Transcriptome Analysis of Interaction Between Gossypium barbadense and Fusarium oxysporum f. sp. vasinfectum

doi:10.13560/j.cnki.biotech.bull.1985.2022-1316

Abstract

Abstract:

Cotton Fusarium wilt is a common disease in cotton production, especially very seriously in island cotton（Gossypium barbadense）, affecting its yield and quality, which pose a great threat to the development of island cotton industry. To understand the molecular mechanism of the interaction between cotton and Fusarium oxysporum, RNA-seq sequencing technology was applied to analyze the gene expression characteristics of the interaction between Fusarium oxysporum and cotton using the resistant and susceptible cotton root tissues and pathogenic bodies infected by Fusarium oxysporum for 48 h as materials. The results showed that 15 218 and 9 358 differentially expressed genes were detected in resistant and susceptible cotton varieties respectively, 3 708 and 3 656 differentially expressed genes were identified in Fusarium oxysporum after infecting the resistant and susceptible cotton varieties. Through GO enrichment analysis, we found that the main processes in cotton after interaction were oxidative stress, auxin-activated signaling pathway, response to stimulus, response to injury and transcription factor activity. KEGG pathways were significantly enriched in endocytosis, plant hormone signal transduction, amino acid biosynthesis, carbon metabolism, plant-pathogen interactions, phenylpropane biosynthesis and other metabolic pathways. Disease-resistant cultivars were significantly up-regulated in responses to stimulation and injury. In the Fusarium oxysporum after interaction, GO enrichment analysis found that differentially expressed genes were mostly involved in membrane components, catalytic activity regulation, ATP binding etc. KEGG was significantly enriched in peroxisome, mitogen-activated protein kinase signaling pathways, valine, leucine and L-Isoleucine degradation, glycine, serine and threonine metabolism, carbon metabolism, amino acid biosynthesis, starch and sucrose metabolism and other metabolic pathways. This study provids an abundant gene resources for studying the responses of cotton to Fusarium wilt and the pathogenicity of F. oxysporum, and laid a foundation for an in-depth analysis of the mechanism of interaction between Fusarium oxysporum and cotton.

Key words: Fusarium oxysporum, cotton, Fusarium wilt, plant-pathogen interactions, RNA-seq, differentially expressed genes

YANG Yang, ZHU Jin-cheng, LOU Hui, HAN Ze-gang, ZHANG Wei. Transcriptome Analysis of Interaction Between Gossypium barbadense and Fusarium oxysporum f. sp. vasinfectum[J]. Biotechnology Bulletin, 2023, 39(6): 259-273.

Figures/Tables 11

Table 1 Primers for RT-qPCR

基因名称Gene name	上游引物 Forward primer（5'-3'）	下游引物 Reverse primer（5'-3'）
Gb2763	TTCCACAGTTCCAGGGTA	GATGATCCAAGGCTTTCT
Gb1474	AAACAAGGTAAGGAGGCT	GTTGGGTAAATAATAGGC
Gb7593	CAACTTGGCATCTTATCC	CTTACATTGAGCAGCAAC
Gb8190	CATGGAGCAAAGGTTTAA	TGTTGGATTCAGGGAGAT
Gb8191	CATGGAGCAAAGGTTTAA	TGTTGGATTCAGGGAGAT
Gb9261	TTTGCCAAAGAGCGTAGA	TTAAAGAATGCGGTGTCG
Gb9263	TTTCGGCAAGTCTATGAT	TCTTTCTGGTCGTGGATG
FOTG10073	GATGCCTGCCGTGGTGGAT	GGGCGAAGAAACAGTGTAAAGC
FOTG05109	TATCGCCCAGATGTTCAA	TACCACGGTGCTGTTCCA
FOTG15482	TTTCTTCATCGCCCTGTA	ACATTGCCGACTTGGATT
FOTG11725	TTGTTGGTTTGCCCTTGT	CGAGCGGTCTGAGTGTAG
FOTG17884	GCAATCTCAGCCTCAAGTT	GACAAGCGTTCATCCATAA
FOTG17663	GCCTTCTCGGATCTTCTA	GCAATGCTGGGATGGTAT
GhUBQ7	GAAGACCTACACCAAGCCCAA	CGGACTCTACTCAATCCCCACC

Fig. 1 Correlation analysis among samples A: Correlation analysis of four samples from cotton root tissues. T14p indicates the treatment sample from Xinhai 14, T42p indicates the treatment sample from Xinhai 42, CKp14 indicates the control sample from Xinhai 14 and CKp42 indicates the control sample from Xinhai 42. B: Correlation analysis of three samples from Fov. CKb refers to the control sample of Fov, T14b to the Fov sample obtained from Xinhai 14, T42b to the Fov sample obtained from Xinhai 42. a and b are the duplications

Fig. 2 Validation of RNA-seq data by RT-qPCR A-C : RNA-seq expression. D and E : RT-qPCR verification of 7 genes in cotton. F and G : RT-qPCR verification of 6 genes in Fusarium oxysporum. CK: Control group. T: Treatment group. CKb: Bacteria control group. T14: Xinhai 14 treatment group.T42: Xinhai 42 treatment group. * indicates difference（P<0.05）, ** indicates significant difference（P<0.01）, and *** indicates extremely significant difference（P<0.001）

Fig. 3 Volcano map of differentially expressed genes in the cotton of different treatments Green is down-regulated gene and red is up- regulated gene. The same below

Fig. 4 Volcano map of differentially expressed genes of Fusarium oxysporum among different treatments A：CKb_T14；B：CKb_T42

Fig. 5 GO analysis of differentially expressed genes in Xinhai 14 after inoculation A-C: GO analysis of up-regulated genes. D-F: GO analysis of down-regulated genes. The abscissa is number of genes enriched for each term, and the ordinate is the term of GO level

Fig. 6 GO analysis of differentially expressed genes in Xinhai 42 after inoculation A-C: GO analysis of up-regulated genes. D-F: GO analysis of down-regulated genes. The abscissa is number of genes enriched for each term,the ordinate is the term of GO level

Fig. 7 KEGG analysis of differentially expressed genes in two cotton cultivars after inoculation A: KEGG analysis of up-regulated genes in Xinhai 14. B: KEGG analysis of down-regulated genes in Xinhai 14. C: KEGG analysis of up-regulated genes in Xinhai 42. D: KEGG analysis of down-regulated genes in Xinhai 42

Fig. 8 GO analysis of differentially expressed genes of Fov after infecting Xinhai 14 A-C: GO analysis of up-regulated genes of Fov in Xinhai 14. D-F: GO analysis of down-regulated genes of Fov in Xinhai 14. The abscissa is number of genes enriched for each term, the ordinate is the term of GO level

Fig. 9 KEGG analysis of differentially expressed genes of Fov after infecting Xinhai 14 and Xinhai 42 A: KEGG analysis of up-regulated genes of Fov（Fusarium oxysporum f. sp. Vasinfectum）in Xinhai 14. B: KEGG analysis of down-regulated genes of Fov in Xinhai 14. C: KEGG analysis of up-regulated genes of Fov in Xinhai 42. D: KEGG analysis of down-regulated genes of Fov in Xinhai 42

Fig. 10 GO analysis of differentially expressed genes of Fov after infecting Xinhai 42 A-C: GO analysis of up-regulated genes of Fov in Xinhai 42. D-F: GO analysis of down-regulated genes of Fov in Xinhai 42. The abscissa is number of genes enriched for each term, the ordinate is the term of GO level

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