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Manual reannotation of benthi PLCPs

JK Jiorgos Kourelis
SM Shivani Malik
OM Oliver Mattinson
SK Sonja Krauter
PK Parvinderdeep S. Kahlon
JP Judith K. Paulus
RH Renier A. L. van der Hoorn
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Amino acid sequences were extracted from the NbDE and Niben1.0.1 annotations based on the Pfam peptidase C1 domain (PF00112). Exhaustive tblastn using the identified PLCPs as a query and the Niben1.0.1 genome as subject was used to identify partial/not annotated PLCPs. Gene models were compared to the top five highest similarity genes identified by blastn with the NCBI RefSeq Nicotiana species as subject. Where needed, exon–exon boundaries and transcription start and termination sites of gene models were adjusted based on the NCBI RefSeq annotation. Truncated PLCP genes with frame-shift mutations were cross-validated against the independent Niben0.4.4, Nbv0.5, and Nbv0.3 genome assemblies to ensure that the mutation was not an artefact of genome assembly.

Copyright and License information: The Author(s) ©2020
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