Genome-Wide Identification and Analysis of DOF Gene Family in Eugenia uniflora L. (Myrtaceae)

Abstract

Eugenia uniflora is a Brazilian native plant species with great ecological and economic importance. It is distributed throughout the Atlantic forest, where two distinct populations show local adaptation to the contrasting conditions of restinga and riparian forest. Among various TFs described in plants, the DOF TF family has been reported to affect flowering and vascular development, making them promising candidates for characterization in E. uniflora. In this study, 28 DOF genes were identified by a genome-wide analysis, of which 20 were grouped into 11 MCOGs by Bayesian phylogeny, suggesting a shared functionallity between members. Based on RNA-seq experiments, we have detected eight drought responsive genes, and SNPs identification revealed population unique polymorphisms, implying a role in local adapatation mechanisms. Finally, analysis of conserved motifs through MEME revealed 15 different protein motifs, and a promoter region analysis returned 40 enriched TF binding motifs, both reporting novel biological functions circa the DOF gene family. In general, the DOF family is found to be conserved both in sequence and expression. Furthermore, this study contributes to both DOF literature and the genetic exploration of native species, elucidating their genetic potential and bringing to light new research topics, paving the way to future studies.

Identification and characterization of Dof genes in Cerasus humilis

“…These genes were named as ChDof1–ChDof25 , according to their chromosomal location. Different number of Dof genes have been reported in plant species; for example, 28 in Eugenia uniflora ( Waschburger et al., 2022 ), 22 in spinach ( Spinacia oleracea ) ( Yu et al., 2021 ), 16 in tea ( Camellia sinensis ) ( Yu et al., 2020 ), 45 in pear ( Pyrus bretschneideri ) ( Liu et al., 2020 ), 24 in rose ( Rosa chinensis ), 40 in Medicago sativa ( Cao et al., 2020 ), 25 in grape, 36 in watermelon ( Citrullus lanatus ) ( Zhou et al., 2020 ), 36 in Areca catechu ( Li et al., 2022a ), and 20 in Chrysanthemum morifolium ( Song et al., 2016 ). However, some plant species possess an exceptionally high number of Dof genes (e.g., 103 in Camelina sativa ) ( Luo et al., 2022 ), which may be related to the large genome size or high sequencing depth of the species.…”

Identification of Dof transcription factors in Dendrobium huoshanense and expression pattern under abiotic stresses

“…However, the regulatory function of Dof on abiotic stress responses was only reported in a limited number of plants ( Zhang et al, 2018 ). RcDOFs expressed at two distinct levels varied in response to ABA ( Waschburger et al, 2022 ). CmDOFs had a role in the response to ABA and SA, which contributed to differential expression patterns.…”

DOF gene family expansion and diversification

“…Moreover, nearly two-thirds of articles studied DOF genes in crop species, while 94 studied model species, including Physcomitrella patens ( Sugiyama et al, 2012 ) and Pinus pinaster ( Rueda-López et al, 2017 ) ( Figure 1C ). Only four articles were published focusing on DOF genes in native species Chrysanthemum morifolium ( Song et al, 2016 ), Tamarix hispida ( Yang et al, 2017 ), Petunia inflata ( Yue et al, 2021 ), and Eugenia uniflora ( Waschburger et al, 2022 ). A preference for studied species is also apparent when comparing the number of published articles considering the major botanical groups ( Figure 1D ).…”