Abstract
MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.
Highlights
MicroRNAs are important regulators of gene expression at the post-transcriptional level in a wide range of species, including plants, animals, algae, and some unicellular organisms [1,2]
Based on the 21 most conserved miRNA families, and using the currently available genome sequence of date palm (Phoenix dactylifera), 81 miRNAs were predicted in the date genome (Table 1)
The majority of miRNAs were located in intergenic regions 4 to 5 kb away from the nearest protein-coding genes, and we determined that duplication events are the major driving force behind the evolution of miRNAs
Summary
MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species, including plants, animals, algae, and some unicellular organisms [1,2]. Conserved miRNA families in plants regulate ancestral transcription factors that specify basic meristem functions, organ polarity and separation, cell division, and hormonal control [6,7]. Based on the miRNAs known to date in plants, Cuperus et al [10] predicted that there are 21 miRNA families conserved between monocots and dicots. These 21 conserved miRNA families were expected to be found using computational methods in a monocot plant like date palm (Phoenix dactylifera)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
