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Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica
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 releas...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601442/ https://www.ncbi.nlm.nih.gov/pubmed/36292581 http://dx.doi.org/10.3390/genes13101696 |
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author | Tabarelli, Mattia Malnoy, Mickael Janik, Katrin |
author_facet | Tabarelli, Mattia Malnoy, Mickael Janik, Katrin |
author_sort | Tabarelli, Mattia |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9601442 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96014422022-10-27 Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica Tabarelli, Mattia Malnoy, Mickael Janik, Katrin Genes (Basel) Article 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. MDPI 2022-09-22 /pmc/articles/PMC9601442/ /pubmed/36292581 http://dx.doi.org/10.3390/genes13101696 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Tabarelli, Mattia Malnoy, Mickael Janik, Katrin Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica |
title | Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica |
title_full | Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica |
title_fullStr | Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica |
title_full_unstemmed | Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica |
title_short | Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica |
title_sort | chasing consistency: an update of the tcp gene family of malus × domestica |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601442/ https://www.ncbi.nlm.nih.gov/pubmed/36292581 http://dx.doi.org/10.3390/genes13101696 |
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