Genome-wide identification and functional analysis of ARF transcription factors in Brassica juncea var. tumida

Abstract

Auxin signalling is vital for plant growth and development, from embryogenesis to senescence. Recent studies have shown that auxin regulates biological processes by mediating gene expression through a family of functionally original DNA-binding auxin response factors, which exist in a large multi-gene family in plants. However, to date, no information has been available about characteristics of the ARF gene family in Brassica juncea var. tumida. In this study, 65 B. juncea genes that encode ARF proteins were identified in the B. juncea whole-genome, classified into three phylogenetical groups and found to be widely and randomly distributed in the A-and B-genome. Highly conserved proteins were also found within each ortholog based on gene structure and conserved motifs, as well as clustering level. Furthermore, promoter cis-element analysis of BjARFs demonstrated that these genes affect the levels of plant hormones, such as auxin, salicylic, gibberellin acid, MeJA, abscisic acid, and ethylene. Expression analysis showed that differentially expressed BjARF genes were detected during the seedling stage, tumor stem development and the flowering period of B. juncea. Interestingly, we found that BjARF2b_A, BjARF3b_A, BjARF6b_A, and BjAR-F17a_B were significantly expressed in tumor stem, and an exogenous auxin assay indicated that these genes were sensitive to auxin and IAA signaling. Moreover, eight of the nine BjARF10/16/17 genes and all of the BjARF6/8 genes were involved in post-transcriptional regulation, targeted by Bj-miR160 and Bj-miR167c, respectively. This analysis provides deeper insight of diversification for ARFs and will facilitate further dissection of ARF gene function in B. juncea.

Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa

“…Phylogeny and synteny analysis revealed that both the segmental duplications and whole-genome duplications contributed to PtrARF gene family expansion. However, it was somewhat inconsistent with the previous conclusion that segmental duplication was the major cause for the ARF gene family expansion [49][50][51].…”

“…In addition, the percentage of CTD-truncated PtrARF (37.5%) was higher than that in Vitis vinifera (10.5%) [14], A. thaliana (17.39%) [15], O. sativa (24%) [9], Brassica rapa (22.6%) [51], and Solanum lycopersicum (28.6%) [56] but lower than that in Hordeum vulgare (45.0%) and M. truncatula (60.9%) [12,57]. It has been reported that the truncated ARF proteins without CTD function, whose activities were regulated through interaction with other transcription factors instead of interaction with Aux/IAA, are likely to be insensitive to auxin [4,8].…”

Genome–Wide Identification and Functional Characterization of Auxin Response Factor (ARF) Genes in Eggplant

“…The functions of ARFs have been studied in Arabidopsis thaliana , tomato ( Solanum lycopersicum ), papaya ( Carica papaya L.), sugar beet, peach, and other plant species [ 13 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ]. AtARF 2 , 3 , 5 , 6 , 7 , 8 , 17 , and 19 regulate apical bud formation, pollen wall synthesis, vascular bundle development, hypocotyl tropic movement, and adventitious root formation [ 26 , 27 , 28 , 29 , 30 ].…”

Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis)

“…The proportion of PkorARF members lacking CTD domains in Korean pine (38.5%) is higher than that in other species, such as Arabidopsis (17.39%) [ 10 ], tomato ( Solanum lycopersicum ) (28.6%) [ 59 ], Brassica juncea var. tumida (22.6%) [ 60 ], and Populus (37.5%) [ 12 ]. However, the proportion of structural domains lacking in PkorARF (38.5%) is similar to that of PtrARF (37.5%), suggesting both variability in structure among different species and similarity in structure among closely related species.…”