Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (8): 1575-1591.doi: 10.3864/j.issn.0578-1752.2024.08.012

• HORTICULTURE • Previous Articles     Next Articles

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

LIN Wei(), WU ShuiJin, LI YueSen   

  1. Subtropical Agriculture Research Institute, Fujian Academy of Agricultural Sciences, Zhangzhou 363005, Fujian
  • Received:2023-09-18 Accepted:2023-12-15 Online:2024-04-16 Published:2024-04-24
  • Contact: LIN Wei

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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

Table1

Primer sequences by qRT-PCR analysis"

基因名称（基因ID）
Gene name (Gene ID)		 引物序列 Primers sequence (5′-3′)
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

Table 2

Quality test of transcriptome sequencing data"

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

Table 3

Genome comparison results"

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%)

Fig. 1

Statistical map of differentially expressed genes"

Fig. 2

Gene ontology classification of DEGs"

Table 4

Classification of COG annotation about DEGs"

功能分类
Functional classification		 Unigene数量 Unigene number
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

Table 5

Some metabolic pathways of DEGs"

代谢通路
Pathway		 代谢通路编号
Pathway ID		 Unigene数目Unigene number
Cold1/CK Cold3/CK
氨基酸代谢
Amino acid metabolism		 map00310 19 21
map00380 30 35
map00260 37 42
map00270 67 88
map00360 16 25
map00280 16 22
脂质代谢
Lipid metabolism		 map00071 12 26
map00061 17 24
map00073 17 13
map00062 26 24
map00564 51 83
map00561 42 75
map00600 17 37
map00591 16 12
map00592 29 35
苯丙素生物合成 Phenylpropanoid biosynthesis map00940 100 116
α-亚麻酸代谢 α-Linolenic acid metabolism map00592 29 35
辅因子和维生素的代谢
Metabolism of cofactors and vitamins		 map00790 12 15
map00860 30 39
map00760 12 17
其他次生代谢产物的生物合成
Biosynthesis of other secondary metabolites		 map00960 11 20
map00941 22 36
map00940 100 116
map00945 11 20
类胡萝卜素生物合成 Carotenoid biosynthesis map00906 16 23
碳水化合物代谢 Carbohydrate metabolism map00040 34 43
map00051 42 62
map00053 38 45
map00052 27 36
光合作用信号途径 Photosynthetic signaling pathway map00719 51 60
能量代谢 Energy metabolism map00196 29 26
map00710 51 60
map00910 19 22
半乳糖代谢 Galactose metabolism map00052 27 36
谷胱甘肽代谢 Glutathione metabolism map00480 40 64

Fig. 3

The KEGG analysis of differentially expressed genes A: Cold1 vs CK; B: Cold3 vs CK; C: Cold1 vs Cold3"

Fig. 4

qRT-PCR validation results"

Fig. 5

Comparative analysis of transcriptome and proteome data A: Correlation analysis between transcription and corresponding protein expression; B: DEGs and DEPs distribution statistics;C:Venn diagram for comparative analysis of DEGs and DEPs"

Fig. 6

GO enrichment analysis of DEPs co-upregulated with DEGs"

Fig. 7

GO enrichment analysis of DEPs co-downregulated with DEGs"

Fig. 8

Association analysis of DEGs and DEPs based on KEGG pathway"

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