Biotechnology Bulletin ›› 2024, Vol. 40 ›› Issue (3): 215-228.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0747
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XIE Qian(), JIANG Lai, HE Jin, LIU Ling-ling, DING Ming-yue, CHEN Qing-xi()
Received:
2023-08-03
Online:
2024-03-26
Published:
2024-04-08
Contact:
CHEN Qing-xi
E-mail:xieq0416@163.com;cqx0246@fafu.edu.cn
XIE Qian, JIANG Lai, HE Jin, LIU Ling-ling, DING Ming-yue, CHEN Qing-xi. Regulatory Genes Mining Related to Transcriptome Sequencing and Phenolic Metabolism Pathway of Canarium album Fruit with Different Fresh Food Quality[J]. Biotechnology Bulletin, 2024, 40(3): 215-228.
基因ID Gene ID | 引物序列Primer sequence(5'-3') | 扩增品种(系)Amplification variety(lines) |
---|---|---|
Cluster-0.119989-F | TGACTTCTGTGTCCTGCTCTT | DQc、TQc |
Cluster-0.119989-R | GGTAGTGCCAACTGCTTCTTC | |
Cluster-0.121834-F | CTTGACATGAATACAGCAGAGGAT | DQc、TQc |
Cluster-0.121834-R | GCACCATCAATTTCAGCAACTT | |
Cluster-0.121871-F | TCTGTGTCCTGCTCTTTGAAG | DQc、TQc |
Cluster-0.121871-R | GCAACCTCAGAGATGGGAAG | |
Cluster-0.121919-F | TAACCATAACGCCTCCATCTCT | DQc、TQc |
Cluster-0.121919-R | TCATCTCACGAGACACAATAGACT | |
Cluster-0.121949-F | TAACCATAACGCCTCCTTCTCT | DQc、TQc |
Cluster-0.121949-R | GCTCCTACAATCACCACATCAG | |
Cluster-0.155662-F | AGACTATGACGAGCAAGACAACT | DQc、TQc |
Cluster-0.155662-R | GTTACCACACCACCGACTCT | |
Cluster-0.119990-F | CTGTTGCCGTAACTTCACTGT | TQc |
Cluster-0.119990-R | CTGAGAGATGGGAAGCGTTTC | |
Cluster-0.120915-F | ATCATTCTCCAGGCATTTCTCAG | TQc |
Cluster-0.120915-R | GGAACAGCCACAGCTTGTAT | |
Cluster-0.121783-F | CAGGAAGTGTCAGCAACATCAA | TQc |
Cluster-0.121783-R | CTGTTCTTCGCAAGGTTCATCT | |
Cluster-0.121896-F | AGGAGTGAAGTGGTTGAAGAGTA | DQc |
Cluster-0.121896-R | ACAATCATCCCAGGCACAATC | |
Cluster-0.122437-F | TAACCATAACGCCTCCATCTCT | DQc |
Cluster-0.122437-R | ATCAGTGTCCGCATGTGTAATC | |
Cluster-0.122522-F | CCTCCATCTCTGCTTCTTCCT | DQc |
Cluster-0.122522-R | TGTACCTGCGTGTCATCTCA | |
18S rRNA-F(内参基因) | CCTGAGAAACGGCTACCACA | DQc、TQc |
18S rRNA-R(内参基因) | CACCAGACTT GCCCTCCA |
Table 1 Primer sequences for RT-qPCR
基因ID Gene ID | 引物序列Primer sequence(5'-3') | 扩增品种(系)Amplification variety(lines) |
---|---|---|
Cluster-0.119989-F | TGACTTCTGTGTCCTGCTCTT | DQc、TQc |
Cluster-0.119989-R | GGTAGTGCCAACTGCTTCTTC | |
Cluster-0.121834-F | CTTGACATGAATACAGCAGAGGAT | DQc、TQc |
Cluster-0.121834-R | GCACCATCAATTTCAGCAACTT | |
Cluster-0.121871-F | TCTGTGTCCTGCTCTTTGAAG | DQc、TQc |
Cluster-0.121871-R | GCAACCTCAGAGATGGGAAG | |
Cluster-0.121919-F | TAACCATAACGCCTCCATCTCT | DQc、TQc |
Cluster-0.121919-R | TCATCTCACGAGACACAATAGACT | |
Cluster-0.121949-F | TAACCATAACGCCTCCTTCTCT | DQc、TQc |
Cluster-0.121949-R | GCTCCTACAATCACCACATCAG | |
Cluster-0.155662-F | AGACTATGACGAGCAAGACAACT | DQc、TQc |
Cluster-0.155662-R | GTTACCACACCACCGACTCT | |
Cluster-0.119990-F | CTGTTGCCGTAACTTCACTGT | TQc |
Cluster-0.119990-R | CTGAGAGATGGGAAGCGTTTC | |
Cluster-0.120915-F | ATCATTCTCCAGGCATTTCTCAG | TQc |
Cluster-0.120915-R | GGAACAGCCACAGCTTGTAT | |
Cluster-0.121783-F | CAGGAAGTGTCAGCAACATCAA | TQc |
Cluster-0.121783-R | CTGTTCTTCGCAAGGTTCATCT | |
Cluster-0.121896-F | AGGAGTGAAGTGGTTGAAGAGTA | DQc |
Cluster-0.121896-R | ACAATCATCCCAGGCACAATC | |
Cluster-0.122437-F | TAACCATAACGCCTCCATCTCT | DQc |
Cluster-0.122437-R | ATCAGTGTCCGCATGTGTAATC | |
Cluster-0.122522-F | CCTCCATCTCTGCTTCTTCCT | DQc |
Cluster-0.122522-R | TGTACCTGCGTGTCATCTCA | |
18S rRNA-F(内参基因) | CCTGAGAAACGGCTACCACA | DQc、TQc |
18S rRNA-R(内参基因) | CACCAGACTT GCCCTCCA |
Fig. 1 Total phenol content in Chinese olive fruit ripening process and maturity period * indicates significant difference at 0.05 level, ** indicates significant difference at 0.01 level, and *** indicates significant difference at 0.001 level
类型Type | 序列条数Number of sequences | 序列平均长度Mean length/bp | N50/bp | N90/bp | 序列总碱基Total bases/bp |
---|---|---|---|---|---|
Unigene | 296 314 | 1 163 | 1 764 | 522 | 344 722 448 |
Table 2 Sequence splicing results of Chinese olive transcriptome
类型Type | 序列条数Number of sequences | 序列平均长度Mean length/bp | N50/bp | N90/bp | 序列总碱基Total bases/bp |
---|---|---|---|---|---|
Unigene | 296 314 | 1 163 | 1 764 | 522 | 344 722 448 |
Fig. 4 Differential genes and KEGG enrichment analysis of Chinese olive in different varieties(lines) A : Up-regulated and down-regulated differential genes, gene up/down-regulated expression refers to low phenolic Chinese olive(DQc, TQc)relative to high phenolic Chinese olive(SPc, HPc); B : common or unique differential genes ;C : KEGG enrichment analysis of common differential genes
Fig. 5 Differential genes and KEGG enrichment analysis of different varieties(lines)of Chinese olive ripening process A: Differential genes in the maturation process of ‘Ziyang 1’ (SP)and ‘Dongshanchangsui’ (DQ). B : Venn of differential genes in different maturation periods. C : KEGG enrichment analysis of differential genes
Fig. 6 Differential gene analysis of shikimic acid and hydrolyzed tannin biosynthesis pathway in different varieties(lines)of Chinese olive during maturation DPS : 3-deoxy-D-arabinoheptulose-7-phosphate synthase; DHQS : 3-dehydroquinic acid synthase; SKDH : shikimate dehydrogenase; UGTs : glycosyltransferase; SK : shikimate kinase; EPSPS : 5-enolpyruvylshikimate-3-phosphate synthase; CS : chorismate synthase; CM : chorismate mutase; pheA2 : prebenzoic acid dehydratase; GOT1 : aspartate aminotransferase; TAT : tyrosine aminotransferase; hisC : phosphohistidine aminotransferase ; Red or blue color blocks represent the value of Log2FC(DQ / SP), red and blue represent the up-regulated and down-regulated genes of low-phenol olive(DQ)compared to high-phenol olive(SP), respectively, and * indicates P.adjust < 0.05, the same below
Fig. 7 Differential gene analysis in phenylpropanes and flavonoids biosynthesis pathways in different varieties(lines)of Chinese olive during maturation PAL : Phenylalanine ammonia lyase; C4H : cinnamic acid-4-hydroxylase; 4CL : 4-coumaroyl-CoA ligase; CHS : chalcone synthase; CHI : chalcone isomerase; IFS : isoflavone synthase; FNS : flavonoid synthase; F3H : flavanone-3-hydroxylase; F3'H : flavonoid 3'-hydroxylase; F3' 5'H : flavonoid 3' 5' -hydroxylase; FLS : flavonol synthase; DFR : dihydroflavonol reductase; LAR : achromatic anthocyanin reductase; ANR : anthocyanin reductase ; aNS : anthocyanin synthase
Fig. 8 Visualization of gene co-expression network A: Determination of the optimal soft threshold. B: Cluster dendrogram of co-expression modules. C: Correlation between co-expression modules
Fig. 9 Module identification of phenolic compounds and mining of their associated transcription factors A:Module and trait correlation heat map,each row corresponds to a module. The values of each lattice indicate the correlation coefficients R and P, respectively. The lattice color indicates correlation, red indicates positive correlation, and blue indicates negative correlation. B:Co-expression network analysis of phenolic synthesis genes and transcription factors. Darker colors indicate that the gene is more important in the interaction network. C:Category statistics of transcription factors related to phenol synthesis
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