Identification and characterization of novel amphioxus microRNAs by Solexa sequencing.
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.
Chen
Xi
X
Jiangsu Diabetes Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Hankou Road, Nanjing, Jiangsu 210093, PR China.
Li
Qibin
Q
Wang
Jin
J
Guo
Xing
X
Jiang
Xiangrui
X
Ren
Zhiji
Z
Weng
Chunyue
C
Sun
Guoxun
G
Wang
Xiuqiang
X
Liu
Yaping
Y
Ma
Lijia
L
Chen
Jun-Yuan
JY
Wang
Jun
J
Zen
Ke
K
Zhang
Junfeng
J
Zhang
Chen-Yu
CY
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
D035683:MicroRNAs