Isolation by the 5′ anchored PCR technique and characterization of eighteen microsatellite loci in horseshoe crab (Tachypleus gigas)

Ling, Liew Pui; Adibah, A.B.; Tan, Soon Guan; Christianus, Annie; Faridah, Q. Z.

doi:10.1007/s12041-011-0115-5

Cited by 5 publications

(3 citation statements)

References 7 publications

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“…For non-model organisms, microsatellite loci were generally identified by 5̕ anchor PCR (Ling et al, 2013), transcriptome sequence analysis (Ariede et al, 2018;Han et al, 2018), and microsatellite library screening (Bazsalovicsová et al, 2018) and development of microsatellite loci through cross-species amplification of closely related species (Gravley et al, 2018). In the present study, RAD-seq method was used for isolating microsatellite loci in C. aculeata.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide assessment and characterization of simple sequence repeats (SSRs) makers for Capoeta aculeata (Valenciennes, 1844) using NGS data

Gandomkar

Nazari

Hosseini

et al. 2022

injoar

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The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemics to Iran. However, the investigation of a population genetic structure of this species is limited by the low number of molecular markers currently described. In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We sequenced 60 individuals from three populations occurring in the Zagros basin. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16. (average=7.89). The results showed that, the polymorphism information content (PIC) of these SSR loci varied from 0.254 to 0.888. The observed heterozygosity (Ho) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (He) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p<0.05). These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate populations and other closely related species.

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Section: Discussionmentioning

confidence: 99%

Genome-wide assessment and characterization of simple sequence repeats (SSRs) makers for Capoeta aculeata (Valenciennes, 1844) using NGS data

Gandomkar

Nazari

Hosseini

et al. 2022

injoar

View full text Add to dashboard Cite

show abstract

“…For non-model organisms, microsatellite loci were generally identi ed by 5 anchor PCR (Ling et al 2013), transcriptome sequence analysis (Ariede et al 2018;Han et al 2018), and microsatellite library screening (Bazsalovicsová et al 2018) and development of microsatellite loci through cross-species ampli cation of closely related species (Gravley et al 2018). In the present study, RAD-seq method was used for isolating microsatellite loci in C. aculeata.…”

Section: Discussionmentioning

confidence: 99%

Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844)

et al. 2021

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The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of a population genetic structure of this species is limited by the low number of molecular markers currently described. In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We sequenced 60 individuals from three populations occurring in the Zagros basin. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16. (average = 7.89). The results showed that, the polymorphism information content (PCI) of these SSR loci varied from 0.254 to 0.888. The observed heterozygosity (Ho) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (He) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated signi cantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p< 0.05). These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate populations and other closely related species.

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“…While the EST-based SSRs still suffer from the drawback that gene / genes not expressing at a particular organ / time are not included, high-throughput DNA sequencing requires substantial investment. The 5’-anchored polymerase chain reaction [ 28 , 29 ] is one of the simplest and fast methodsfor developing SSR enriched genomic libraries and subsequent isolation of microsatellites that does not require substantial investment.…”

Section: Introductionmentioning

confidence: 99%

Development and characterization of a new set of genomic microsatellite markers in rice bean (Vigna umbellata (Thunb.) Ohwi and Ohashi) and their utilization in genetic diversity analysis of collections from North East India

et al. 2017

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Rice bean [Vigna umbellate (Thumb.) Ohwi and Ohashi] is an underutilized crop believed to be domesticated in the Myanmar-Thailand region of Asia. In India, rice bean is mainly cultivated in the North-Eastern Hills, which is a hotspot for biological diversity. A 5' anchored PCR was used to develop microsatellite markers in rice bean. Twenty-eight specific primer pairs were designed and employed to characterize sixty five ricebean accessions collected from North East India. A total of 179 alleles were amplified with an average of 6.393 alleles per locus. The gene diversity was high (mean 0.534) in the accessions collected from Darjeeling, Nagaland and Manipur, which are bordering areas with East Nepal and Myanmar, respectively. Exceptionally high outcrossing rate was observed in the entire population. Population structure analysis identified three distinct clusters in which accessions collected from areas bordering Myanmar and East Nepal grouped separately. Using a combination of STRUCTURE and Principal Coordinate Analysis, relative affinity of the intermediate accessions could be established. However, differences in allelic counts among populations were non-significant. The results showed that there is a high level of genetic diversity within the accessions, with high outcrossing rate.

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Isolation by the 5′ anchored PCR technique and characterization of eighteen microsatellite loci in horseshoe crab (Tachypleus gigas)

Cited by 5 publications

References 7 publications

Genome-wide assessment and characterization of simple sequence repeats (SSRs) makers for Capoeta aculeata (Valenciennes, 1844) using NGS data

Genome-wide assessment and characterization of simple sequence repeats (SSRs) makers for Capoeta aculeata (Valenciennes, 1844) using NGS data

Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844)

Development and characterization of a new set of genomic microsatellite markers in rice bean (Vigna umbellata (Thunb.) Ohwi and Ohashi) and their utilization in genetic diversity analysis of collections from North East India

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