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

Aleksia Fanni Maria Vaattovaara; Jarkko Tapani Salojärvi; Michael Alois Wrzaczek

doi:10.1007/978-1-4939-7063-6_8

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

Aleksia Fanni Maria Vaattovaara, Jarkko Tapani Salojärvi, Michael Alois Wrzaczek

Research output: Chapter in Book/Report/Conference proceeding › Chapter › Scientific › peer-review

Abstract

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 language	English
Title of host publication	Plant Receptor Kinases : Methods and Protocols
Editors	Reidunn Aalen
Number of pages	79
Place of Publication	New York
Publisher	Springer
Publication date	2017
Pages	79-91
ISBN (Print)	978-1-4939-7062-9
ISBN (Electronic)	978-1-4939-7063-6
DOIs	https://doi.org/10.1007/978-1-4939-7063-6_8
Publication status	Published - 2017
MoE publication type	A3 Book chapter

Publication series

Name	Methods in Molecular Biology
Number	1621
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Fields of Science

1183 Plant biology, microbiology, virology

Access to Document

10.1007/978-1-4939-7063-6_8

Cite this

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title = "Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis",

abstract = "Analysis of gene families and identification of homologous genes are important for phylogenetic analysisand for translating results from model to crop species. While numerous plant genomes have been sequencedand made available, the identification of gene models can be difficult, in particular for large gene familiesarranged in tandem repeats or encoding proteins with a variable number of internal repeats. Thus, correctannotation 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 fromnon-annotated DNA regions. This protocol allows the efficient identification of gene family member ofPRK from most available plant genomes.",

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Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis. / Vaattovaara, Aleksia Fanni Maria ; Salojärvi, Jarkko Tapani ; Wrzaczek, Michael Alois.
Plant Receptor Kinases : Methods and Protocols. ed. / Reidunn Aalen. New York: Springer, 2017. p. 79-91 (Methods in Molecular Biology; No. 1621).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › Scientific › peer-review

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PY - 2017

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