转录组和蛋白质组关联分析解析巴西蕉幼苗响应低温的分子机制

doi:10.3864/j.issn.0578-1752.2024.08.012

Abstract

Abstract:

【Objective】 Low temperature is a significant natural disaster that affects banana production. In this study, based on transcriptome and proteome association analysis, the regulatory network of genes, proteins, signals and metabolic pathways involved in banana cold resistance was investigated. The aim was to explore the molecular mechanism of banana cold resistance. 【Methods】 ‘Baxi’ banana (Musa nana Lour) was treated at 7 ℃ for 1 and 3 d, and a control group was treated at 28 ℃. Based on the proteome data obtained in the previous study, the transcriptome sequencing technology was used to detect changes in the gene regulatory network of banana under cold stress. Simultaneously, the correlation analysis was conducted with proteomics to analyze the molecular mechanism of banana response to cold stress. 【Result】 Transcriptome analysis revealed that 11 370, 15 460 and 9 619 differentially expressed genes were identified in the three comparison groups of Cold1 vs CK, Cold3 vs CK and Cold1 vs Cold3, respectively. KEGG enrichment analysis of these genes revealed that the differentially expressed genes were enriched in several key signaling metabolic pathways, such as photosynthesis signal, glutathione metabolism, α-linolenic acid metabolic pathway and phenylpropanoid biosynthesis under low temperature stress. Moreover, there were significant differences in the enrichment degree of glutathione metabolic pathway between Cold1 d vs CK and Cold3 d vs CK. Real-time quantitative PCR analysis (qRT-PCR) was performed on several differentially expressed genes. Among them, the expression levels of key low-temperature regulatory genes, such as DREB, MAPK and MYB, were significantly increased after the low-temperature treatment. The expression trend of the selected 20 genes was essentially consistent with that of RNA-seq, confirming the accuracy of RNA-seq. The results of the transcriptome and proteome association analysis showed a positive correlation between the transcriptome and proteomics. A total of 6 211 proteins corresponding to transcripts were identified. Among these, 105 transcripts and their proteins were up-regulated, while 218 transcripts and their proteins were down-regulated. GO enrichment analysis showed that the differentially expressed genes and proteins were enriched in functions, such as photoresponse, chloroplast and oxidoreductase activity. Furthermore, the correlation analysis of differentially expressed genes and protein KEGG pathway revealed that the low temperature treatment suppressed the expression of genes and proteins related to phenylpropanoid biosynthesis and photosynthesis signaling pathway, while promoting the expression of proteins associated with α-linolenic acid metabolism and the glutathione pathway. 【Conclusion】 The transcriptome and proteomics were used to map the regulatory network of banana cold resistance at the gene and protein levels. It was found that the signal pathway of banana response to low temperature mainly involved photosynthesis signal, glutathione metabolism, α-linolenic acid metabolism and phenylpropanol biosynthesis.

Key words: Musa nana Lour, low temperature stress, transcriptome, proteome, comparative analysis

LIN Wei, WU ShuiJin, LI YueSen. Transcriptome and Proteome Association Analysis to Revealthe Molecular Mechanism of Baxi Banana Seedlings in Response to Low Temperature[J].Scientia Agricultura Sinica, 2024, 57(8): 1575-1591.

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References 39

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基因名称（基因ID） Gene name (Gene ID)	引物序列 Primers sequence (5′-3′)
基因名称（基因ID） Gene name (Gene ID)	正向 Forward	反向 Reverse
MaMYB (LOC103972162)	CTGCCCTTTCGTCTGTCTTC	CAGTTCTCGGCAGGAGGTAG
MaDREB (LOC103990508)	GACAGAGAGCTCAGCACACG	AGCATCGACATCATCCCAAT
MaWRKY45 (LOC108952331)	AGTGGGTCAGAGCCTTGAGA	TGCACTCCGTCGTAAGTGAC
MaMYBP (LOC103998926)	GCTCATCATCAAGCTCCACA	CTCGAAATGGGTGGCTGTAT
MaWRKY33 (LOC103989687)	CGGGTTGTCTTCCATGAGAT	CCTCCAGTTGTATCCGTCGT
MaMYC (LOC103985317)	TCTCCATGACCCAGTCCTTC	GAAGAGGACGCTGATCTTGC
MaCPK29 (LOC103995457)	GCAATTCAGAGCGATGAACA	CCAGCCTTCTCAGTCCAGTC
MaMAPK5 (LOC103996929)	AACCCGAGCTTGGATTTCTT	AGAAAGGGTCCATGCAAGTG
MaWRKY24 (LOC103989687)	CGGGTTGTCTTCCATGAGAT	CCTCCAGTTGTATCCGTCGT
MaGST U17 (LOC103994768)	TGGTTTGACAGCCACCATTA	CACTTCCGCCATCTCTTCTC
MaGST F12 (LOC103981216)	CAACAAGGTCCTGGAGGTGT	TTGACGTGCTTCTTGTCGTC
MaGST F10 (LOC103982403)	TGGTCGAACAGAGCATGAAG	TCCCACCACCTGTACACCTT
MaGST zeta (LOC103995971)	TCGGCTCGAGTATTCAACCT	TTTGGAAGCGCACTAATCCT
MaGST T1 (LOC103973270)	TTTCGAGGAGGTGAGGATTG	GATACCAATGGTCCGGAATG
Ma14-3-3 (LOC103985456)	TGAGGATCATGTTTCCGTGA	GCCTCCTTCCTTTCATTTCC
MaMKK5 (LOC103981573)	GGATCAACACCGACCTCAAC	CAGATGGCCACCATGAGAC
MaCML49 (LOC103972901)	CCCAAAGGAAGGGAAGACTC	TGTTGCAGCTCCTTGTCATC
MaCML18 (LOC103994211)	GCTTTGAACGCGTCTTCTTC	GGTCAAGCAAGGAGACCTCA
MaCML31 (LOC104000196)	TGATTCTCGTCAATCCAACG	TTTGTCGTGCTGCTTATTGG
MaCML10 (LOC103995933)	TTCGTCGAACTCAACACCAG	GGTCATCATGGCCTTGAACT
MaACTIN (LOC103992883)	CGTAGCACCAGAAGAACA	CATAAAGGGAGAGGACAG

样品名称 Sample name	过滤后序列 Clean reads	过滤后总数据量 Clean bases	碱基错误率 Error rate (%)	Q20 (%)	Q30 (%)	GC (%)
CK1	55962510	8251833288	0.0266	97.39	92.72	54.51
CK2	54693020	7946130178	0.0267	97.38	92.69	53.64
CK3	46556340	6760589819	0.0273	97.16	92.15	53.30
Cold1-1	43765858	6433985244	0.0268	97.34	92.49	50.46
Cold1-2	49835534	7319445856	0.0275	97.07	91.89	50.12
Cold1-3	45665780	6692564466	0.0272	97.21	92.18	50.38
Cold3-1	43171118	6347773723	0.0275	97.07	91.9	50.69
Cold3-2	47440180	6960515302	0.0276	97.04	91.83	50.43
Cold3-3	43284622	6385904142	0.0276	97.06	91.86	50.56

样品名称 Sample	过滤序列总数 Clean reads	总比对（对比率） Totalmapped (Mapping ratio, %)	多方比对（对比率） Multiple mapped (Mapping ratio, %)	唯一比对（对比率） Uniquely mapped (Mapping ratio, %)
CK1	55962510	51136284 (91.38%)	853090 (1.52%)	50283194 (89.85%)
CK2	54693020	49654543 (90.79%)	792871 (1.45%)	48861672 (89.34%)
CK3	46556340	42271280 (90.8%)	647597 (1.39%)	41623683 (89.4%)
Cold1-1	43765858	38887517 (88.85%)	553404 (1.26%)	38334113 (87.59%)
Cold1-2	49835534	44029762 (88.35%)	605472 (1.21%)	43424290 (87.14%)
Cold1-3	45665780	40473620 (88.63%)	548796 (1.2%)	39924824 (87.43%)
Cold3-1	43171118	38239493 (88.58%)	596851 (1.38%)	37642642 (87.19%)
Cold3-2	47440180	42055866 (88.65%)	728177 (1.53%)	41327689 (87.12%)
Cold3-3	43284622	38397112 (88.71%)	702198 (1.62%)	37694914 (87.09%)

功能分类 Functional classification	Unigene数量 Unigene number
功能分类 Functional classification	Cold1/CK	Cold3/CK	Cold1/Cold3
RNA加工和修饰 RNA processing and modification	29	58	25
染色质结构与动力学 Chromatin structure and dynamics	74	98	53
能源生产和转换 Energy production and conversion	185	250	164
细胞周期控制、细胞分裂 Cell cycle control, cell division	118	154	89
氨基酸运输和代谢 Amino acid transport and metabolisS	255	385	251
核苷酸运输和代谢 Nucleotide transport and metabolism	63	87	59
碳水化合物运输和代谢 Carbohydrate transport and metabolism	505	604	413
辅酶转运与代谢 Coenzyme transport and metabolism	85	123	74
脂质运输和代谢 Lipid transport and metabolism	195	275	179
核糖体结构与生物发生 Ribosomal structure and biogenesis	240	417	242
转录 Transcription	1093	1396	898
复制、重组和修复 Replication, recombination and repair	136	228	145
细胞壁、膜、包膜生物发生 Cell wall, membrane,envelope biogenesis	168	224	148
细胞运动 Cell motility	5	5	5
翻译后修饰 Posttranslational modification	763	1176	760
无机离子运输和代谢 Inorganic ion transport and metabolism	176	250	165
次生代谢产物生物合成 Secondary metabolites biosynthesis	166	235	169
信号传导机制 Signal transduction mechanisms	784	1107	673
胞内运输 Intracellular trafficking	338	522	315
防御机制 Defense mechanisms	80	99	72
核结构 Nuclear structure	0	2	1
细胞骨架 Cytoskeleton	133	173	98

Transcriptome and Proteome Association Analysis to Revealthe Molecular Mechanism of Baxi Banana Seedlings in Response to Low Temperature

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