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Abstract：
Auxin response factors (ARFs), as the main components of auxin signaling, play a crucial role in various processes of plant growth and development, as well as in stress response. So far, there have been no reports on the genome-wide identification of the ARF transcription factor family in Cyclocarya paliurus, a deciduous tree plant in the family Juglaceae. In this study, a total of 34 CpARF genes were identified based on whole genome sequence, and they were unevenly distributed on 16 chromosomes, with the highest distribution on chromosome 6. Domain analysis of CpARF proteins displayed that 31 out of 34 CpARF proteins contain a typical B3 domain (DBD domain), except CpARF12/ CpARF14/CpARF31, which all belong to Class VI. And 20 CpARFs (58.8%) contain an auxin_IAA binding domain, and are mainly distributed in classes I, and VI. Phylogenetic analysis showed that CpARF was divided into six classes (I-VI), each containing 4, 4, 1, 8, 4, and 13 members, respectively. Gene duplication analysis showed that there are 14 segmental duplications and zero tandem repeats were identified in the CpARF gene family of the C. paliurus genome. The Ka/Ks ratio of duplicate gene pairs indicates that CpARF genes are subjected to strong purification selection pressure. Synteny analysis showed that C. paliurus shared the highest homology in 74 ARF gene pairs with Juglans regia, followed by 73, 51, 25, and 11 homologous gene pairs with Populus trichocarpa, Juglans cathayensis, Arabidopsis, and rice, respectively. Promoter analysis revealed that 34 CpARF genes had cis-elements related to hormones, stress, light, and growth and development except for CpARF12. The expression profile analysis showed that almost all CpARF genes were differentially expressed in at least one tissue, and several CpARF genes displayed tissue-specific expression. Furthermore, 24 out of the 34 CpARF genes have significantly response to drought stress (P < 0.05), and most of them (16) being significantly down-regulated under moderate drought treatment. Meanwhile, the majority of CpARF genes (28) have significantly response to drought stress (P < 0.05), and most of them (26) are significantly down-regulated under severe drought treatment. Furthermore, 32 out of the 34 CpARF genes have significantly response to high, middle, and low salt stress under salt treatment (P < 0.05). Additionally, subcellular localization analysis confirmed that CpARF16 and CpARF32 were all localized to nucleus. Thus, our findings expand the understanding of the function of CpARF genes and provide a basis for further functional studies on CpARF genes in C. paliurus.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s12298-024-01474-1.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s12298-024-01474-1.
摘要：
生长素反应因子（ARFs），作为生长素信号的主要组成部分，在植物生长发育的各种过程中起着至关重要的作用，以及应激反应。到目前为止,目前还没有关于全基因组鉴定青钱柳ARF转录因子家族的报道，胡桃木科中的一种落叶乔木植物。在这项研究中,根据全基因组序列共鉴定了34个CpARF基因，它们不均匀地分布在16条染色体上，在6号染色体上分布最高。CpARF蛋白的结构域分析显示，34个CpARF蛋白中有31个含有典型的B3结构域（DBD结构域），除CpARF12/CpARF14/CpARF31外，均属于VI类。20个CpARFs(58.8%)含有生长素_IAA结合域,主要分布在I班，和VI。系统发育分析表明，CpARF分为6类(I-VI)，每个包含4、4、1、8、4和13个成员，分别。基因重复分析表明，在C.paliurus基因组的CpARF基因家族中鉴定出14个节段重复和零串联重复。重复基因对的Ka/Ks比率表明CpARF基因经受强的纯化选择压力。综合分析表明，在74个ARF基因对中，黄柳与核桃属地区的同源性最高。其次是73、51、25和11个与毛果杨同源的基因对，核桃,拟南芥,还有米饭,分别。启动子分析显示34个CpARF基因存在与激素相关的顺式元件,压力，光,以及除CpARF12外的生长发育。表达谱分析显示几乎所有的CpARF基因在至少一个组织中差异表达,和几个CpARF基因显示组织特异性表达。此外，34个CpARF基因中有24个对干旱胁迫有显著响应(P<0.05),在中度干旱处理下，它们中的大多数(16)被显著下调。同时,大多数CpARF基因(28个)对干旱胁迫有显著响应(P<0.05),其中大多数(26)在严重干旱处理下显著下调。此外，34个CpARF基因中有32个对高，中间,和盐处理下的低盐胁迫(P<0.05)。此外,亚细胞定位分析证实CpARF16和CpARF32均位于细胞核。因此，本研究拓展了人们对CpARF基因功能的认识,为进一步研究黄柳CpARF基因的功能奠定了基础。
■在线版本包含补充材料，可在10.1007/s12298-024-01474-1获得。
■在线版本包含补充材料，可在10.1007/s12298-024-01474-1获得。
