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Open Access Research article

Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)

Hu Zheng, Jiang Qiyan, Ni Zhiyong and Zhang Hui*

Author Affiliations

The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

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BMC Genomics 2013, 14:280  doi:10.1186/1471-2164-14-280

Published: 24 April 2013

Additional files

Additional file 1:

The cis-NATs in soybean. The overlap length and types of cis-NATs are shown.

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Additional file 2:

The trans-NATs in soybean. The overlap length is shown.

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Additional file 3:

Identification of NATs in soybean. The transcripts were amplified by RT-PCR and sequenced. The overlapping regions are shown at the location of the transcript sequence.

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Additional file 4:

The small RNAs and degradome cDNAs of NATs. Unique and total small RNAs and unique and total degradome cDNAs are shown.

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Additional file 5:

Identification of nat-siRNA targets in soybean. The degradome, their abundance, and the genes from which they were derived are shown. nat-siRNAs, nat-siRNA target sites, nat-siRNA abundance, and the origin of the nat-siRNAs are indicated. nat-siRNAs can target the sense or antisense transcript of a given NAT and other transcripts. The origins of nat-siRNAs are shown as a, s, and o. a: the nat-siRNA derived from the antisense transcript of a given NAT targets the sense transcript; s: the nat-siRNA derived from the sense transcript of a given NAT targets the sense transcript; o: the nat-siRNA derived from a given NAT guides the expression of another gene. Searches for genes that generate the nat-siRNAs identified nat-siRNAs derived from different genes. Nat-siRNAs that identically matched more than five sense or antisense transcripts are denoted as multiple.

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Additional file 6:

Secondary structures of five NAT-related pre-miRNAs. Five NAT transcripts had the stem-loop structure that is characteristic of pre-miRNAs. Of these five transcripts, two were miR166 pre-miRNA and one was miR319 pre-miRNA. The miRNAs are indicated in red.

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Additional file 7:

The small RNAs were matched to the five NAT-related pre-miRNAs. The small RNAs are shown along with information on their length, abundance, and location in the pre-miRNAs.

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Additional file 8:

The miRNA targets containing antisense transcripts. The miRNA targets could form cis- and trans-NATs with other genes. a: These targets were validated previously by the analysis of the degradome in soybean [31,32].

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Additional file 9:

RT-PCR primers used for the amplification of NATs.

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Additional file 10:

The sequences of transcripts identified by RT-PCR.

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