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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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Venn diagrams showing unique and shared novel transcripts detected between (A) Velvet-Oases, Trinity, and TopHat-Cufflinks assemblers, (B) de novo (Velvet-Oases and Trinity), and reference-based (TopHat-Cufflinks) pipelines.
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fig3: Venn diagrams showing unique and shared novel transcripts detected between (A) Velvet-Oases, Trinity, and TopHat-Cufflinks assemblers, (B) de novo (Velvet-Oases and Trinity), and reference-based (TopHat-Cufflinks) pipelines.

Mentions: A comparison of the Velvet-Oases, Trinity, and TopHat-Cufflinks assemblers was performed using standard assembly statistics. The result showed that Velvet-Oases outperformed Trinity and TopHat-Cufflinks for all assembly parameters except for the percentage of annotated transcripts (Table 7). A higher percentage of annotated transcripts are generated by TopHat-Cufflinks even though fewer reads were used, consistent with the benefits of using the reference genome to anchor assemblies. We compared the novel transcripts of the three assemblers and found that there is only a marginal overlap, indicating that each transcriptome assembler has their own strengths (Figure 3A). The possible reasons for the marginal overlap are differences in the specifics of the assembly graphs, determination and weighting of graph edges, approaches to handle sequence errors, and approaches to handle diverse expression level.


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)

Venn diagrams showing unique and shared novel transcripts detected between (A) Velvet-Oases, Trinity, and TopHat-Cufflinks assemblers, (B) de novo (Velvet-Oases and Trinity), and reference-based (TopHat-Cufflinks) pipelines.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Venn diagrams showing unique and shared novel transcripts detected between (A) Velvet-Oases, Trinity, and TopHat-Cufflinks assemblers, (B) de novo (Velvet-Oases and Trinity), and reference-based (TopHat-Cufflinks) pipelines.
Mentions: A comparison of the Velvet-Oases, Trinity, and TopHat-Cufflinks assemblers was performed using standard assembly statistics. The result showed that Velvet-Oases outperformed Trinity and TopHat-Cufflinks for all assembly parameters except for the percentage of annotated transcripts (Table 7). A higher percentage of annotated transcripts are generated by TopHat-Cufflinks even though fewer reads were used, consistent with the benefits of using the reference genome to anchor assemblies. We compared the novel transcripts of the three assemblers and found that there is only a marginal overlap, indicating that each transcriptome assembler has their own strengths (Figure 3A). The possible reasons for the marginal overlap are differences in the specifics of the assembly graphs, determination and weighting of graph edges, approaches to handle sequence errors, and approaches to handle diverse expression level.

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