Genome-wide characterization of simple sequence repeats in Palmae genomes

Badr M Al-Shomrani,Manee M Manee,Mohamed B Al-Fageeh

doi:10.1007/s13258-020-00924-w

Abstract

BackgroundMicrosatellites 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.ObjectiveThis is the first comprehensive study examining and comparing microsatellites in completely-sequenced draft genomes of Palmae species.MethodsWe 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.ResultsA 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.ConclusionWe 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.

Highlights

Plants in the palm family (Arecaceae or Palmae) are important economic crops that are widely cultivated in arid and semi-arid regions of North Africa, the Sahara, the Middle East, and eastward to the Indus Valley
Despite the increasing number of genomic studies on Palmae trees, little genome-wide characterization has been performed on these plants for the purposes of conservation and genetic assessment
We adopted the Benchmarking Universal Single Copy Ortholog (BUSCO) plant lineage dataset, which consisted of 1440 single-copy orthologs for the Embryophyta lineage, to assess the completeness of each of the five genome assemblies

Summary

Introduction

Plants in the palm family (Arecaceae or Palmae) are important economic crops that are widely cultivated in arid and semi-arid regions of North Africa, the Sahara, the Middle East, and eastward to the Indus Valley. 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. 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. The current study contributes a detailed characterization of simple sequence repeats in palm genomes

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Conclusion