Chasing Consistency: An Update of the <i>TCP</i> Gene Family of <i>Malus</i> × <i>Domestica</i>
The 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in <i>Malus</i> × <i>domestica</i> (<i>M.</i> × <i>domestica</i>) were identified in 2014 on the first genome assembly, which was rele...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-09-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/10/1696 |
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| author | Mattia Tabarelli Mickael Malnoy Katrin Janik |
| author_facet | Mattia Tabarelli Mickael Malnoy Katrin Janik |
| author_sort | Mattia Tabarelli |
| collection | DOAJ |
| description | The 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in <i>Malus</i> × <i>domestica</i> (<i>M.</i> × <i>domestica</i>) 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 <i>TCP</i> genes were named based on the relative position of the genes on the chromosomes. The present work consists of an update of the <i>TCP</i> gene family based on the latest genome assembly of <i>M.</i> × <i>domestica</i>. Compared to the previous classification, the number of <i>TCP</i> 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 <i>Arabidopsis thaliana</i> (<i>A. thaliana</i>) <i>TCPs</i> in an effort to set a common standard for the <i>TCP</i> classification that will facilitate any future interspecific analysis. |
| first_indexed | 2024-03-09T20:11:46Z |
| format | Article |
| id | doaj.art-8d0583a2b3cb47c9995ef45ec954cb07 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T20:11:46Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-8d0583a2b3cb47c9995ef45ec954cb072023-11-24T00:14:32ZengMDPI AGGenes2073-44252022-09-011310169610.3390/genes13101696Chasing Consistency: An Update of the <i>TCP</i> Gene Family of <i>Malus</i> × <i>Domestica</i>Mattia Tabarelli0Mickael Malnoy1Katrin Janik2Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, ItalyResearch and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, ItalyLaimburg Research Centre, Institute of Agricultural Chemistry and Food Quality, Molecular Biology and Microbiology, Laimburg 6–Vadena/Pfatten, 39040 Ora/Auer, ItalyThe 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in <i>Malus</i> × <i>domestica</i> (<i>M.</i> × <i>domestica</i>) 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 <i>TCP</i> genes were named based on the relative position of the genes on the chromosomes. The present work consists of an update of the <i>TCP</i> gene family based on the latest genome assembly of <i>M.</i> × <i>domestica</i>. Compared to the previous classification, the number of <i>TCP</i> 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 <i>Arabidopsis thaliana</i> (<i>A. thaliana</i>) <i>TCPs</i> in an effort to set a common standard for the <i>TCP</i> classification that will facilitate any future interspecific analysis.https://www.mdpi.com/2073-4425/13/10/1696<i>Malus</i> × <i>domestica</i><i>TCP</i> gene familyGDDH13v1.1 genome assembly |
| spellingShingle | Mattia Tabarelli Mickael Malnoy Katrin Janik Chasing Consistency: An Update of the <i>TCP</i> Gene Family of <i>Malus</i> × <i>Domestica</i> Genes <i>Malus</i> × <i>domestica</i> <i>TCP</i> gene family GDDH13v1.1 genome assembly |
| title | Chasing Consistency: An Update of the <i>TCP</i> Gene Family of <i>Malus</i> × <i>Domestica</i> |
| title_full | Chasing Consistency: An Update of the <i>TCP</i> Gene Family of <i>Malus</i> × <i>Domestica</i> |
| title_fullStr | Chasing Consistency: An Update of the <i>TCP</i> Gene Family of <i>Malus</i> × <i>Domestica</i> |
| title_full_unstemmed | Chasing Consistency: An Update of the <i>TCP</i> Gene Family of <i>Malus</i> × <i>Domestica</i> |
| title_short | Chasing Consistency: An Update of the <i>TCP</i> Gene Family of <i>Malus</i> × <i>Domestica</i> |
| title_sort | chasing consistency an update of the i tcp i gene family of i malus i i domestica i |
| topic | <i>Malus</i> × <i>domestica</i> <i>TCP</i> gene family GDDH13v1.1 genome assembly |
| url | https://www.mdpi.com/2073-4425/13/10/1696 |
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