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Research paper

Polyploidy events shaped the expansion of transcription factors in Cucurbitaceae and exploitation of genes for tendril development

Yu Zhanga,1, Yingchao Zhanga,1, Bing Lib,1, Xiao Tana, Changping Zhua, Tong Wua, Shuyan Fenga, Qihang Yanga, Shaoqin Shena, Tong Yua, Zhuo Liua, Xiaoming Songa,c,d( )
College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei 050051, China
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA

1 The authors contributed equally to the work.

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Abstract

Cucurbitaceae is one of the most important plant families distributed worldwide. Transcription factors (TFs) regulate plant growth at the transcription level. Here, we performed a systematic analysis of 42 641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species. Whole-genome duplication (WGD) was the dominant event type in almost all Cucurbitaceae plants. The TF families were divided into 1 210 orthogroups (OGs), of which, 112 were unique to Cucurbitaceae. Although the loss of several gene families was detected in Cucurbitaceae, the gene families expanded in five species that experienced a WGD event comparing with grape. Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families. The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families, AUX/IAA, NAC, NBS, HB, and NF-YB. Finally, we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related (TEN) genes in 11 Cucurbitaceae species. Interestingly, the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene (Bhi06M000087) of Benincasa hispida. Furthermore, we identified a new characteristic sequence, YNN, which could be used for TEN gene exploitation in Cucurbitaceae. In conclusion, this study will serve as a reference for studying the relationship between gene family evolution and genome duplication. Moreover, it will provide rich genetic resources for functional Cucurbitaceae studies in the future.

Keywords

CucurbitaceaeTranscription factors (TFs)Whole-genome duplication (WGD)Expansion and contractionTCP gene familyTendril-related genes (TEN)

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Horticultural Plant Journal
Volume 8 Issue 5,
September 2022
Pages 562-574
DOI: 10.1016/j.hpj.2022.07.004
Cite this article:
Zhang Y, Zhang Y, Li B, et al. Polyploidy events shaped the expansion of transcription factors in Cucurbitaceae and exploitation of genes for tendril development. Horticultural Plant Journal, 2022, 8(5): 562-574. https://doi.org/10.1016/j.hpj.2022.07.004

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Received: 28 January 2022
Revised: 12 April 2022
Accepted: 24 June 2022
Published: 21 July 2022
© 2022 Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS).

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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