MicroRNA expression analysis of rosette and folding leaves in Chinese cabbage using high-throughput Solexa sequencing

Abstract

In this study, a global analysis of miRNA expression from rosette leaves (RLs) and folding leaves (FLs) of Chinese cabbage (Brassica rapa L. ssp. pekinensis) was conducted using high-throughput Solexa sequencing. In total, over 12 million clean reads were obtained from each library. Sequence analysis identified 64 conserved miRNA families in each leaf type and 104 and 95 novel miRNAs from RLs and FLs, respectively. Among these, 61 conserved miRNAs and 61 novel miRNAs were detected in both types of leaves. Furthermore, six conserved and 21 novel miRNAs were differentially expressed between the two libraries. Target gene annotation suggested that these differentially expressed miRNAs targeted transcription factors, F-box proteins, auxin and Ca(2+) signaling pathway proteins, protein kinases and other proteins that may function in governing leafy head formation. This study advanced our understanding of the important roles of miRNAs in regulating leafy head development in Chinese cabbage.

Keywords: AFB3; AGL; AP2; APETALA2; ARF; AUX/IAA; Agamous-like; Auxin response factors; Auxin signaling F-box3; Auxin/indole-3-acetic acid; Basic region/leucine zipper motif; BcpLH; Brassica campestris ssp. pekinensis leafy heads; CDPK; CaLB; CaM; Calcium-dependent lipid binding; Calcium-dependent protein kinases; Calmodulin; Chinese cabbage; Folding leaves; GH3; GRF; Gretchen hagen3; Growth-regulation factor; HD-ZIP III; High-throughput Solexa sequencing; Homeodomain-leucine zipper protein III; LBD; Lateral organ boundaries domain; MYB; MicroRNA; Myeloblastosis; PIN; PIN-formed; Rosette leaves; TCP; Teosinte branched1/Cycloidia/PCF; bZIP.