Vaattovaara Aleksia, Salojärvi Jarkko, Wrzaczek Michael
Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1 (POB65), FI-00014, Helsinki, Finland.
Methods Mol Biol. 2017;1621:79-91. doi: 10.1007/978-1-4939-7063-6_8.
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.
基因家族分析和同源基因鉴定对于系统发育分析以及将模型物种的研究结果转化到作物物种中非常重要。虽然已经对众多植物基因组进行了测序并公开，但基因模型的鉴定可能具有挑战性，特别是对于以串联重复排列或编码具有可变数量内部重复的蛋白质的大型基因家族。因此，正确注释植物受体激酶（PRK）是一项挑战。在这里，我们描述了一种用于从注释的基因模型以及未注释的DNA区域中半自动提取、注释和验证基因的工作流程。该方案能够从大多数现有植物基因组中高效鉴定PRK基因家族成员。
