Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica

Mattia Tabarelli; Mickael Malnoy; Katrin Janik

doi:10.3390/genes13101696

Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica

Genes (Basel). 2022 Sep 22;13(10):1696. doi: 10.3390/genes13101696.

Authors

Mattia Tabarelli^{1

2

3}, Mickael Malnoy², Katrin Janik³

Affiliations

¹ Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy.
² Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all'Adige, Italy.
³ Laimburg Research Centre, Institute of Agricultural Chemistry and Food Quality, Molecular Biology and Microbiology, Laimburg 6-Vadena/Pfatten, 39040 Ora/Auer, Italy.

Abstract

The 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in Malus × domestica (M. × domestica) were identified in 2014 on the first genome assembly, which was released in 2010. In 2017, a higher quality genome assembly for apple was released and is now considered to be the reference genome. Moreover, as in several other species, the identified TCP genes were named based on the relative position of the genes on the chromosomes. The present work consists of an update of the TCP gene family based on the latest genome assembly of M. × domestica. Compared to the previous classification, the number of TCP genes decreased from 52 to 40 as a result of the addition of three sequences and the deduction of 15. An analysis of the intragenic identity led to the identification of 15 pairs of orthologs, shedding light on the forces that shaped the evolution of this gene family. Furthermore, a revised nomenclature system is proposed that is based both on the intragenic identity and the homology with Arabidopsis thaliana (A. thaliana) TCPs in an effort to set a common standard for the TCP classification that will facilitate any future interspecific analysis.

Keywords: GDDH13v1.1 genome assembly; Malus × domestica; TCP gene family.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Arabidopsis* / genetics
Arabidopsis* / metabolism
Gene Expression Regulation, Plant
Malus* / genetics
Transcription Factors / genetics
Transcription Factors / metabolism

Substances

Transcription Factors

Grants and funding

The work was partially performed as part of the projects APPLIII and APPLIV within the framework agreement in the field of invasive species in fruit growing and major pathologies, which is co-funded by the South Tyrolean Apple Consortium and the Autonomous Province of Bozen/Bolzano, Italy. The authors thank the Department of Innovation, Research, University and Museums of the Autonomous Province of Bozen/Bolzano for covering the Open Access publication costs.