MicroRNAs (miRNAs) are ~21 nucleotide (nt), endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that miRNAs play an important role in species-specific development in plants. However, the detailed miRNA profile divergence has not been performed among tomato species. In this study, the small RNA (sRNA) profiles of Solanum lycopersicum cultivar 9706 and Solanum habrochaites species PI 134417 were obtained by deep sequencing. Sixty-three known miRNA families were identified from these two species, of which 39 were common. Further miRNA profile comparison showed that 24 known non-conserved miRNA families were species-specific between these two tomato species. In addition, six conserved miRNA families displayed an apparent divergent expression pattern between the two tomato species. Our results suggested that species-specific, non-conserved miRNAs and divergent expression of conserved miRNAs might contribute to developmental changes and phenotypic variation between the two tomato species. Twenty new miRNAs were also identified in S. lycopersicum. This research significantly increases the number of known miRNA families in tomato and provides the first set of small RNAs in S. habrochaites. It also suggests that miRNAs have an important role in species-specific plant developmental regulation.

Document Type


Publication Date


Notes/Citation Information

Published in Journal of Integrative Agriculture, v. 14, issue 1.

Copyright © 2015 Chinese Academy of Agricultural Sciences. All rights reserved.

Under a Creative Commons license.

Digital Object Identifier (DOI)


Funding Information

This work was supported by the National Basic Research Program of China (2009CB11900) and the Special Fund for Agro-Scientific Research in the Public Interest, China (201003065).

Related Content

Appendix associated with this paper can be available on http://www.ChinaAgriSci.com/V2/En/appendix.htm

Included in

Horticulture Commons