Mining of microsatellites in mitochondrial genomes of order Hypnales (Bryopsida)
DOI:
https://doi.org/10.14719/pst.2019.6.sp1.697Keywords:
Bryophytes, Hypnales, Microsatellites, Simple Sequence RepeatsAbstract
Microsatellites or SSRs are the markers of selection due to their reproducibility, degree of polymorphism, distribution throughout the genome and co-dominant nature. Microsatellites are used primarily to study the genetic variability in various species and marker aided selection. Since microsatellites can be readily amplified by PCR, they have been utilized most extensively. To reduce time and cost to a great extent, the computational approach for identifying and developing microsatellite markers by mining nucleotide sequences is preferred over the conventional methods. In the present analysis, an in-silico method was used to detect microsatellites effectively in mitochondrial genomes of Anomodon rugelii (Müll. Hal.) Keissl., Anomodon attenuatus (Hedw.) Hueb., Climacium americanum (Renauld & Cardot) Kindberg, and Hypnum imponens Hedw. (Bryopsida; Hypnales). A total of 101 perfect microsatellites were mined with an average density of 1 microsatellite/4.21 kb. The hexa-nucleotide repeats were not detected in mitochondrial genomes of studied taxa. Di-nucleotides were seen to be the most frequent repeats followed by tetra-nucleotides. The identified microsatellites were also checked for variability in length between species. The mined microsatellites will be used for gene tagging, species identification and population genetic studies.
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