Open Access Highly Accessed Research article

Identification of microRNAs from Amur grape (vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics

Chen Wang1, Jian Han1, Chonghuai Liu2, Korir Nicholas Kibet1, Emrul Kayesh1, Lingfei Shangguan1, Xiaoying Li1 and Jinggui Fang1*

Author Affiliations

1 College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China

2 Zhengzhou Institute of Pomology, Chinese Academy of Agricultural Sciences, 11 Hanghai East Road, Zhengzhou 450009, People's Republic of China

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BMC Genomics 2012, 13:122  doi:10.1186/1471-2164-13-122

Published: 29 March 2012

Additional files

Additional file 1:

Size distribution of unique small RNA sequences from Amur grape.

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Additional file 2:

Identified conserved miRNAs from Amur grape.

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Additional file 3:

Predicted secondary structure of new potential miRNAs from Amur grape.

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Additional file 4:

3'RACE and 5' RACE products of Vv-miRNAs amplified by PCR shown in an ethidium bromide-stained agarose gel. Sizes of the molecular weight markers of the bottom and the second bottom bands are 50 bp and 100 bp on A, B, C and D, respectively. Lanes 1-20 are 3'RACE (A) and 5'RACE (B) products of 20 lower abundance va-miRNAs (va-miR398b, va-miR399c, va-miR828a, va-miR005, va-miR011, va-miR020, va-miR028, va-miR029, va-miR032, va-miR037, va-miR045, va-miR048, va-miR052, va-miR063, va-miR066, va-miR074, va-miR077, va-miR082, va-miR095 and va-miR098, respectively). Lanes 1'-20' are 3'RACE (C) and 5'RACE (D) products of 20 higher abundance va-miRNAs (va-miR156e, va-miR160c, va-miR162, va-miR164c, va-miR166c, va-miR169m, va-miR171c, va-miR172c, va-miR408, va-miR535a, va-miR001, va-miR007, va-miR016, va-miR018, va-miR023, va-miR046, va-miR047, va-miR049, va-miR057 and va-miR062, respectively). The sizes of 3'RACE products are about 83 bp while the size of 5'RACE products are about 57 bp.

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Additional file 5:

List of SNPs of conserved miRNAs in Amur grape.

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Additional file 6:

List of miR-LDs of conserved miRNAs in Amur grape.

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Additional file 7:

List of predicted target genes of non-conserved miRNAs identified in Amur grape.

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Additional file 8:

List of primers of miRNAs used for miR-5'RACE and miR-3'RACE.

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Additional file 9:

List of primers of va-miR-LDs used for miR-RACE.

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