scholarly journals Genome-wide analysis and expression characterization of zinc finger homeodomain (ZHD) family genes responsed to different abiotic stresses and hormonal treatments in grape (Vitis vinifera L.)

2020 ◽  
Author(s):  
Guojie Nai ◽  
Juan Mao ◽  
Shixiong Lu ◽  
Yanmei Li ◽  
Zonghuan Ma ◽  
...  
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Defense Mechanisms ◽  
Treatment Time ◽  
Expression Profiles ◽  
Vitis Vinifera L ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Expression Characterization

Abstract Background Zinc finger homeodomain (ZHD) proteins transcription factors (TFs) family occupy a crucial role in regulating plant growth and development. The ZHD TFs family had been studied in diverse organisms such as humans, Drosophila, nematode worms and plants. Especially in plants there is an extensive exploration involved in photosynthesis, defense mechanisms and responses to stress. In this further research, we will provide a better understanding of the ZHD gene family in grape. Results In this study, a total of 12 VvZHD genes were identified from the Grape Genome. The exploration of detailed bioinformatics found that the full length of VvZHD genes ranges from 150 bp (base pair) to 26706 bp, isoelectric points (pIs) were 6.25–9.68, molecular weights (MWs) ranged from 10.28 kilodaltons (KDa) to 97.93 kDa. Also, analysis of phylogenetic evolution showed there existed a common ancestor between Arabidopsis and grape. Ka (Nonsynonymous) / Ks (Synonymous) was lower than 1 and strong collinearity showed there were tandem duplications of genes between Arabidopsis and grape. Codon bias levels of ZHD gene family were relatively higher overall. Gene chip data analysis of cabernet sauvignon seedlings showed VvZHD genes had different expression under different time of different treatments, and with the prolongation of treatment time, most of VvZHD genes were slightly downregulated. The qRT-PCR was carried out under different hormones and stresses to verify expression profiles in grape roots and leaves. Results revealed that most VvZHD genes had higher expressions in roots but lower expressions in leaves. Also, most of the VvZHD gene members were responsed with high expressions after the treatment of ABA, IAA and MeJA in roots. However, VvZHD9, VvZHD11 and VvZHD12 were highly expressed by inducing of PEG in leaves. Conclusions Through genome-wide analysis and expression characterization of ZHD family genes, results showed 12 members had the diversity of function, structure and unique expression characterization under various abiotic stress and hormone treatments. This study will provide us with a newer insight on ZHD gene family of grape and promote to explore the biological functions of ZHD genes in other plants.

scholarly journals Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yuzhu Huo ◽  
Wangdan Xiong ◽  
Kunlong Su ◽  
Yu Li ◽  
Yawen Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Panicum Virgatum ◽  
Expression Profiles ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

Genome-wide analysis and characterization of molecular evolution of the HCT gene family in pear (Pyrus bretschneideri)

2016 ◽  
Vol 303 (1) ◽  
pp. 71-90 ◽  
Author(s):  
Ce Ma ◽  
Huping Zhang ◽  
Jiaming Li ◽  
Shutian Tao ◽  
Xin Qiao ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Gene Family ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance

2020 ◽  
Author(s):  
Yinbo Ma ◽  
Sushil Satish Chhapekar ◽  
Lu Lu ◽  
Sangheon Oh ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Raphanus Sativus ◽  
Expression Profiles ◽  
Recent Common Ancestor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Encoding Genes ◽  
Identification And Characterization

Abstract Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.

Sign in / Sign up

Export Citation Format

Share Document