Transcriptome Sequencing and Gene Expression Analysis of Watermelon Peel with Different Firmness

doi:10.7668/hbnxb.20192957

Abstract

Abstract:

In order to analyze the molecular mechanism of different watermelon peel firmness,and provided a theoretical basis for discovering key genes related to watermelon peel firmness,the high firmness(901)4-1-1-M and low firmness BSH with similar growth period but significant difference in peel hardness were used as experimental materials.The peel with the maximum difference 30 days after pollination was selected for transcriptome sequencing analysis and the Illumina HiSeq^TM sequencing platform was used to analyze the molecular mechanism of different watermelon peel firmness,Real-time fluorescence quantitative PCR (qRT-PCR) was used to verify the sequencing results.A total of 1 085 differentially expressed genes (DEGs) were screened by transcriptome sequencing,including 555 up-regulated genes and 530 down-regulated genes.Gene Ontology(GO)analysis showed that 1 085 DEGs were significantly enriched in cell components,molecular functions and biological processes,including cell wall,cell periphery,external encapsulation structure,extracellular region,tetrapyrrole skeleton,redox enzyme activity,transferase activity and pectin esterase activity.Kyoto Encyclopedia of Genes and Genomes (KEGG)analysis indicated that 19 DEGs,including Cla97C04G075800,Cla97C02G044950,Cla97C09G165820,Cla97C10G195660,Cla97C01G025380,etc.,were enriched in the most significant enrichment biosynthesis of phenylpropanoid,which eventually lead to the metabolites of Syringyl lignin,5-Hydroxy-guaiacy lifnin,Guaiacy lifnin and P-Hydroxy-phenyl lifnin.The correlation coefficient of DEGs expression levels by qRT-PCR and RNA-seq data was 0.791,which indicated that the transcriptome test data were reliable.This study explained the reason of watermelon peel firmness difference between(901)4-1-1-M and BSH from the transcriptional level.

Key words: Watermelon, Peel firmness, Transcriptomic, Differentially expressed genes, Styrene acrylic pigment, Lignin

ZHANG Jingjing, LI Bing, SHI Yufan, GAO Xiurui, PAN Xiuqing, SONG Xue, WU Yanrong. Transcriptome Sequencing and Gene Expression Analysis of Watermelon Peel with Different Firmness[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(3): 44-52. doi: 10.7668/hbnxb.20192957.

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References 23

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基因 Gene ID	正向引物(5'-3') Forward primer sequence(5'-3')	反向引物(5'-3') Reverse primer sequence(5'-3')	扩增片段长度/bp Product size
Actin	TCAACCCAAAGGCAAACAGG	AAAACGGCCTGGATTGCAAC	91
Cla97C04G075800	TGGCTTCGAGTTTTGCATCG	AATGGCTTCCCTTCAACGAC	92
Cla97C02G044950	ATCGCCATTTCCAAGCTTCG	TTGCGGTGGTTCAAGTCATC	110
Cla97C10G195660	TTGCAAAGGAGCCATTTCCG	TGTTTCGAGGCAATGAGCTG	108
Cla97C09G165820	AAGCGTGGCTCAACAAATGG	ATGTGGAAAAACGGCAGCAC	90
Cla97C09G165630	AAAACGGCAACACCACCAAC	CGTCGGTGGCAATGTAAAGC	123
Cla97C02G032910	ACGGACAAGAAGACCAGAACC	ACAGAGCATCGCTTTGCAAC	78
Cla97C07G144540	TTTGACAGCGTTCCAAAGGG	TGCATTCCGCCACAATTACC	139
Cla97C02G045070	AGACGCTTCATTCGCAAAGC	AAAGCTTTGGGGTAGCAACG	95
Cla97C07G139710	ACATGAAACCGAGCAAGCTC	TCGCCGCTATGATCTTCAAC	138

基因 Gene ID	正向引物(5'-3') Forward primer sequence(5'-3')	反向引物(5'-3') Reverse primer sequence(5'-3')	扩增片段长度/bp Product size
Actin	TCAACCCAAAGGCAAACAGG	AAAACGGCCTGGATTGCAAC	91
Cla97C04G075800	TGGCTTCGAGTTTTGCATCG	AATGGCTTCCCTTCAACGAC	92
Cla97C02G044950	ATCGCCATTTCCAAGCTTCG	TTGCGGTGGTTCAAGTCATC	110
Cla97C10G195660	TTGCAAAGGAGCCATTTCCG	TGTTTCGAGGCAATGAGCTG	108
Cla97C09G165820	AAGCGTGGCTCAACAAATGG	ATGTGGAAAAACGGCAGCAC	90
Cla97C09G165630	AAAACGGCAACACCACCAAC	CGTCGGTGGCAATGTAAAGC	123
Cla97C02G032910	ACGGACAAGAAGACCAGAACC	ACAGAGCATCGCTTTGCAAC	78
Cla97C07G144540	TTTGACAGCGTTCCAAAGGG	TGCATTCCGCCACAATTACC	139
Cla97C02G045070	AGACGCTTCATTCGCAAAGC	AAAGCTTTGGGGTAGCAACG	95
Cla97C07G139710	ACATGAAACCGAGCAAGCTC	TCGCCGCTATGATCTTCAAC	138

样品 Sample	原始reads/条 Raw reads	滤后reads/条 Clean reads	错误率/% Error rate	Q20百分率/% Q20 percentage	Q30百分率/% Q30 percentage	GC 含量/% GC percentage
A1	41 758 886	41 376 900	0.02	98.13	94.40	43.83
A2	43 554 750	43 143 786	0.02	98.18	94.47	43.80
A3	50 305 470	49 846 930	0.02	98.08	94.24	43.67
B1	45 484 004	44 895 382	0.03	97.35	92.63	43.72
B2	47 849 050	47 228 278	0.02	98.25	94.61	43.67
B3	46 091 088	45 586 596	0.02	98.22	94.55	43.48

样品 Sample	原始reads/条 Raw reads	滤后reads/条 Clean reads	错误率/% Error rate	Q20百分率/% Q20 percentage	Q30百分率/% Q30 percentage	GC 含量/% GC percentage
A1	41 758 886	41 376 900	0.02	98.13	94.40	43.83
A2	43 554 750	43 143 786	0.02	98.18	94.47	43.80
A3	50 305 470	49 846 930	0.02	98.08	94.24	43.67
B1	45 484 004	44 895 382	0.03	97.35	92.63	43.72
B2	47 849 050	47 228 278	0.02	98.25	94.61	43.67
B3	46 091 088	45 586 596	0.02	98.22	94.55	43.48

样品 Sample	总数/条 Total reads	数量/条(比对率/%) Quantity (ratio)			外显子比对率/% Exon mapped ratio
样品 Sample	总数/条 Total reads	定位到基因组上序列 Total mapped	唯一比对位置序列 Uniquely mapped	多个比对位置序列 Multiple mapped	外显子比对率/% Exon mapped ratio
A1	41 376 900	33 568 170(81.13)	32 939 299(79.61)	628 871(1.52)	76.50
A2	43 143 786	35 596 732(82.51)	34 956 941(81.02)	639 791(1.48)	75.60
A3	49 846 930	40 630 024(81.51)	39 734 776(79.71)	895 248(1.80)	76.03
B1	44 895 382	35 359 625(78.76)	34 779 983(77.47)	579 642(1.29)	75.23
B2	47 228 278	35 818 334(75.84)	35 071 296(74.26)	747 038(1.58)	76.03
B3	45 586 596	32 768 449(71.88)	32 165 238(70.56)	603 211(1.32)	76.31

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