Genome-Wide Identification and Characterization of the NAC Gene Family and Its Involvement in Cold Response in Dendrobium officinale

Abstract

The NAC (NAM, ATAF1/2 and CUC2) gene family is one of the largest plant-specific transcription factor families, functioning as crucial regulators in diverse biological processes such as plant growth and development as well as biotic and abiotic stress responses. Although it has been widely characterized in many plants, the significance of the NAC family in Dendrobium officinale remained elusive up to now. In this study, a genome-wide search method was conducted to identify NAC genes in Dendrobium officinale (DoNACs) and a total of 110 putative DoNACs were obtained. Phylogenetic analysis classified them into 15 subfamilies according to the nomenclature in Arabidopsis and rice. The members in the subfamilies shared more similar gene structures and conversed protein domain compositions. Furthermore, the expression profiles of these DoNACs were investigated in diverse tissues and under cold stress by RNA-seq data. Then, a total of five up-regulated and five down-regulated, cold-responsive DoNACs were validated through QRT-PCR analysis, demonstrating they were involved in regulating cold stress response. Additionally, the subcellular localization of two down-regulated candidates (DoNAC39 and DoNAC58) was demonstrated to be localized in the nuclei. This study reported the genomic organization, protein domain compositions and expression patterns of the NAC family in Dendrobium officinale, which provided targets for further functional studies of DoNACs and also contributed to the dissection of the role of NAC in regulating cold tolerance in Dendrobium officinale.

Genome-wide identification, evolution, and expression analysis of the NAC gene family in chestnut (Castanea mollissima)

“…However, the NAC gene family in many plants has been identified, but there have been no relevant reports on the NAC genes in chestnut. Here, 115 non-redundant NACs were identified in the chestnut genome, similar to the number of NACs in pepper ( Capsicum annuum ) (104) ( Diao et al, 2018 ) and Dendrobium officinale (110) ( Yang et al, 2023 ), but less than that in cabbage ( Brassica rapa ) (188) ( Ma et al, 2014 ), Malus pumila (180) ( Su et al, 2013 ), sunflower ( Helianthus annuus ) (150) ( Li et al, 2021 ) and rice (151) ( Nuruzzaman et al, 2010 ). The difference in size may be due to differences in WGD and other gene duplication events that accompany species evolution and differentiation.…”

“…For example, the CmNAC115 in the OsNAC7 subgroup lacked motif 3, which was preserved in other members of the OsNAC7 subgroup ( Figure 3B ). Indeed, the specific functions of these motifs required further in-depth research ( Yang et al, 2023 ).…”

“…There is ample evidence to suggest that the NAC gene family already existed in early plants such as moss and ferns, and its origin is closely related to the formation of the multicellular structure and complex life cycle of plants ( Hu et al, 2022 ; Yang et al, 2023 ). The expansion of the NAC gene family is mainly achieved through gene duplication and selective preservation ( Diao et al, 2018 ; Jin et al, 2020 ).…”

Characterization of NAC Gene Family in Ammopiptanthus mongolicus and Functional Analysis of AmNAC24, an Osmotic and Cold-Stress-Induced NAC Gene

“…Here, 86 NAC proteins were identified in A. mongolicus. Compared with the genomes of other species, the count of NAC genes in other species such as M. sativa [58], Glycine max [59], Dendrobium officinale [60], and Zanthoxylum bungeanum [29] stands at 421, 269, 111, and 109, respectively. A. mongolicus exhibits a relatively modest count of NAC family members compared to these plants, potentially indicative of evolutionary adaptations in distinct species amid varying habitat conditions.…”

Physiological and transcriptomic comparisons shed light on the cold stress response mechanisms of Dendrobium spp

“…Transcription factors plays key roles in stress response and tolerance by regulating the expression of stress-related genes in plants [ 7 ]. There are several transcription factors ( NAC58/39 and MYB75 ) verified to be involved in cold tolerance of Dendrobium orchids in previous study [ 61 , 62 ]. These transcription factors belong to the homologue genes of NAC68/53 and MYB58 respectively identified in our co-expression network, which further supports the critical role of the NAC and MYB transcription factor families in improving the low temperature tolerance of Dendrobium spp.…”