Maybe, Next-Gen Sequencing and Microarrays…

Two recent studies (published as early access papers from the Journal of Experimental Botany) describe the combined use of RNA-Seq and custom microarrays to uncover more transcriptomics information about agriculturally important species.

MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response.

1In the first study, researchers characterize the miRNA profile of the shoot apical meristem (SAM) of an important legume crop, soybean, by integrating high-throughput sequencing data with miRNA microarray analysis.

A total of 8423 non-redundant sRNAs were obtained from two libraries derived from micro-dissected SAM or mature leaf tissue. Sequence analysis allowed the identification of 32 conserved miRNA families as well as 8 putative novel miRNAs.

A custom soybean miRNA microarray was designed containing miRNA and several miRNA* sequences derived from this RNA-Seq data as well as other soybean miRNAs available in the public miRNA database (miRBase). This microarray was subsequently utilized to compare the repertoire of miRNAs in the SAM and mature leaf as well as to verify the expression of novel miRNA candidates identified.

2The second study presents an efficient method for genome-wide discovery of new drought stress responsive miRNAs in Populus euphratica, a typical abiotic stress-resistant woody species, through the combined use of RNA-Seq and miRNA microarray profiling data.

High-throughput sequencing of P. euphratica leaves found 197 conserved miRNAs between P. euphratica and Populus trichocarpa. Additionally, 58 new miRNAs belonging to 38 families were identified, an increase in the number of P. euphratica miRNAs.

Comparison of high-throughput sequencing with miRNA microarray profiling data indicated that 104 miRNA sequences were up-regulated, whereas 27 were down-regulated under drought stress. The method of combining high-throughput sequencing and microarray technologies allowed the successful discovery of new and stress responsive miRNAs and will serve as a basis for future comparative functional genomic analyses using syntenic orthologues.

  1. Chui E. Wong, Ying-Tao Zhao, Xiu-Jie Wang, Larry Croft, Zhong-Hua Wang, Farzad Haerizadeh, John S. Mattick, Mohan B. Singh, Bernard J. Carroll, and Prem L. Bhalla. (2011) MicroRNAs in the shoot apical meristem of soybean. J Exp Bot [Epub ahead of print]. [article]
  2. Bosheng Li, Yurong Qin, Hui Duan, Weilun Yin, and Xinli Xia (2011) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J Exp Bot [Epub ahead of print]. [article]