Dig-up primers : a pipeline for identification of polymorphic microsatellites loci within assemblies of related species

Turudić, Ante (author), Liber, Zlatko (author), Grdiša, Martina (author), Jakše, Jernej (author), Varga, Filip (author), Poljak, Igor (author), Šatović, Zlatko (author)

Simple sequence repeats (SSRs) have become one of the most popular molecular markers and are used in numerous fields, including conservation genetics, population genetic studies, and genetic mapping. Advances in next-generation sequencing technology and the growing amount of genomic data are driving the development of bioinformatics tools for SSR marker design. These tools work with different combinations of input data, which can be raw reads or assemblies, and with one or more input datasets. We present here a new strategy and implementation of a simple standalone pipeline that utilizes more than one assembly for the in silico design of PCR primers for microsatellite loci in more than one species. Primers are tested in silico to determine if they are polymorphic, eliminating the need to test time-consuming cross-species amplification in the laboratory. The end result is a set of markers that are in silico polymorphic in all analyzed species and have great potential for the identification of interspecies hybrids. The efficiency of the tool is demonstrated using two examples at different taxonomic levels and with different numbers of input assemblies to generate promising, high-quality SSR markers.

• Language: English
• Keywords: SSRs, NGS, SSR primer design, in silico PCR
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2024
• Number of pages: 10 str.
• Numbering: Vol. 25, iss. 6, art. 3169
• PID: 20.500.12556/RUL-156393
• UDC: 577.2
• ISSN on article: 1422-0067
• DOI: 10.3390/ijms25063169
• COBISS.SI-ID: 196357123
• Publication date in RUL: 23.05.2024

Record is a part of a journal

• Title: International journal of molecular sciences
• Shortened title: Int. j. mol. sci.
• Publisher: MDPI
• ISSN: 1422-0067
• COBISS.SI-ID: 2779162

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: bioinformatika, molekularna genetika, molekularni markerji, mikrosateliti, SSR markerji, genom

Projects

• Funder: HRZZ - Croatian Science Foundation
• Project number: PK.1.1.02.0005
• Name: Research and Development of Plant Genetic Resources for Sustainable Agriculture