Genome-Wide Identification of the ARF Gene Family in Three Dendrobium Species and Its Expression Pattern Analysis in D. nobile Flower

Cuili Zhang; Wenjun Lin; Shijie Ke; Deqiang Chen; Linying Wang; Qinyao Zheng; Ye Huang; Zhong-Jian Liu; Weilun Yin; Siren Lan

doi:10.3390/horticulturae10060568

Horticulturae (May 2024)

Genome-Wide Identification of the ARF Gene Family in Three Dendrobium Species and Its Expression Pattern Analysis in D. nobile Flower

Cuili Zhang,
Wenjun Lin,
Shijie Ke,
Deqiang Chen,
Linying Wang,
Qinyao Zheng,
Ye Huang,
Zhong-Jian Liu,
Weilun Yin,
Siren Lan

Affiliations

Cuili Zhang: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Wenjun Lin: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Shijie Ke: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Deqiang Chen: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Linying Wang: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Qinyao Zheng: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Ye Huang: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Zhong-Jian Liu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Weilun Yin: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Siren Lan: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China

DOI: https://doi.org/10.3390/horticulturae10060568
Journal volume & issue: Vol. 10, no. 6
p. 568

Abstract

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The ARF gene family is a representative transcription factor that plays a crucial role in the regulation of various growth and development processes in plants. Although the ARF gene family has been identified in five Orchidaceae species, limited research has been conducted on the ARF gene within Dendrobium. To explore ARF family genes in different Dendrobium species, we selected chromosome-level genomic data from D. nobile, D. chrysotoxum, and D. huoshanense for genome-wide identification, and to analyze expression patterns in the D. nobile flower. In this study, 13, 18, and 23 ARF genes were identified in the genomes of D. chrysotoxum, D. huoshanense, and D. nobile, respectively. These genes were then subsequently classified into four classes (Classes I, II, III, and IV) based on our phylogenetic analysis. Additional protein sequence analysis found that 30 ARF proteins with three classically conserved structural domains (BDB, MR, and RD) were present in the three Dendrobium species. Our gene structure comparative analysis also found the same evolutionary branch with similar intron-exon structural features. Specifically, Class I and Class III display longer introns that potentially constitute a distinctive characteristic of Dendrobium. Gene expression patterns analysis showed the potential involvement of DnoARF 5, 7, 10, 11, 12, 13, 16, 17, and 23 in initial differentiation and flower bud formation. Likewise, transcriptomic analysis and RT-qPCR expression profiles indicated flower-specific expression patterns for four ARF genes (DnoARF5, DnoARF6, DnoARF16, and DnoARF22), which suggest an important impact on flower development and regulation. Ultimately, this study provides comprehensive data to elucidate the potential functions of ARF genes in three Dendrobium species and suggests new insights for further exploration concerning the function and regulatory mechanisms in Dendrobium during flower development.

Published in Horticulturae

ISSN: 2311-7524 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Agriculture: Plant culture
Website: http://www.mdpi.com/journal/horticulturae

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