ArticleMarine biotechnology (New York, N.Y.)
Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy.
Article in Marine biotechnology (New York, N.Y.). The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
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- Genomic Analysis of the Giant Red Shrimp (Genes · 2024Article
- Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management ofAnimals : an open access journal from MDPI · 2024Article
- Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome.PloS one · 2024Article
- Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing.Molecular biology reports · 2021Article
- Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei).BMC genomics · 2020Article
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- The First Genome Survey of the Antarctic Krill (Marine drugs · 2020Article
- Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis.Scientific reports · 2019Article
- Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes.World journal of microbiology & biotechnology · 2016Article
- First haploid genetic map based on microsatellite markers in Senegalese sole (Solea senegalensis, Kaup 1858).Marine biotechnology (New York, N.Y.) · 2015Article
- Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla).PloS one · 2015Article
- Microsatellites in Pursuit of Microbial Genome Evolution.Frontiers in microbiology · 2015Review
- Genome-wide analysis of simple sequence repeats in marine animals-a comparative approach.Marine biotechnology (New York, N.Y.) · 2014Article
- Current status of genetics and genomics of reared penaeid shrimp: information relevant to access and benefit sharing.Marine biotechnology (New York, N.Y.) · 2013Review
- Use of comparative genomics to develop EST-SSRs for red drum (Sciaenops ocellatus).Marine biotechnology (New York, N.Y.) · 2012Article
- Development of type I genetic markers from expressed sequence tags in highly polymorphic species.Marine biotechnology (New York, N.Y.) · 2011Article
- Sixteen polymorphic simple sequence repeat markers from expressed sequence tags of the Chinese Mitten Crab Eriocheir sinensis.International journal of molecular sciences · 2010Article
- Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis.BMC genomics · 2007Article
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Authors and funding
6 authors.
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Abstract
We report on the data mining of publicly available Litopenaeus vannamei expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers and on their transferability between related Penaeid shrimp species. Repeat motifs were found in 3.8% of the evaluated ESTs at a frequency of one repeat every 7.8 kb of sequence data. A total of 206 primer pairs were designed, and 112 loci were amplified with the highest success in L. vannamei. A high percentage (69%) of EST-SSRs were transferable within the genus Litopenaeus. More than half of the amplified products were polymorphic in a small testing panel of L. vannamei. Evaluation of those primers in a larger testing panel showed that 72% of the markers fit Hardy-Weinberg equilibrium, which shows their utility for population genetic analysis. Additionally, a set of 26 of the EST-SSRs were evaluated for Mendelian segregation. A high percentage of monomorphic markers (46%) proved to be polymorphic by singles-stranded conformational polymorphism analysis. Because of the high number of ESTs available in public databases, a data mining approach similar to the one outlined here might yield high numbers of SSR markers in many animal taxa.
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