Open Access Highly Accessed Research article

Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars

Jungeun Kim12, June Hyun Park7, Chan Ju Lim1, Jae Yun Lim7, Jee-Youn Ryu34, Bong-Woo Lee1, Jae-Pil Choi1, Woong Bom Kim1, Ha Yeon Lee1, Yourim Choi7, Donghyun Kim7, Cheol-Goo Hur12, Sukweon Kim5, Yoo-Sun Noh3, Chanseok Shin7* and Suk-Yoon Kwon16*

Author Affiliations

1 Green Bio Research Center, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea

2 Bioinformatics, University of Science & Technology, 217 Gajung-ro, Yuseong-gu, Daejeon, 305-350, Republic of Korea

3 School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-747, Republic of Korea

4 Korea Ocean Research & Development Institute, 787 Haeanro, Sangrok-gu, Ansan, 426-744, Republic of Korea

5 Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea

6 Biosystems and Bioengineering Program, University of Science & Technology, 217 Gajungno, Yuseong-gu, Daejeon, 305-350, Republic of Korea

7 Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-921, Republic of Korea

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BMC Genomics 2012, 13:657  doi:10.1186/1471-2164-13-657

Published: 21 November 2012

Additional files

Additional file 1:

The statistics of sRNA and its distribution.

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Additional file 2:

Raw data of miRNAs identified in Vital, Maroussia, Sympathy, and Haedang. This file provides mapped known/novel and unmapped known miRNAs. In addition, major miRNAs with miRNA/miRNA* pairs were also provided.

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Additional file 3:

The miRNA lists conserved in Rosaceae families. miRNA libraries for strawberry, peach, apples were downloaded from GEO database and re-analyzed.

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Additional file 4:

Gene-specific primers used for target validation using 5' RACE.

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Additional file 5:

Schematic diagram of flavonoid biosynthetic pathways and miRNA profiles targeting flavonoid biosynthetic genes. Colours represent enrichment genes in specific Rosa measured by applying Audic’s test (p value < 0.001).* miRNA cleavage were experimentally validated (Figure 5).

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Additional file 6:

Gene list involved in Carotenoid pathway.

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Additional file 7:

Gene list involved in Flavonoid pathway.

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Additional file 8:

The 2 * 2 contingency table and the probability equation for Audic’s test.

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