ArticleBMC plant biology2014
Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera.
Article in BMC plant biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 28 citations in OpenAlex.
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- The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence.The plant genome · 2021Article
- De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism.BMC genomics · 2021Article
- Development of EST-SSR markers and their application in an analysis of the genetic diversity of the endangered species Magnolia sinostellata.Molecular genetics and genomics : MGG · 2019Article
- Characterization and Application of EST-SSR Markers Developed From the Transcriptome ofFrontiers in genetics · 2019Article
- Characterization of the Rosa roxburghii Tratt transcriptome and analysis of MYB genes.PloS one · 2019Article
- Generation and characterization of expressed sequence tags (ESTs) from coralloid root cDNA library ofPlant diversity · 2018Article
- De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila.Scientific reports · 2016Article
- Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing.Molecules (Basel, Switzerland) · 2016Article
- Intraspecific variations in cardamom (Elettaria cardamomum Maton): assessment of genomic diversity by flow cytometry, cytological studies and ISSR analysis.SpringerPlus · 2016Article
- Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda).BMC genetics · 2015Article
- Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.).BMC plant biology · 2015Article
- Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants.BMC genomics · 2015Article
- Microsatellite resources of Eucalyptus: current status and future perspectives.Botanical studies · 2014Review
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Authors and funding
5 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSimple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).
resultsOur analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.
conclusionsOur analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
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