FullSSR: Microsatellite Finder and Primer Designer

Metz, Sebastián; Cabrera, Juan Manuel; Rueda, Eva Carolina; Giri, Federico; Amavet, Patricia Susana

doi:10.1155/2016/6040124

Cited by 19 publications

(11 citation statements)

References 15 publications

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“…A large number of perfect SSR with mono-, di-, tri-, tetra-, penta-, and hexa-motifs were found, but their numbers varied with MISA and FULL SSR (Metz et al 2016). The average numbers of SSRs were 2329 with MISA and 7870 with FULL SSR.…”

Section: The Abundance Of Ssrs In Rubus Ellipticus Sequencesmentioning

confidence: 95%

“…SSR motifs were identified in assembled sequenced data using MISA (http://pgrc.ipk-gater slebe n.de/misa) (Xu et al 2013) and with FULL SSR (Metz et al 2016). Only perfect SSRs of mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide (nt) motifs with default parameters (number of uninterrupted repeat units) of more than 10, 7, 6, 5, 4, and 4, respectively, were targeted.…”

Section: Unigene Analysis and Ssr Developmentmentioning

confidence: 99%

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Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers

et al. 2019

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Key message Rubus ellipticus is a wild crop having less number of EST-SSR markers. First attempt was made towards the transcriptomics data analysis and generation of EST-SSR markers which were used in genetic diversity and transferability studies. Abstract Rubus ellipticus is a raspberry with yellow fruits, native to tropical and subtropical India and Asia. Leaves of Rubus ellipticus 'Kumarhatti' collection were utilized for cDNA library construction. More than 15 million sequencing reads were generated using NextSeq 500 Illumina RNA-seq technology. The DNASTAR software was used for de novo assembly from which 7777 unigenes with an average length of 500 bp was obtained. These unigenes were annotated using public databases, including NCBI non-redundant and gene ontology. De novo assembly of R. ellipticus unigenes found the highest similarity to apple than to other members of Rosaceae. This is the first attempt to use the Illumina platform of RNA sequencing and de novo assembly for R. ellipticus without a reference genome. In this study, unigenes were used for SSR marker development. ESTs containing SSR motifs were extracted using an online Microsatellite Identification Tool (MISA). SSR primers were designed from the SSR containing 704 EST sequences using the Websat software. Total 304 EST-SSRs primers were successfully designed, out of which 68 randomly selected primer pairs were custom synthesized and used for validation. Real-time PCR was also performed to analyze the relationship of transcriptional factors with fruit ripening. Out of 68 primer pairs, 61 were found to be informative in R. ellipticus, whereas 65 primer pairs were informative in the five tested genera of Rosaceae, i.e., pear, peach, apple, rose, and strawberry with 95.3% and 93.5% polymorphism, leading to the conclusion that these marker systems are very efficient to carryout diversity and cross transferability study in Rosaceae genera.

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Section: The Abundance Of Ssrs In Rubus Ellipticus Sequencesmentioning

confidence: 95%

Section: Unigene Analysis and Ssr Developmentmentioning

confidence: 99%

Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers

et al. 2019

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“…Its research goal is focused on population genetics studies, with emphasis in conservation questions related to non-model wetland organisms that are endangered or managed. The laboratory has obtained molecular markers (microsatellites) with traditional methods and NGS technologies (Rueda et al, 2011a,b ;Metz et al, 2016;Ojeda et al, 2017). The fieldwork comprises the area of the La Plata basin, which it is the second-largest river basin of South America, including major rivers such as the Parana, Paraguay, and Uruguay systems.…”

Section: Rabid Fishmentioning

confidence: 99%

“…The fieldwork comprises the area of the La Plata basin, which it is the second-largest river basin of South America, including major rivers such as the Parana, Paraguay, and Uruguay systems. The research group obtained and analyzed fish samples from different migratory and commercially exploited species (Rueda et al, 2011a(Rueda et al, ,b, 2013(Rueda et al, , 2017Metz et al, 2016;Ojeda et al, 2017) resulting in a huge collection of samples donated by many collaborators, with different biological issues, and including more than 20 sites from five countries and four species: Prochilodus lineatus, Salminus brasiliensis, Leporinus obtusidens, and Pseudoplatystoma corruscans.…”

Section: Rabid Fishmentioning

confidence: 99%

Tools for Evolutionary and Genetic Analysis (TEGA): A new platform for the management of molecular and environmental data

Elías

Rueda

2020

Genet. Mol. Biol.

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Population genetics studies the distributions and changes in population allele frequencies in response to processes, such as mutation, natural selection, gene flow, and genetic drift. Researchers daily manage genetic, biological, and environmental data of the samples, storing them in text files or spreadsheets, which makes it difficult to maintain consistency and traceability. Here we present TEGA, a WEB-based stand-alone software developed for the easy analysis and management of population genetics data. It was designed to: 1) facilitate data management, 2) provide a way to execute the analysis procedures, and 3) supply a means to publish data, procedures, and results. TEGA is distributed under the GNU AGPL v3 license. The documentation, source code, and screenshots are available at https://github.com/darioelias/TEGA. In addition, we present Rabid Fish, the first implementation of TEGA in the Genetics Labortory of the Faculty of Humanities and Sciences at the National University of the Litoral, where research focuses on population genetics studies applied to non-model organisms.

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“…PERF (Avvaru et al, 2017) matches each potential substring in accordance with a set of pre-computed repeat strings. Other programs including TROLL (Castelo et al, 2002), MfSAT (Chen et al, 2011), ProGeRF (Silva et al, 2015), and FullSSR (Metz et al, 2016) have also been developed. In addition, imperfect SSR detection algorithms have also been reported, such as IMEx (Mudunuri and Nagarajaram, 2007), and Krait (Du et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences

Gou

Shi

et al. 2020

Front. Genet.

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Microsatellites or simple sequence repeats (SSRs) are short tandem repeats of DNA widespread in genomes and transcriptomes of diverse organisms and are used in various genetic studies. Few software programs that mine SSRs can be further used to mine polymorphic SSRs, and these programs have poor portability, have slow computational speed, are highly dependent on other programs, and have low marker development rates. In this study, we develop an algorithm named Simple Sequence Repeat Molecular Marker Developer (SSRMMD), which uses improved regular expressions to rapidly and exhaustively mine perfect SSR loci from any size of assembled sequence. To mine polymorphic SSRs, SSRMMD uses a novel threestage method to assess the conservativeness of SSR flanking sequences and then uses the sliding window method to fragment each assembled sequence to assess its uniqueness. Furthermore, molecular biology assays support the polymorphic SSRs identified by SSRMMD. SSRMMD is implemented using the Perl programming language and can be downloaded from https://github.com/GouXiangJian/SSRMMD.

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FullSSR: Microsatellite Finder and Primer Designer

Cited by 19 publications

References 15 publications

Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers

Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers

Tools for Evolutionary and Genetic Analysis (TEGA): A new platform for the management of molecular and environmental data

SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences

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