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Identification of candidate flavonoid pathway genes using transcriptome correlation network analysis in ripe strawberry (Fragaria × ananassa) fruits.

Pillet J, Yu HW, Chambers AH, Whitaker VM, Folta KM - J. Exp. Bot. (2015)

Bottom Line: The results suggest that two of the newly-identified regulators likely contribute to discrete nodes of the flavonoid pathway.The third putative transcription factor appears to be a universal regulator of flavonoid-pathway genes, as many pathway transcripts decrease in abundance when this gene is silenced.This report demonstrates that such systems-level approaches may be especially powerful when connected to an effective transient expression system, helping to provide rapid and strong evidence of gene function in key fruit-ripening processes.

View Article: PubMed Central - PubMed

Affiliation: Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.

No MeSH data available.


Phylogenetic analysis using the Neighbor–Joining method and based on closest amino acid sequences of gene17673 from different plant species. Bootstrap values are based on 1000 replicates. Bars, 0.1 amino acid substitutions per site.
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Figure 3: Phylogenetic analysis using the Neighbor–Joining method and based on closest amino acid sequences of gene17673 from different plant species. Bootstrap values are based on 1000 replicates. Bars, 0.1 amino acid substitutions per site.

Mentions: Three candidates (gene09614, gene17673 and gene13212) were selected based on potential inferred roles in ripening or due to their expression levels. Based on sequence and domain similarity compared to Arabidopsis, gene09614 was named FaTCP11. Phylogenetic analysis of gene17673 reveals that this gene belongs to a cluster of PCL1-like genes (Fig. 3). Closest orthologues from related species such as Malus domestica, Prunus persica and Cucumis sativus were used for cluster analysis and also family genes from Arabidopsis thaliana. Based on this analysis, we named gene17673 ‘PCL1-like’. The transcript noted as gene13212 is most similar to AtSCL8 in Arabidopsis, a member of the SCARECROW-LIKE gene family, and was named ‘FaSCL8’.


Identification of candidate flavonoid pathway genes using transcriptome correlation network analysis in ripe strawberry (Fragaria × ananassa) fruits.

Pillet J, Yu HW, Chambers AH, Whitaker VM, Folta KM - J. Exp. Bot. (2015)

Phylogenetic analysis using the Neighbor–Joining method and based on closest amino acid sequences of gene17673 from different plant species. Bootstrap values are based on 1000 replicates. Bars, 0.1 amino acid substitutions per site.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4507756&req=5

Figure 3: Phylogenetic analysis using the Neighbor–Joining method and based on closest amino acid sequences of gene17673 from different plant species. Bootstrap values are based on 1000 replicates. Bars, 0.1 amino acid substitutions per site.
Mentions: Three candidates (gene09614, gene17673 and gene13212) were selected based on potential inferred roles in ripening or due to their expression levels. Based on sequence and domain similarity compared to Arabidopsis, gene09614 was named FaTCP11. Phylogenetic analysis of gene17673 reveals that this gene belongs to a cluster of PCL1-like genes (Fig. 3). Closest orthologues from related species such as Malus domestica, Prunus persica and Cucumis sativus were used for cluster analysis and also family genes from Arabidopsis thaliana. Based on this analysis, we named gene17673 ‘PCL1-like’. The transcript noted as gene13212 is most similar to AtSCL8 in Arabidopsis, a member of the SCARECROW-LIKE gene family, and was named ‘FaSCL8’.

Bottom Line: The results suggest that two of the newly-identified regulators likely contribute to discrete nodes of the flavonoid pathway.The third putative transcription factor appears to be a universal regulator of flavonoid-pathway genes, as many pathway transcripts decrease in abundance when this gene is silenced.This report demonstrates that such systems-level approaches may be especially powerful when connected to an effective transient expression system, helping to provide rapid and strong evidence of gene function in key fruit-ripening processes.

View Article: PubMed Central - PubMed

Affiliation: Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.

No MeSH data available.