Genome-wide characterization of simple sequence repeats in Palmae genomes

Background Microsatellites or simple sequence repeats (SSRs) have become the most significant DNA marker technology used in genetic research. The availability of complete draft genomes for a number of Palmae species has made it possible to perform genome-wide analysis of SSRs in these species. Palm...

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Bibliographic Details
Published in:Genes & genomics 2020, 42(5), , pp.597-608
Main Authors: Manee, Manee M., Al-Shomrani, Badr M., Al-Fageeh, Mohamed B.
Format: Article
Language:English
Subjects:
Animal Genetics and Genomics
Arecaceae - classification
Arecaceae - genetics
Biomedical and Life Sciences
Computer applications
Cultivars
Economic importance
Genome, Plant
Genomes
Human Genetics
Life Sciences
Microbial Genetics and Genomics
Microsatellite Repeats
Microsatellites
Nucleotide sequence
Phylogeny
Plant Genetics and Genomics
Research Article
Simple sequence repeats
Species
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Summary:Background Microsatellites or simple sequence repeats (SSRs) have become the most significant DNA marker technology used in genetic research. The availability of complete draft genomes for a number of Palmae species has made it possible to perform genome-wide analysis of SSRs in these species. Palm trees are tropical and subtropical plants with agricultural and economic importance due to the nutritional value of their fruit cultivars. Objective This is the first comprehensive study examining and comparing microsatellites in completely-sequenced draft genomes of Palmae species. Methods We identified and compared perfect SSRs with 1–6 bp nucleotide motifs to characterize microsatellites in Palmae species using PERF v0.2.5. We analyzed their relative abundance, relative density, and GC content in five palm species: Phoenix dactylifera , Cocos nucifera , Calamus simplicifolius , Elaeis oleifera , and Elaeis guineensis . Results A total of 118241, 328189, 450753, 176608, and 70694 SSRs were identified, respectively. The six repeat types were not evenly distributed across the five genomes. Mono- and dinucleotide SSRs were the most abundant, and GC content was highest in tri- and hexanucleotide SSRs. Conclusion We envisage that this analysis would further substantiate more in-depth computational, biochemical, and molecular studies on the roles SSRs may play in the genome organization of the palm species. The current study contributes a detailed characterization of simple sequence repeats in palm genomes.
ISSN:1976-9571
2092-9293
DOI:10.1007/s13258-020-00924-w