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An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?

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Abstract

Microsatellites (SSRs) are tandem repeat sequences in eukaryote genomes, including plant cytoplasmic genomes. The mitochondrial genome (mtDNA) has been shown to vary in size, number, and distribution of SSRs among different plant groups. Thus, SSRs contribute with genomic diversity in mtDNAs. However, the abundance, distribution, and evolutionary significance of SSRs in mtDNA from a wide range of algae and plants have not been explored. In this study, the mtDNAs of 204 plant and algal species were investigated related to the presence of SSRs. The number of SSRs was positively correlated with genome size. Its distribution is dependent on plant and algal groups analyzed, although the cluster analysis indicates the conservation of some common motifs in algal and terrestrial plants that reflect common ancestry of groups. Many SSRs in coding and non-coding regions can be useful for molecular markers. Moreover, mitochondrial SSRs are highly abundant, representing an important source for natural or induced genetic variation, i.e., for biotechnological approaches that can modulate mtDNA gene regulation. Thus, this comparative study increases the understanding of the plant and algal SSR evolution and brings perspectives for further studies.

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Funding

This research received no external funding from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) -Finance Code 001, the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq -process n° 407591/2018-4), and from Fundação de Amparo a Pesquisa do Rio Grande do Sul (FAPERGS).

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  1. Plant Genomics and Breeding Center, Technology Development Center, Federal University of Pelotas, Pelotas, RS, Brazil

    Karine E. Janner de Freitas, Carlos Busanello, Vívian Ebeling Viana, Camila Pegoraro, Luciano Carlos da Maia & Antonio Costa de Oliveira

  2. Center for Antarctic Vegetation Studies (NEVA), Federal University of Pampa, São Gabriel, RS, Brazil

    Filipe de Carvalho Victoria

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  1. Karine E. Janner de Freitas
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  2. Carlos Busanello
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Contributions

K.E.J.F. wrote the main manuscript text and C.B. prepared figures. F.C.V. conducted the RE analysis and contributed to the main manuscript text. V.E.V, C. P., and L.C.M. made contributions to the discussion. A.C. led the research. All the authors reviewed the manuscript.

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Correspondence to Antonio Costa de Oliveira.

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de Freitas, K.E.J., Busanello, C., Viana, V.E. et al. An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?. Funct Integr Genomics 22, 35–53 (2022). https://doi.org/10.1007/s10142-021-00815-7

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