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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (11): 2944-2957.doi: 10.3724/SP.J.1006.2025.54062

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Identification of RAV family in 25 different plant species and expression analysis of RAV genes in potato

LI Wan1,*(), CHANG Zi-Rui1, LU Yao2, SHEN Ri-Min2, ZHAO Yong-Ping1,*(), BAI Xiao-Dong2,*()   

  1. 1 School of Biomedicine and Food Engineering, Shangluo University, Shangluo 726000, Shaanxi, China
    2 Key Laboratory of Potato Genetic Improvement and Germplasm Innovation in Shanxi Province, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
  • Received:2025-05-17 Accepted:2025-08-13 Online:2025-11-12 Published:2025-08-22
  • Contact: *E-mail: 599092122@qq.com; E-mail: zhaoyp2008@sina.com; E-mail: bxd5561@126.com
  • Supported by:
    Natural Science Basic Research Program of Shaanxi(2025JC-YBMS-245);Key Laboratory of Potato Genetic Improvement and Germplasm Innovation in Shanxi Province(202304010921003-K06)

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Abstract:

Plants are susceptible to various environmental factors such as extreme temperatures, high salinity, and drought, which can hinder their development and significantly reduce crop yields. The RAV (Related to ABI3/VP1) gene family is unique to plants and is closely associated with growth, development, and responses to both biotic and abiotic stresses. In this study, RAV genes/proteins (RAVs) from 25 plant species, ranging from Chlorophyta to Angiosperms, were identified and analyzed using bioinformatics tools and multiple databases. The results revealed that RAVs are more abundant in Gymnosperms and Angiosperms, present in smaller numbers in Bryophytes and Lycophytes, and absent in Chlorophyta. Phylogenetic analysis classified the RAVs into three main clades: Clade I included RAVs from Bryophytes to Angiosperms (excluding Monocots); Clade II contained only RAVs from Eudicots; Clade III comprised RAVs from Monocots and Marchantia polymorpha. Further analysis of RAVs in potato showed that although the number of RAV family members was limited, they exhibited significant functional divergence and played important roles in responses to abiotic stress. Overall, this study provides a comprehensive identification and characterization of RAVs across 25 plant species, offering a valuable reference for future functional studies of the RAV gene family.

Key words: RAV family, transcription factors, bioinformatics, Solanum tuberosum, abiotic stresses

Table 1

Number of RAVs, gene duplication events, and clade of RAVs in 25 plant species"

植物门类
Plant lineage		 物种
Species		 RAVs蛋白数量
Numbers of
RAV protein		 片段复制
Segmental duplication		 串联复制
Tandem
duplication		 Clade I Clade II Clade III
藻类
Chlorophyta		 衣藻
Chlamydomonas reinhardtii (Cr)		 0 0 0 0 0 0
胶球藻
Coccomyxa subellipsoidea (Co)		 0 0 0 0 0 0
杜氏盐藻
Dunaliella salina (Ds)		 0 0 0 0 0 0
微胞藻
Micromonas pusilla (Mi)		 0 0 0 0 0 0
鞭毛藻
Ostreococcus lucimarinus (Ol)		 0 0 0 0 0 0
团藻Volvox carteri (Vc) 0 0 0 0 0 0
苔藓类
Bryophyta		 地钱
Marchantia polymorpha (Mp)		 1 0 0 0 0 1
小立碗藓
Physcomitrella patens (Ph)		 2 0 0 2 0 0
假泥炭藓Sphagnum fallax (Sf) 2 0 0 2 0 0
石松类
Lycophyte		 卷柏
Selaginella moellendorffii (Sm)		 2 0 0 2 0 0
裸子植物
Gymnospermae		 云杉Picea abies (Pa) 16 0 0 16 0 0
被子植物
Angiosperm
 无油樟
Amborella		 无油樟
Amborella trichopoda (Ar)		 1 0 0 1 0 0
双子叶植物
Eudicots		 拟南芥
Arabidopsis thaliana (At)		 6 3 0 2 4 0
芸薹Brassica rapa (Br) 14 18 1 7 7 0
黄瓜Cucumis sativus (Cs) 4 0 0 3 1 0
荠菜Capsella rubella (Cb) 5 2 0 2 3 0
大豆Glycine max (Gm) 5 6 0 1 4 0
棉花Gossypium raimondii (Gr) 10 4 2 7 3 0
番茄
Solanum lycopersicum (Sl)		 3 1 0 1 2 0
马铃薯Solanum tuberosum (St) 2 0 0 0 2 0
单子叶植物
Monocots		 二穗短柄草
Brachypodium distachyon (Bd)		 4 2 1 0 0 4
大麦Hordeum vulgare (Hv) 8 0 1 0 0 8
水稻Oryza sativa (Os) 4 3 1 0 0 4
小麦Triticum aestivum (Ta) 5 0 0 0 0 5
玉米Zea mays (Zm) 3 2 0 0 0 3

Fig. 1

Phylogenetic tree (A), gene structure (B), conserved domain (C), and motif analysis (D) of RAVs In panel A, three subgroups and different plant species are distinguished by different colors. In panel B, red boxes indicate coding sequences (CDS), black lines represent introns, and blue boxes denote upstream/downstream untranslated regions (UTRs). In panel C, different conserved domains are shown in various colors."

Fig. 2

Phylogenetic tree of 97 RAVsThe three subgroups and different plant species were distinguished by different colors. Colored circles at the branch nodes represented different root value ranges."

Fig. 3

Hypothetical evolutionary models for RAVs in 25 plant species In panel A, different plant species are represented by different colors. In the pie charts, the numbers in the green and yellow segments indicate the number of tandem and segmental duplication events, respectively, in each species. In panel B, the numbers represent the total number of RAV proteins, gene duplication events, and the number of tandem or segmental duplications in each species."

Fig. 4

GO annotation information of whole RAVs Different types of gene annotation are shown in different colors."

Fig. 5

Sequence alignment (A) and tertiary structure prediction (B) of StRAV1 and StRAV2"

Fig. 6

CAE prediction in promoter regions, and expression analysis of StRAV1 and StRAV2 under different stresses and tissues A: CAEs prediction. Green and red boxes indicated the absence and inclusion of the CAE, respectively, and the number represented the quantity of the corresponding CAE. B: expression patterns of StRAV1 and StRAV2 under different stress treatments. The vertical coordinate (Times) represented the ratio of the gene expression level under a certain stress to that of the control group. C: expression patterns of StRAV1 and StRAV2 in different tissues. The data in the figure (gene expression level) was equal to the logarithm of the original data with base 2. # indicated that the expression level of this gene in this tissue was 0."

Fig. 7

Analysis of the expression levels of StRAV1 and StRAV2 under different stress conditions Quantitative data were detected by taking three biological replicates and three technical replicates, and the relative expression level of each gene was calculated using the 2-ΔΔCt method. Significance analysis was conducted using the t-test. * and ** indicate significant differences compared to the control at P < 0.05 and P < 0.01, respectively."

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