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

Freitas, Karine Elise Janner de; Busanello, Carlos; Viana, Vívian Ebeling; Pegoraro, Camila; Victoria, Filipe de Carvalho; Maia, Luciano Carlos da; Oliveira, Antônio Costa de

doi:10.1007/s10142-021-00815-7

Cited by 10 publications

(13 citation statements)

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“…Repetitive sequences, especially abundant SSRs ( Freitas et al., 2022 ), increase the mitogenome size, generation of multiple copies of genes, genome diversification, and structural variations ( Fang et al., 2021 ). SSRs are characterized by cross-species transfer and high polymorphism, which allow them to be applied as molecular markers in phylogenetic analyses ( Rossetto et al., 2002 ).…”

Section: Discussionmentioning

confidence: 99%

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Liu,

Wu,

Tian

et al. 2023

Front. Plant Sci.

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IntroductionPrunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome.MethodsIn the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated.Results and discussionThe P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.

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Section: Discussionmentioning

confidence: 99%

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Liu,

Wu,

Tian

et al. 2023

Front. Plant Sci.

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“…Interspecific, but not intraspecific, variation for a G n microsatellite is present in the genus Pinus ( Soranzo et al., 1999 ), whereas a compound, highly polymorphic microsatellite region reveals both intra- and interspecific variation in Abies ( Jaramillo-Correa et al., 2013 ). Tandemly repeat mitochondrial loci are not generally conserved across diverse plant taxa and are not always polymorphic between related taxa, but recent work has identified extensive mitochondrial microsatellites among plant species ( de Freitas et al., 2022 ; Xiong et al., 2022 ). These studies and databases of plant mitochondrial microsatellite repeats ( Kumar et al., 2014 ; Sablok et al., 2015 ) facilitate the experimental search for loci that are polymorphic in specific taxa.…”

Section: Introductionmentioning

confidence: 99%

Plant mitochondrial introns as genetic markers - conservation and variation

et al. 2023

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Plant genomes are comprised of nuclear, plastid and mitochondrial components characterized by different patterns of inheritance and evolution. Genetic markers from the three genomes provide complementary tools for investigations of inheritance, genetic relationships and phenotypic contributions. Plant mitochondrial genomes are challenging for universal marker development because they are highly variable in terms of size, gene order and intergenic sequences and highly conserved with respect to protein-coding sequences. PCR amplification of introns with primers that anneal to conserved, flanking exons is effective for the development of polymorphic nuclear genome markers. The potential for plant mitochondrial intron polymorphisms to distinguish between congeneric species or intraspecific varieties has not been systematically investigated and is possibly constrained by requirements for intron secondary structure and interactions with co-evolved organelle intron splicing factors. To explore the potential for broadly applicable plant mitochondrial intron markers, PCR primer sets based upon conserved sequences flanking 11 introns common to seven angiosperm species were tested across a range of plant orders. PCR-amplified introns were screened for indel polymorphisms among a group of cross-compatible Citrus species and relatives; two Raphanus sativus mitotypes; representatives of the two Phaseolus vulgaris gene pools; and congeneric pairs of Cynodon, Cenchrus, Solanum, and Vaccinium species. All introns were successfully amplified from each plant entry. Length polymorphisms distinguishable by gel electrophoresis were common among genera but infrequent within genera. Sequencing of three introns amplified from 16 entries identified additional short indel polymorphisms and nucleotide substitutions that separated Citrus, Cynodon, Cenchrus and Vaccinium congeners, but failed to distinguish Solanum congeners or representatives of the Phaseolus vulgaris major gene pools. The ability of primer sets to amplify a wider range of plant species’ introns and the presence of intron polymorphisms that distinguish congeners was confirmed by in silico analysis. While mitochondrial intron variation is limited in comparison to nuclear introns, these exon-based primer sets provide robust tools for the amplification of mitochondrial introns across a wide range of plant species wherein useful polymorphisms can be identified.

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“…SSRs are ubiquitous in the genome of higher organisms and exhibit genetic polymorphism at inter- and intra-species levels (Bruford and Wayne 1993; Ellegren, 2004; Amiteye, 2021). Therefore, they have been widely used in population genetics (Chen et al, 2022; Sapkota et al, 2022;), genotyping, marker-assisted breeding, genome-wide association analysis (Li et al, 2014; Jha et al, 2021; Kim et al, 2021), forensic investigation (Li et al, 2021; Wang et al, 2022), evolutionary studies (Nowicki et al, 2021; Song et al, 2021; de Freitas et al, 2022), and conservation genetics (Rodríguez-Peña et al, 2018; Dong et al, 2022; Ming et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

Diouf

Zoclanclounon

Mboup

et al. 2023

Preprint

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Background: Microsatellite markers represent a low-cost and efficient tool for rapid genotyping as compared to single nucleotide polymorphism markers in laboratories with limited resources. For the economically important yam species widely cultivated in developing countries, very few microsatellite markers are available and no marker database has been developed to date. Herein, we conducted a genome-wide microsatellite marker development among four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam breeder community. Results: The screening of yam genomes resulted in 318,713; 322,501; 307,040 and 253,856 microsatellites in Dioscorea alata, D. rotundata, D. dumetorum, and D. zingiberensis, respectively. Mono-, di- and tri-nucleotides were the most important types of repeats in the different species and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, a subset of 17 markers were experimentally validated with good discriminatory power regarding the species and the ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at http://yamdb.42web.io/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. Conclusions: The present work is the first comprehensive microsatellite marker mining across several yam species and will contribute to advance yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam breeders, especially those in developing countries. Keywords: genotyping; Dioscoreacea; database; microsatellite; transferable markers

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

Cited by 10 publications

References 90 publications

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Plant mitochondrial introns as genetic markers - conservation and variation

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

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