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Identification and characterization of novel amphioxus microRNAs by Solexa sequencing

Xi Chen1, Qibin Li234, Jin Wang1, Xing Guo1, Xiangrui Jiang1, Zhiji Ren1, Chunyue Weng1, Guoxun Sun1, Xiuqiang Wang15, Yaping Liu1, Lijia Ma3, Jun-Yuan Chen15, Jun Wang3, Ke Zen1, Junfeng Zhang1* and Chen-Yu Zhang1*

Author Affiliations

1 Jiangsu Diabetes Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Hankou Road, Nanjing, Jiangsu 210093, PR China

2 Beijing Institute of Genomics, Chinese Academy of Sciences, Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

3 Beijing Genomics Institute, Beishan Road, Yantian District, Shenzhen 518083, PR China

4 Graduate University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing 100049, PR China

5 Nanjing Institute of Palaeontology and Geology, East Beijing Road, Nanjing, Jiangsu 210008, PR China

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Genome Biology 2009, 10:R78  doi:10.1186/gb-2009-10-7-r78

Published: 17 July 2009

Abstract

Background

microRNAs (miRNAs) are endogenous small non-coding RNAs that regulate gene expression at the post-transcriptional level. While the number of known human and murine miRNAs is continuously increasing, information regarding miRNAs from other species such as amphioxus remains limited.

Results

We combined Solexa sequencing with computational techniques to identify novel miRNAs in the amphioxus species B. belcheri (Gray). This approach allowed us to identify 113 amphioxus miRNA genes. Among them, 55 were conserved across species and encoded 45 non-redundant mature miRNAs, whereas 58 were amphioxus-specific and encoded 53 mature miRNAs. Validation of our results with microarray and stem-loop quantitative RT-PCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. Analyzing the evolutionary history of amphioxus miRNAs, we found that amphioxus possesses many miRNAs unique to chordates and vertebrates, and these may thus represent key steps in the evolutionary progression from cephalochordates to vertebrates. We also found that amphioxus is more similar to vertebrates than are tunicates with respect to their miRNA phylogenetic histories.

Conclusions

Taken together, our results indicate that Solexa sequencing allows the successful discovery of novel miRNAs from amphioxus with high accuracy and efficiency. More importantly, our study provides an opportunity to decipher how the elaboration of the miRNA repertoire that occurred during chordate evolution contributed to the evolution of the vertebrate body plan.