Identification and transcriptome data analysis of ARF family genes in five Orchidaceae species

Abstract

The Orchidaceae is a large family of perennial herbs especially noted for the exceptional diversity of specialized owers adapted for insect pollination. Elucidating the genetic regulation of owering and seed development of orchids is an important research goal with potential utility in orchid breeding programs. Auxin Response Factor (ARF) genes encode auxin-responsive transcription factors, which are involved in the regulation of diverse morphogenetic processes, including owering and seed development. However, limited information on the ARF gene family in the Orchidaceae is available. In this study, 112 ARF genes were identi ed in the genomes of ve orchid species (Phalaenopsis aphrodite, Phalaenopsis equestris, Vanilla planifolia, Apostasia shenzhenica, and Dendrobium catenatum). These genes were grouped into seven subfamilies based on their phylogenetic relationships. Compared with the ARF family in model plants, such as Arabidopsis thaliana and Oryza sativa, one subfamily of ARF genes involved in pollen wall synthesis has been lost during evolution of the Orchidaceae. This loss corresponds with absence of the exine in the pollinia. Transcriptome analysis indicated that the ARF genes of subfamily 4 may play an important role in ower formation and plant growth, whereas those of subfamily 3 are potentially involved in pollen wall development. Through mining of the published genomic and transcriptomic data for the ve species, the present results provide novel insights into the genetic regulation of unique morphogenetic phenomena of orchids. This study lays a foundation for further analysis of the regulatory mechanisms and functions of sexual reproduction-related genes in orchids. Key MessageGenome wide analysis and expression pattern analysis of ARF genes in ve 20 Orchidaceae species highlight their Evolutionary characteristics and roles in IAA response.

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

“…The number of ARF family genes varies among different plant species. For example, ARF gene family members in A. thaliana (23) [4], S. lycopersicum (21) [30], P. equestris (16) [14], Zea mays (31) [11], and Medicago sativa (81) [31] are known to vary among these species. In this investigation, 13, 18, and 23 ARF genes were identified in the genomes of D. chrysotoxum, D. huoshanense, and D. nobile, respectively.…”

“…The protein sequence of ARF from Arabidopsis thaliana was obtained from TAIR2 (https://www.arabidopsis.org/, accessed on 15 August 2023), and four species (Ap. shenzhenica, P. equestris, P. aphrodite, D. catenatum) of ARF proteins sequence were downloaded from prior investigations [14].…”

“…BLAST and HMM results were combined to eliminate false-positive sequences, and any truncated or redundant proteins were manually removed. Subsequently, all ARF genes were subjected to analysis using the NCBI Batch-CDD (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi, accessed on 3 September 2023) and SMART (http://smart.embl-heidelberg.de/, accessed on 3 September 2023) databases to confirm the presence of the B3 and Auxin_resp conserved domain in the candidate orchid ARFs [14]. Additionally, several physicochemical properties that include protein molecule, aliphatic index (AI), theoretical isoelectric point (pI), and grand average of hydropathicity (GRAVY) within the ARF genes were predicted using the ExPASy online tool (http://www.expasy.org, accessed on 10 September 2023) [23].…”

“…Previously, whole genome-level studies on ARF genes have been conducted in various plants, including Zea mays, Ginkgo biloba, Populus trichocarp, Apostasia shenzhenica, Phalaenopsis equestris, P. aphrodite, and Dendrobiu catenatum [11][12][13][14]. Although the ARF gene family has been identified in Orchidaceae, ARF genes among closely related species have not been studied of Dendrobium.…”

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

“…The ARF gene family has been examined in several plant taxa, including flowering plants, bryophytes, and lycophytes, but ARF gene numbers are highly variable among plant species, ranging from 3 genes in Marchantia polymorpha to 51 genes in Glycine max ( Chandler, 2016 ; Li et al, 2016 , 2023 ). Recently, a total of 112 ARFs were identified in five genomes of orchid species, namely, Apostasia shenzhenica (17 AsARFs ), Dendrobium catenatum (21 DcARFs ), Phalaenopsis aphrodite (16 PaARFs ), Phalaenopsis equestris (34 PeARFs ), and Vanilla planifolia (24 VpARFs ) ( Bai et al, 2023 ). Sixty-seven TaARFs were identified in bread wheat ( Triticum aestivum ), distributed across six clades ( Chaudhary et al, 2023 ).…”