title: Identification and characterization of novel amphioxus microRNAs by Solexa sequencing.
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.
authors.affiliation: Jiangsu Diabetes Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Hankou Road, Nanjing, Jiangsu 210093, PR China.
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.forename: Qibin
authors.initials: Q
authors.lastname: Li
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
authors.forename: Xing
authors.initials: X
authors.lastname: Guo
authors.forename: Xiangrui
authors.initials: X
authors.lastname: Jiang
authors.forename: Zhiji
authors.initials: Z
authors.lastname: Ren
authors.forename: Chunyue
authors.initials: C
authors.lastname: Weng
authors.forename: Guoxun
authors.initials: G
authors.lastname: Sun
authors.forename: Xiuqiang
authors.initials: X
authors.lastname: Wang
authors.forename: Yaping
authors.initials: Y
authors.lastname: Liu
authors.forename: Lijia
authors.initials: L
authors.lastname: Ma
authors.forename: Jun-Yuan
authors.initials: JY
authors.lastname: Chen
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Ke
authors.initials: K
authors.lastname: Zen
authors.forename: Junfeng
authors.initials: J
authors.lastname: Zhang
authors.forename: Chen-Yu
authors.initials: CY
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001483:Base Sequence; D002816:Chordata, Nonvertebrate / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D015723:Gene Library; D035683:MicroRNAs / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D035683:MicroRNAs