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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (11): 2765-2773.doi: 10.3724/SP.J.1006.2022.14143

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Downstream target gene network regulated by AhGLK1 and AhHDA1 using ChIP-seq in peanut

LIU Xing1(), SU Liang-Chen1, LI Li-Mei2, LI Ling2,*()   

  1. 1Department of Bioengineening, Zhuhai Campus, Zunyi Medical University, Zhuhai 519041, Guangdong, China
    2Guangdong Provincial Key Laboratory of Biotechnology for Plant Development / School of Life Sciences, South China Normal University, Guangzhou 510631, Guangdong, China
  • Received:2021-08-10 Accepted:2021-11-29 Online:2022-11-12 Published:2021-12-17
  • Contact: LI Ling E-mail:liuxingas@126.com;Liling502@126.com
  • Supported by:
    The Department of Science and Technology of Guizhou Province(ZK2021-127);The National Natural Science Foundation of China(31671600)

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Abstract:

Peanut (Arachis hypogaea L.) is an important economic and edible oil crop whose growth, yield and quality are seriously affected by drought stress. In order to further investigate the mechanism of drought tolerance in peanut, chromatin immunoprecipitation sequence (ChIP-seq) was conducted to analyze immunoaffinity separation of specific binding DNA fragments with AhHDA1 (Arachis hypogaea L. histone deacetylase 1) and transcription factor AhGLK1 (Arachis hypogaea L. Golden2-like 1) for sequence identification, revealing the downstream target gene networks regulated by AhHDA1 and AhGLK1. Through alignment and analysis, 65.71, 63.90, and 70.06 million clean beads were obtained for GLKHDA and input IP from the sequencing run, respectively. The unique alignment of reads to the reference genome sequence were 74.97%, 76.81%, and 76.75%, respectively. GLK-IP obtained 714 peaks and HDA-IP obtained 543 peaks. Peaks were distributed into exons, introns, upstream, downstream, intergenic and other functional elements. GO enrichment revealed that 35.1% and 32.8% of the peak-related genes of AhGLK1-IP and AhHDA1-IP were enriched in “molecular function”. 39.3% and 44.2% were enriched in “biological process” and 25.5% and 22.8% were enriched in “cellular components”, respectively. KEGG pathway enrichment showed that AhGLK1-IP related genes were significantly enriched in metabolic, biosynthesis of antibiotics, glyoxylate and dicarboxylate metabolism, microbial metabolism in diverse environments, carbon metabolism, biosynthesis of secondary metabolites and biosynthesis of amino acids pathways. Whereas, AhHDA1-IP related genes were significantly enriched in N-glycan biosynthesis, arginine, proline and phenylalanine metabolism pathways. Moreover, there were four common peaks enriched both in AhGLK1-IP and AhHDA1-IP. A common conserved motif sequences (AGAA/T) was presented in the motif sequences specifically enriched by AhGLK1-IP and AhHDA1-IP. These results of the study have some reference value for further understanding the functions of AhGLK1 and AhHDA1 genes and the regulatory mechanism of peanuts in response to drought stress and post-drought recovery growth.

Key words: Arachis hypogaea L., chromatin immunoprecipitation sequence, AhGLK1, AhHDA1, target gene

Table 1

Statistics of ChIP-seq data output"

样品名
Sample name		 序列总数
No. of total sequences		 碱基总数
No. of total bases		 GC
(%)		 Q20
(%)		 Q30
(%)
GLK-IP 65,712,234 9,856,835,100 41.50 97.60 93.96
HDA-IP 63,903,912 9,85,586,800 40.73 97.61 93.96
Input 70,062,804 10,509,420,600 40.49 97.43 93.58

Table 2

Statistics of data comparison results"

样品名
Sample		 总序列数
No. of total
sequences		 比对序列数
No. of aligned
sequences		 比对率
Aligned rate
(%)		 唯一比对序列数
No. of unique aligned
sequences		 唯一比对率
Unique aligned rate
(%)
GLK-IP 65,133,710 60,248,717 92.50 48,828,873 74.97
HDA-IP 63,362,432 59,643,659 94.13 48,666,448 76.81
Input 69,408,066 68,607,870 98.85 53,268,396 76.75

Table 3

Peak information statistics"

样品名
Sample name		 Peak数
Peak number		 Peak总长度
Peak total
length		 Peak平均长度
Peak average length		 Peak总序列深度
Peak total sequence depth		 Peak平均序列度
Peak average sequence degree		 基因组比例
Genome rate
(%)
GLK-IP 714 416,446 583 11,224 15 0.02
HDA-IP 543 298,118 549 7764 14 0.01

Fig. 1

Peak distribution of AhGLK1 and AhHDA1 enriched genes"

Fig. 2

GO classification of AhGLK1 and AhHDA1 enriched genes"

Fig. 3

KEGG pathway of AhGLK1 and AhHDA1 enriched genes A: AhGLK1-IP related genes; B: AhHDA1-IP related genes."

Table 4

Distribution of AhGLK1 and AhHDA1-IP related genes in different KEGG pathways"

样品
Sample name		 KEGG通路
KEGG pathway		 基因个数
Gene number		 基因ID
Gene ID
AhGLK-IP 代谢途径
Metabolic pathways		 20 Arahy.14YEDZ, Arahy.46RTPJ, Arahy.46W7S4, Arahy.6Q1KS5, Arahy.8T1UF6, Arahy.C0Q7J8, Arahy.CQFZ3U, Arahy.D1ZPVC, Arahy.IC3HGI, Arahy.LT225G, Arahy.MY1TBE, Arahy.NDL7Z2, Arahy.S45BII, Arahy.S8DJY1, Arahy.SKV00U, Arahy.SP7CPF, Arahy.U4VZKL, Arahy.VD5UEC, Arahy.YS6PIM, Arahy.ZZNJ3G
抗生素生物合成
Biosynthesis of antibiotics		 8 Arahy.46W7S4, Arahy.8T1UF6, Arahy.C0Q7J8, Arahy.CQFZ3U, Arahy.NDL7Z2, Arahy.S45BII, Arahy.SP7CPF, Arahy.U4VZKL
二羧酸代谢
Glyoxylate and dicarboxylate metabolism		 3 Arahy.NDL7Z2, Arahy.S45BII, Arahy.VD5UEC
不同环境中微生物代谢
Microbial metabolism in diverse environments		 6 Arahy.CQFZ3U, Arahy.NDL7Z2, Arahy.S45BII, Arahy.SP7CPF, Arahy.U4VZKL, Arahy.VD5UEC
碳代谢
Carbon metabolism		 5 Arahy.CQFZ3U, Arahy.NDL7Z2, Arahy.S45BII, Arahy.U4VZKL, Arahy.VD5UEC
次生代谢生物合成
Biosynthesis of secondary metabolites		 12 Arahy.46W7S4, Arahy.6Q1KS5, Arahy.8T1UF6, Arahy.C0Q7J8, Arahy.CQFZ3U, Arahy.IC3HGI, Arahy.NDL7Z2, Arahy.S45BII, Arahy.SP7CPF, Arahy.U4VZKL, Arahy.YS6PIM, Arahy.ZZNJ3G
AhHDA-IP N聚糖生物合成
N-Glycan biosynthesis		 3 Arahy.6B4W14,Arahy.7LT28F, Arahy.YXCZ83
精氨酸和脯氨酸代谢
Arginine and proline metabolism		 3 Arahy.EJ6Q9X, Arahy.GRS0A1, Arahy.UIG78U
苯丙氨酸代谢
Phenylalanine metabolism		 2 Arahy.21PEZK, Arahy.SGZ2CH

Fig. 4

Common peak distribution of the ChIP-seq reads of AhGLK1 and AhHDA1"

Fig. 5

Motif sequence of AhGLK1 and AhHDA1-IP"

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