In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

Tambarussi, Evandro Vagner; Melotto-Passarin, Danila Montewka; Gonzalez, Simone Guidetti; Brigati, Joice Bissoloti; Jesus, Frederico Almeida de; Barbosa, André Luís; Dressano, K.; Carrer, Helaine

doi:10.12702/1984-7033.v09n04a09

Cited by 18 publications

(10 citation statements)

References 31 publications

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“…Molecular techniques have made it possible to enlarge our understanding of the cytoplasmic genome by detecting the genetic variation in the two organelles viz., chloroplast and mitochondria. The chloroplast genome is widely used in plant systematic as well as taxonomic studies (Rajendrakumar et al 2007;Tambarussi et al 2009), as it is assumed to be slow-evolving, non-recombining (Clegg 1993) and densely populated with microsatellite repeats. The discovery of highly polymorphic SSRs in the chloroplast genome of plants has provided new opportunities for cytoplasmic analysis and phylogenetic studies (Powell et al 1996).…”

Section: Introductionmentioning

confidence: 99%

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

et al. 2015

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A basic understanding of the cytoplasmic diversity of Saccharum complex comprising of Saccharum species and related genera is essential for broadening the cytoplasmic base of sugarcane cultivars. In the present study markers generated by nine chloroplast microsatellite primer pairs designed from sugarcane chloroplast genome were used to establish the genetic relationship and phylogeny among 43 accessions belonging to different species of Saccharum and related genera representing the Saccharum complex. The polymorphic primer pairs amplified an average of six alleles per loci and possess relatively high polymorphism information content. Molecular diversity was estimated using 54 polymorphic markers. The overall chloroplast genetic diversity in the Saccharum complex was found to be 53 %. The genetic diversity among Saccharum species was 22 %. Among the Saccharum species S. spontaneum was found to be distinct from other species of Saccharum and cpSSR markers could efficiently distinguish S. spontaneum from rest of the Saccharum spcies. Ripidium, one of the most primitive among the Saccharum complex showed the highest genetic diversity (90 %) with Saccharum. Miscanthus, another primitive genus of Saccharum complex was found to be more closely related to Saccharum than Erianthus. In view of the high genetic diversity, the present study supports the utilization of different species of Erianthus in the sugarcane breeding programmes for broadening the cytoplasmic base of the sugarcane varieties.

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Section: Introductionmentioning

confidence: 99%

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

et al. 2015

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“…The main objective of this study was to analysis SSRs in chloroplast genome (cpDNA) of Olea species for their occurrence and distribution in both coding and noncoding regions. (Tambarussi et al 2009), Solanum lycopersicum EST-SSRs (1.3 SSR per kb) (Gupta et al 2010). However, an average frequency of SSRs in Olea species in present study (1.47 SSR per kb) is lower than found in loblolly pine EST-SSRs (42.9 SSR per kb), some cereal species EST-SSRs (6 SSR per kb) (Varshney et al 2002), palm EST-SSRs (4.4 SSR per kb) (Palliyarakkal et al 2011).…”

Section: Introductionmentioning

confidence: 99%

In Silico chloroplast SSRs mining of Olea species

Filiz

Koç

2012

Biodiversitas

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Filiz E, Koc E. 2012. In Silico chloroplast SSRs mining of Olea species. Biodiversitas 13: 114-117. Simple sequence repeat (SSR) markers are highly informative and have been widely applied as molecular markers in genetic studies. The purpose of present study is to analyze the occurrence and distribution of chloroplast SSRs in genic and intergenic regions from Olea species viz., Olea europaea, Olea europaea subsp. cuspidate, Olea europaea subsp. europaea, Olea europaea subsp. maroccana, Olea woodiana subsp. woodiana by using bioinformatics tools. We identified 1149 chloroplast SSRs (cpSSRs) in all genome and a total of 340 (29.6%) was located in genic regions. It was observed that the most abundant repeat types were found mononucleotide SSR (66.7 %) followed by trinucleotide SSR (28.3 %), dinucleotide (2.7%), tetranucleotide (1.5%) and pentanucleotide (0.8%). cpSSRs located in genic regions were identified only mono-and trinucleotide motifs, the most abundant of which was trinucleotide (16.2%) followed by mononucleotide (14.3%). All types of repeat motif (mono-, di-, tri-, tetra-and pentanucleotide) were detected except hexanucleotide motifs. According to SSRs analysis, the most abundant observed motifs were identified for mono-, di-, tri-, tetra-and pentanucleotide cpSSRs A/T, AT/TA, AAG/CTT, AAAG/AGTTT, and AATCC/ATTGG respectively. This study results provided scientific base for phylogenetics, evolutionary genetics and diversity studies on different Olea species in future.

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“…The plastome is widely used in plant systematic studies to infer plant phylogenies at different taxonomic levels (Rajendrakumar et al, 2007;Tambarussi et al, 2009), in part because it is slowly evolving and is assumed to be non-recombining (Clegg, 1993).…”

Section: Introductionmentioning

confidence: 99%

Characterization of chloroplast DNA microsatellites from Saccharum spp and related species

Melotto-Passarin¹,

Tambarussi²,

Dressano³

et al. 2011

Genet. Mol. Res.

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ABSTRACT. Microsatellites, or simple sequence repeats (SSRs), and their flanking regions in chloroplast genomes (plastomes) of some species of the family Poaceae were analyzed in silico to look for DNA sequence variations. Comparison of the complete chloroplast DNA sequences (cpDNAs) of sugarcane (Saccharum hybrid cv. SP-80-3280 and S. officinarum cv. NCo310) and related species, Agrostis stolonifera, Brachypodium distachyon, Hordeum vulgare subsp vulgare, Lolium perenne, Oryza nivara, O. sativa subsp indica, O. sativa subsp japonica, Sorghum bicolor, Triticum aestivum, Zea mays, and Z. mays cv. B73, allowed us to examine the organization of chloroplast SSRs (cpSSRs) in genic and intergenic regions. We identified 204 cpSSRs in the sugarcane cpDNA; 22.5% were in genic regions. The ndh, rps, trn, and rpl gene clusters of the chloroplasts had the most repeats. Mononucleotide repeats were the most abundant cpSSRs in these species; however, di-, tri-, tetra-, penta-, and hexanucleotide repeats were also identified. Chloroplast SSRs in Poaceae variability possible; repeat motifs are not uniformly distributed across the Poaceae plastomes, but are mostly confined to intergenic regions. Phylogeny was determined by maximum parsimony and neighborjoining inference methods. The cpSSRs of these species were found to be polymorphic. It appears that individual cpSSRs in the Poaceae are stable, at least over short periods of evolutionary time. We conclude that the plastome database can be exploited for phylogenetic analysis and biotechnological development.

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In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

Abstract: -

Cited by 18 publications

References 31 publications

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

In Silico chloroplast SSRs mining of Olea species

Characterization of chloroplast DNA microsatellites from Saccharum spp and related species

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