Genome-wide microsatellites and species specific markers in genus Phytophthora revealed through whole genome analysis
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ORIGINAL ARTICLE
Genome‑wide microsatellites and species specific markers in genus Phytophthora revealed through whole genome analysis Deepu Mathew1 · P. S. Anju1 · Amala Tom1 · Neethu Johnson1 · M. Lidia George1 · Sangeetha P. Davis1 · V. Ravisankar1 · K. N. Asha1 Received: 11 March 2020 / Accepted: 8 September 2020 © King Abdulaziz City for Science and Technology 2020
Abstract Genome wide microsatellite maps shall support Phytophthora systematics through the development of reliable markers, enabling species discrimination and variability analyses. Whole genome sequences of 17 Phytophthora accessions belonging to 14 species were retrieved from GenBank and the genome-wide microsatellites in each species were mined. A total of 51,200 microsatellites, including dinucleotide to decanucleotide motifs, have been identified across all the species and each one was characterized for uniqueness and repeat number. The P. infestans T30-4 genome had the highest (6873) and P. multivora 3378 had the lowest number of microsatellites (1802). Dinucleotide motifs (63.6%) followed by trinucleotide motifs (30.1%) were most abundant in all the genome. From 14 species, 250 microsatellites which are unique for the respective genomes are detailed along with their primer combinations and product sizes. P. sojae had the highest number of unique microsatellite motifs. Genome wide microsatellite maps for all the 14 Phytophthora species including the chromosome, position, motif, repeat number, forward and reverse primer sequences and expected PCR product size, for every microsatellite are presented. Markers based on the unique microsatellites could be used to identify each species, whereas the ones common to all species could be used to identify the genetic variability. Furthermore, to confirm the results, pure cultures of P. capsici, P. nicotianae and P. palmivora were procured from the Phytophthora Repository, DNA was isolated and the unique markers were screened across the species. The characteristic markers developed have confirmed the genome analysis results. Keywords Fungal taxonomy · Genome annotation · Microsatellite markers · Next generation sequencing (NGS) data analysis · Species identification · Simple sequence repeats (SSR)
Introduction Genus Phytophthora accommodates phytopathogenic oomycetes causing devastation in multiple crops. Even after describing more than 170 species, nearly 500 species are expected to be identified (Brasier 2009). Each species is found to have limited host range with characteristic symptoms. In the humid tropics, quick wilt of black pepper caused by P. capsici, bud rot of coconut caused by P. palmivora, late Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13205-020-02430-y) contains supplementary material, which is available to authorized users. * Deepu Mathew [email protected] 1
DBT‑Distributed Information Centre, IT‑BT Complex, Kerala Agricultural University, Thrissur, Kerala 680 656, India
blight of potato and tomato caused by P. infestans
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