Development of genomic resources for four potential environmental bioindicator species: Isoperla grammatica, Amphinemura sulcicollis, Oniscus asellus and Baetis rhodani

AbstractA low-coverage genome was generated for each of four environmental key-species of macroinvertebrate taxa for the primary purpose of microsatellite marker development. De novo assemblies and microsatellite markers were designed for the freshwater species Isoperla grammatica, Amphinemura sulcicollis, and Baetis rhodani but have not been completed for the common shiny woodlice Oniscus asellus. Here, the data is made available, and the methods and pipeline are described which led to the creation of this resource. As widespread and functionally important organisms, which are often neglected in favour of studies on vertebrates, this data will be a useful resource for further research.

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De novo assembly and microsatellite marker development of the transcriptome of the endangered Brachymystax lenok tsinlingensis

Genes & Genomics ◽

10.1007/s13258-020-00939-3 ◽

2020 ◽

Vol 42 (7) ◽

pp. 727-734

Author(s):

Sien Wen ◽

Ping Li ◽

Feng Wang ◽

Jiale Li ◽

Haixia Liu ◽

...

Keyword(s):

Microsatellite Marker ◽

De Novo Assembly ◽

De Novo ◽

Marker Development ◽

Brachymystax Lenok Tsinlingensis ◽

Brachymystax Lenok

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Microsatellite markers for Eucalyptus pilularis (Subgenus Eucalyptus); sourcing genetic markers outside the subgenus

Silvae Genetica ◽

10.1515/sg-2013-0030 ◽

2013 ◽

Vol 62 (1-6) ◽

pp. 246-255 ◽

Cited By ~ 1

Author(s):

M. Shepherd ◽

C. Bihua ◽

R. Henry

Keyword(s):

Molecular Marker ◽

Microsatellite Markers ◽

Microsatellite Marker ◽

Genetic Markers ◽

De Novo ◽

Sequence Divergence ◽

Economic Importance ◽

Evolutionary Divergence ◽

Species Markers ◽

Efficient Transfer

AbstractMicrosatellite markers remain the most broadly used molecular marker in eucalypt genetics. A major advantage of microsatellite markers is that they often transfer readily between related taxa circumventing the need to develop new markers de novo in each species. Markers have been developed for a number of species of major economic importance, mainly from the Subgenus Symphyomyrtus, but these may also be available for use in species of lesser economic importance from other subgenera. Here we report on the sourcing of microsatellite markers for E. pilularis (Subgenus Eucalyptus (Formerly Monocalyptus)) from species outside the subgenus. Ninety-seven precent (60 out of 62) of loci that amplified in the source taxon (E. grandis) also amplified in the target taxon E. pilularis. By characterising them on a diversity panel (n=24) and a pedigree, a subset of 41 loci were distilled out that could be scored reliably and were polymorphic (Mean unbiased heterozygosity= 0.81). Predictions of efficient microsatellite marker transfer among eucalypts based on low evolutionary divergence have largely been borne out and are congruent with accumulating evidence of low sequence divergence within Eucalyptus. Upon this favourable background for microsatellite marker transfer, this study indicates highly efficient transfer is possible by identifying loci with broad PCR optima and adoption of approaches that favour cross-species transfer.

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