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Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa deep-sequencing technology

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Abstract

microRNAs (miRNAs) perform critical roles in various biological and metabolic processes by regulating gene expression at the post-transcriptional level. To investigate the functional roles of miRNAs in the lactating mammary gland of Capra hircus, a library was constructed from the lactating mammary glands of Laoshan dairy goats (C. hircus) during early lactation. The miRNA expression profiles were systematically screened, and miRNAs were identified and characterized using Solexa deep-sequencing technology and bioinformatics. As a result, a total of 18,031,615 clean reads were obtained representing 305,711 unique sRNAs. A total of 12,086,616 sRNAs representing 3,701 unique sRNAs matched the known Bos taurus miRNA precursors in miRBase 17.0, and 300 known miRNAs and 15 miRNA* were discovered. In addition, 131 novel miRNAs sequences were also obtained, and 147,703 putative targets were predicted. GO and KEGG pathway analysis showed that the majority of targets were involved in cellular processes and metabolic pathways. The 290 known miRNAs, 14 miRNA* and 38 novel miRNAs were validated by sequencing a second library that was constructed from the same tissues as the first library. Our study provided the first large-scale identification and characterization of miRNAs in the mammary gland tissue of the dairy goat. The results indicate that the regulation of miRNA-mediated gene expression occurs during early lactation in dairy goats. This study significantly enriches the C. hircus miRNA repertoire and provides a reference for the elucidation of complex miRNA-mediated regulatory networks for gene expression in the physiology and developmental progression of the lactating mammary gland.

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Acknowledgments

We thank Prof. Jianming Wang for revising the language and for valuable comments on the manuscript. We thank the Laoshan dairy goat foundation seed farm and the Qingdao Animal Husbandry and Veterinary Research Institute for providing the experimental goats and assisting in sample collection. This work was financially supported by the Special Fund for Agro-scientific Research in the Public Interest (No. 201103038) and the Innovation Research of Agriculture and Biology Resources (No. 2011186125).

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Correspondence to Jianmin Wang.

Electronic supplementary material

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11033_2012_1779_MOESM1_ESM.xls

S-File 1: Summary of clean reads from small RNA sequencing data. From up to down for each sequence: the ID of the tag obtained by sequencing, reads, and sequence. (XLS 3688 kb)

11033_2012_1779_MOESM2_ESM.rar

S-File 2: Sequence mapping on the Ovis aries genome. From left to right: the IDs of sequences obtained by sequencing, chromosome, starting position in the genome, the terminal position in the genome, sense/antisense strand, sequences, and reads. (RAR 10848 kb)

S-File 3: Annotation of small RNAs into different categories. (RAR 2699 kb)

11033_2012_1779_MOESM4_ESM.xls

S-File 4: Partial sequences matching known miRNA. From up to down for each miRNA: the ID, the precursor sequence, hairpin secondary structure, the mature sequence, and the sequences obtained by sequencing. The IDs, sequence length and reads for the sequences are shown on the right. (XLS 755 kb)

S-File 5: Conserved miRNAs and expression abundance (XLS 32 kb)

S-File 6: Novel miRNAs predicted by Mireap (XLS 27 kb)

S-File 7: Summary of the characteristics of novel miRNAs (XLS 71 kb)

S-File 8: Precursor structures of novel miRNAs (RAR 728 kb)

S-File 9: Target genes of novel miRNAs (XLS 4697 kb)

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Ji, Z., Wang, G., Xie, Z. et al. Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa deep-sequencing technology. Mol Biol Rep 39, 9361–9371 (2012). https://doi.org/10.1007/s11033-012-1779-5

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