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Entomophthora muscae strain UCB genome assembly, annotation, genome completeness, and transposon content

Assembly

Primary nanopore data was generated at the Harvard Bauer Core facility and initially assembly by C. Elya and then later scaffolded with 10X data.

Repeat Masking was run in the RM_Run folder which provides an archive of the repeat modeler results. Archives of the produced repeat libraries and reports are also provided in the (repeatmasker_plots)[/repeatmasker_plots] and (repeatmasker_reports)[repeatmasker_reports] folders.

Annotation

Archive of genome repeat masking and genome annotation process with Funannotate for Entomopthora muscae genome and comparisons among related species. The annotation folder contains pipeline folder for slurm job running on the UCR HPCC.

The approach uses public RNASeq data for transcript production and training gene predictors. Note that the public RNASeq are from different isolate which may be a cryptic species.

This workflow includies re-annotating public genomes in order to test hypotheses that gene content differences are due to real biological differences and not simply annotation pipeline differences.

Citation

This annotation and repeat data is used in the Emuscae_Comparative repository which is tightly linked to this one for the associated manuscript.

Jason E Stajich, Brian Lovett, Emily Lee, Angie M. Macias, Ann E Hajek, Benjamin L de Bivort, Matt T. Kasson, Henrik H. De Fine Licht, Carolyn Elya. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. Submitted.

Curated by Jason Stajich - jason.stajich[AT]ucr.edu @hyphaltip Lab Site