Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review


Analysis of gene families and identification of homologous genes are important for phylogenetic analysis
and for translating results from model to crop species. While numerous plant genomes have been sequenced
and made available, the identification of gene models can be difficult, in particular for large gene families
arranged in tandem repeats or encoding proteins with a variable number of internal repeats. Thus, correct
annotation of plant receptor kinases (PRK) is a challenge. Here, we describe a workflow for the semi-­
manual extraction, annotation, and verification of genes from annotated gene models as well as from
non-­annotated DNA regions. This protocol allows the efficient identification of gene family member of
PRK from most available plant genomes.
Original languageEnglish
Title of host publicationPlant Receptor Kinases : Methods and Protocols
EditorsReidunn Aalen
Number of pages79
Place of PublicationNew York
Publication date2017
ISBN (Print)978-1-4939-7062-9
ISBN (Electronic)978-1-4939-7063-6
Publication statusPublished - 2017
MoE publication typeA3 Book chapter

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fields of Science

  • 1183 Plant biology, microbiology, virology

Cite this

Vaattovaara, A. F. M., Salojärvi, J. T., & Wrzaczek, M. A. (2017). Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis. In R. Aalen (Ed.), Plant Receptor Kinases : Methods and Protocols (pp. 79-91). (Methods in Molecular Biology; No. 1621). Springer. https://doi.org/10.1007/978-1-4939-7063-6_8