Microsatellite analysis in the genome of Acanthaceae: An in silico approach

Abstract

Background:Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes.Objective:The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences.Materials and Methods:The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing.Results:Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome.Conclusion:The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future.

Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

“…Earlier, Wee et al [ 33 ] sequenced 192 clones, and 102 colonies were obtained with desirable SSRs. Furthermore, Kaliswamy et al [ 34 ] also reported that di- and trinucleotide repeats had more occurrences in the Acanthaceae family, which is similar to our findings. In addition to that, Lagercrantz et al [ 35 ] and La Rota et al [ 36 ] noticed that GA/CT microsatellite motifs are more abundant than the CA/GT motif in the plant species, which is similar to the present investigation.…”

Characteristic and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Medicinal Plants of Schisandraceae

“…Because of the characteristics of neutral markers, the highly variable numbers of repeats, and the relative conservatism of flanking sequences of SSRs, they are widely distributed in the genome of organisms. Microsatellites or SSRs play a major role in polymorphism analysis and in marker-assisted selection [ 39 ].…”