Abstract
Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs. Mononucleotide repeats were the most abundant, followed by di- and trinucleotide repeats. Tetra-, penta-, and hexarepeats were rare. A total of 9,498 (57.46%) microsatellite loci had potential as pre-miRNA SSR markers. Of the markers, 3,573 (37.62%) were non-redundant, and 2,341 (65.51%) primer pairs could be transferred to at least one of the plant taxonomic groups. All data and primer pairs were deposited in a user-friendly, freely accessible plant miRNA SSR marker database. The data presented in this study, accelerate the understanding of pre-miRNA evolution and serve as valuable genomic treasure for genetic improvements in a wide range of crops, including legumes, cereals, and cruciferous crops.
Highlights
At least 1.2 simple sequence repeat (SSR) were found per plant, pre-miRNA sequence
Class II (SSR length shorter than 20 bp) SSRs were more frequent than Class I
8651 (51%) pre-miRNA SSR candidates were identified from 292 plant species
Summary
Microsatellites, called simple sequence repeats (SSRs), consist of tandemly repeated units of one to six nucleotides. They are abundant elements in both prokaryotic and eukaryotic genomes, their frequency varies greatly among different organisms [1]. Mutations in SSRs can affect the function of sequence segments and lead to phenotypic changes [8,9]. In this sense, SSRs are described as potential evolutionary tuning knobs [10,11], allowing for a fast adaptation under selection pressure
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.
