Abstract
Main conclusion
Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm.
Abstract
Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon’s Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.
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Data availability
Downloadable dataset is available at https://usegalaxy.org/u/rioswillars/h/angiosperm-dataset.
Code availability
The code of Mfind tool is available at https://github.com/riosew/Mfind in a file named Mfind_script.txt).
Abbreviations
- CR:
-
Conserved region
- MSA:
-
Multiple sequence alignment
- SMI:
-
Shannon’s Measure of Information
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The authors thank the Faculty of Systems from the Autonomous University of Coahuila and the Instituto de Genética Barbara McClintock (IGBM) for their support in scientific research.
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Rios-Willars, E., Chirinos-Arias, M.C. Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm. Planta 259, 134 (2024). https://doi.org/10.1007/s00425-024-04420-3
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DOI: https://doi.org/10.1007/s00425-024-04420-3