Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in brown trout (Salmo trutta)

Ma, Haibing; Huang, Tianqing; Gu, Wei; Liu, Enhui; Wang, Gaochao; Wang, Bingqian; Zhou, Jianshe; Xu, Gefeng

doi:10.1007/s12686-023-01341-3

Cited by 1 publication

(1 citation statement)

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“…GMATA software allows for the analysis of large sequences with large capacity and fast processing [13]. For SSR mining and marker development, the GMATA tool has been used for various organisms: Acacia pachyceras Schwartz [31], spinach [32], brown trout (Salmo trutta) [33], Nicotiana [34], and olive (Olea europaea L.) [35]. However, the distribution of SSRs for Monilinia spp.…”

Section: Discussionmentioning

confidence: 99%

One Step Forwards in Knowledge of Blossom Blight Brown Rot Disease: Monilinia spp. SSR Marker Database

Antanynienė,

Stanys,

Frercks

2024

Microorganisms

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A freely available Monilinia spp. marker database was created, containing microsatellite (SSR) data of the three most essential European fungal pathogens: M. fructigena, M. laxa, and M. fructicola. These pathogens cause brown rot blossom blight. Microsatellites were identified using the bioinformatics tool Genome-wide Microsatellite Analyzing Toward Application (GMATA). The database provides information about SSR markers: forward and reverse sequences of the primers, fragment sizes, SSR motifs (and repeats), and the exact locations with the coordinates in the reference genome. This database currently contains information about 39,216 SSR motifs and 26,366 markers. In total, eight primers generated in silico were validated experimentally and they are marked in the database. All scientists can join this collaboration by adding their experimental data. This database is the initial start of organizing Monilinia spp. molecular data worldwide and, in the future, it could be extended by adding more molecular and genomic information.

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