 to reduce computational requirements.


Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN - G3 (Bethesda) (2014)

Pipeline illustrating the overall transcriptome assembly and annotation of Brassica rapa genotype R500.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232532&req=5

fig2: Pipeline illustrating the overall transcriptome assembly and annotation of Brassica rapa genotype R500.
Mentions: The pipeline for R500 transcriptome assembly and re-annotation of B. rapa genome involved three steps. First, transcriptome sequence libraries were assembled and novel transcripts were detected and annotated. Second, the current genome annotation of B. rapa was updated and annotated. Third, both the novel annotated transcripts and updated annotated transcripts were combined to generate a final improved transcriptome assembly and genome annotation of B. rapa (Figure 2). For assembling and re-annotation purposes, we used reads from one genotype only (R500) to avoid mis-assemblies that could be caused by the approximately 330,000 SNPs existing between the two genotypes. In addition, we only used a subset of total reads for R500 to reduce computational requirements.

Bottom Line: An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation.The deep RNA-Seq reassembled Brassica rapa transcriptome identified 44,239 protein-coding genes.Gaps in the current genome assembly of B. rapa are highlighted by our identification of 780 unmapped transcripts.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of California, Davis, California 95616.

Show MeSH