SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences

Abstract

Microsatellites or simple sequence repeats (SSRs) are short tandem repeats of DNA widespread in genomes and transcriptomes of diverse organisms and are used in various genetic studies. Few software programs that mine SSRs can be further used to mine polymorphic SSRs, and these programs have poor portability, have slow computational speed, are highly dependent on other programs, and have low marker development rates. In this study, we develop an algorithm named Simple Sequence Repeat Molecular Marker Developer (SSRMMD), which uses improved regular expressions to rapidly and exhaustively mine perfect SSR loci from any size of assembled sequence. To mine polymorphic SSRs, SSRMMD uses a novel threestage method to assess the conservativeness of SSR flanking sequences and then uses the sliding window method to fragment each assembled sequence to assess its uniqueness. Furthermore, molecular biology assays support the polymorphic SSRs identified by SSRMMD. SSRMMD is implemented using the Perl programming language and can be downloaded from https://github.com/GouXiangJian/SSRMMD.

The Insights into Mitochondrial Genomes of Sunflowers

“…SSR loci were identified by SSRMMD tool [ 63 ] using simple regular expression mode and 10, 6, 5, 4, 4, and 4 repeat number thresholds for mono, di-, tri-, tetra-, penta-, and hexanucleotide motifs, respectively. Common and polymorphic SSR loci were identified pairwise between mitogenomes by conservativeness of 100 bp SSR flanking sequences scored with Needleman–Wunsch alignment.…”

Oil Palm SSR Resource Interface (Opsri) – Web-Based Bioinformatic Analysis Pipeline for SSR Mining

“…The existing EST collection and increasing availability of transcriptome and other related sequences, suggest that mining of SSRs from this enormous resource requires considerable technical skills, time and cost for successful execution. A number of software and scripts are available to assist in identifying SSR in sequences such as FullSSR (Metz et al, 2016), GMATA (Wang and Wang, 2016), Krait (Du et al, 2018) and recently reported Simple Sequence Repeat Molecular Marker Developer (SSRMMD) (Gou et al, 2020). Nevertheless, data mining of SSRs would be more practical and cheaper when retrieved from an organised database (Vieira et al 2016), especially one with detailed information on the polymorphism of the SSR markers in selected breeding lines.…”

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

“…To date, molecular markers including isozyme ( Fan et al, 2009 ), random amplified polymorphic DNA (RAPD) ( Chi et al, 2010 ), amplified fragments length polymorphism (AFLP) ( Liu et al, 2013 ; Liu et al, 2014 ), mitochondrial DNA ( Guo et al, 2012 ; Shan et al, 2017 ; Hui et al, 2018 ), microsatellites DNA ( Lee et al, 2013 ; Yue et al, 2022 ), and single nucleotide polymorphism (SNP) ( Duan et al, 2022a ) were developed and used in population genetic analysis of P. trituberculatus . Among these markers, microsatellite DNA markers (simple sequence repeats, SSRs) have become an ideal molecular marker in population genetics research because of their co-dominant inheritance, high polymorphism, reproducibility, hyper-variable, transferability, random distribution in the genome, and ease of analysis via PCR ( Gou et al, 2020 ; Pavan Kumara et al, 2020 ; Zhu et al, 2021 ; Lu et al, 2022 ). Such markers are often used to obtain genetic diversity coefficients, which can provide a basis for genetic protection strategies.…”