GMATo: A novel tool for the identification and analysis of microsatellites in large genomes

Wang, Xuewen; Lü, Peng; Luo, Zhou

doi:10.6026/97320630009541

Cited by 95 publications

(72 citation statements)

References 8 publications

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“…GMATo comes with a Java graphical interface and is ready to execute immediately after downloading (Wang et al, 2013). GMATo results are presented as a table of SSR loci statistics.…”

Section: Software For Microsatellite Developmentmentioning

confidence: 99%

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The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century

et al. 2016

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Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers.

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“…GMATo comes with a Java graphical interface and is ready to execute immediately after downloading (Wang et al, 2013). GMATo results are presented as a table of SSR loci statistics.…”

Section: Software For Microsatellite Developmentmentioning

confidence: 99%

“…Its results are in tabular form, giving a summary of different statistics, such as the frequency of a specific microsatellite type. However, some studies indicate that MISA may have mined redundantly in overlapped microsatellites (e.g., Wang et al, 2013; Hodel et al, 2016). …”

Section: Software For Microsatellite Developmentmentioning

confidence: 99%

The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century

et al. 2016

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“…All reads of seven accessions were also combined and used to assembly transcripts, which is called the 'pool' of transcripts. Functional annotation (Gene Ontology-GO and Kyoto Encyclopedia of Genes and Genomes-KEGG) was performed by means of sequence similarity (e-value cutoff of 10 -5 ) using Trapid (Van Bel et al, 2013), and SSRs were identified using GMATo (Wang et al, 2013) and SSRIT (http://www.gramene.org/db/markers/ ssrtool). Transcripts were aligned to Japanese apricot (Prunus mume) and peach (Prunus persica) genomes using Blast2go software (Conesa et al, 2005).…”

Section: De Novo Transcriptome Assembly and Functional And Structuralmentioning

confidence: 99%

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Köse¹,

Çetinsağ²,

Gürcan³

2017

Turk J Agric For

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Apricot (Prunus armeniaca) is an important fruit crop worldwide. We have performed a de novo transcriptome assembly for 7 apricot accessions ('Stark Early Orange' (SEO), 'Hacıhaliloğlu' (HH), 'Perfection' , 'Iğdır' , 'Roxana' , 'Esen1' , and 'Esen2'), which yielded a total number of transcripts ranging from 30,363 for 'SEO' to 59,751 for 'Iğdır' . The pool of the reads produced from 7 accessions were assembled into 85,766 transcripts, with an average of 1165.69 nt. Functional annotation (Gene Ontology-GO and Kyoto Encyclopedia of Genes and Genomes-KEGG) was performed successfully for the transcripts. Simple sequence repeats (SSRs) were searched in the transcript pool and 14,722 di-, tri-tetra-, penta-, and hexanucleotide motif loci with a minimum of 5 repetitions for all motifs were identified. Primers were designed for 206 loci, and 72 of them were found to be polymorphic by amplifying diverse 24 apricot accessions, including 7 Plum Pox Virus (PPV)-resistant and 17 PPV-susceptible accessions. In order to test the amplification success of publicly available genomic SSRs (gSSRs) for diverse apricot accessions, an additional 88 published Prunus gSSRs were characterized amplifying the same 24 apricots and only 54 (62%) produced polymorphic bands. The new EST-SSRs could be a reliable source of primers for characterization and mapping studies of apricots, especially because they mostly flank easily scorable tri-and tetranucleotide repeats.

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“…We will then be able to mine the genomes in silico using software such as GMATo (Genome Microsatellite Analyzing Tool) (Wang et al 2013) or Phobos (Mayer 2006) for more robust microsatellite markers such as tetranucleotide repeats within these species. This will be particularly useful for the blue wildebeest which appears to need more informative microsatellite markers most urgently.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of microsatellites for common ungulates in the South African wildlife industry

Miller

Clarke

Bloomer

et al. 2016

Conservation Genet Resour

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Wildlife is a multi-million dollar industry in South Africa ranging from intensively farmed animals on small properties to free-roaming animals in large functional ecosystems. Specific concerns surrounding the conservation value of the intensively managed wildlife have been raised. Increasingly it is recognised that genetics must be considered when developing conservation policy and management practices. Minimal genetic data are available to assist with decisions within the industry.Microsatellite markers have been developed for some species and are currently used for individual identification, parentage assessment and to inform translocation decisions. However, validation for standardized application in wildlife management has not been completed. Common species for which conservation management decisions have to be made include: Cape buffalo (Syncerus caffer), blue wildebeest (Connochaetes taurinus taurinus), common impala (Aepyceros melampus) and sable antelope (Hippotragus niger). Using existing microsatellite markers for domestic and wild species, we have developed multiplex panels for use in these species. We discriminated between 751 buffalo (four pairs were not distinguishable), 1307 blue wildebeest (three pairs were not distinguishable), 580 impala and 493 sable antelope. We determined parentage in four case studies using a combination of microsatellite and demographic data. We also tested microsatellite markers on roan antelope (Hippotragus equinus), gemsbok (Oryx gazella) and eland (Tragelaphus oryx) and report preliminary data. Further research to improve this validation includes: extensive sampling from more diverse areas, targeted or full genome sequencing to identify additional microsatellite loci, development of sampling kits and training of veterinarians, as well as expansion of the species tested.

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GMATo: A novel tool for the identification and analysis of microsatellites in large genomes

Cited by 95 publications

References 8 publications

The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century

The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Evaluation of microsatellites for common ungulates in the South African wildlife industry

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