Xinjiang Agricultural Sciences ›› 2023, Vol. 60 ›› Issue (2): 389-398.DOI: 10.6048/j.issn.1001-4330.2023.02.016
• Horticultural Special Local Products·Plant Protection·Microbes·Soil Fertilizer· Water Saving Irrigation • Previous Articles Next Articles
SONG Jindi(), LIU Jun(), SUN Yufang, Youlituzi Naibi, CHEN Baoqiang, XIE Bingbing
Received:
2022-06-22
Online:
2023-02-20
Published:
2023-03-31
Correspondence author:
LIU Jun (1970-), female, born in Urumqi, Xinjiang, Associate professor, postgraduate supervisor, research interest: plant pathogenic bacteriology, (E-mail)liujem@126.com
Supported by:
宋金迪(), 刘君(), 孙玉芳, 优丽图孜·乃比, 陈宝强, 颉兵兵
通讯作者:
刘君(1970-),女,新疆乌鲁木齐人,副教授,硕士研究生导师,研究方向为植物病原细菌学,(E-mail)liujem@126.com
作者简介:
宋金迪(1994-),男,河南洛阳人,硕士研究生,研究方向为植物病原细菌学,(E-mail)sjddog@126.com
基金资助:
CLC Number:
SONG Jindi, LIU Jun, SUN Yufang, Youlituzi Naibi, CHEN Baoqiang, XIE Bingbing. Transcriptome Analysis of Acidovorax citrulli against Copper Stress[J]. Xinjiang Agricultural Sciences, 2023, 60(2): 389-398.
宋金迪, 刘君, 孙玉芳, 优丽图孜·乃比, 陈宝强, 颉兵兵. 铜胁迫下的西瓜食酸菌转录组分析[J]. 新疆农业科学, 2023, 60(2): 389-398.
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URL: http://www.xjnykx.com/EN/10.6048/j.issn.1001-4330.2023.02.016
基因ID Gene ID | 本地数据库基因ID Local database gene ID | 正向引物(5'~3') Forward primer | 反向引物(5'~3') Reverse primer |
---|---|---|---|
NMDCN0000J7Q | GE00642 | GCGTGACCGCCATCCAG | CCTTGCGGGCGATGATG |
NMDCN0000J7N | GE00282 | AACAACTACCAGGTGGGACT | GGTGAGCTGCACGGATT |
NMDCN0000J7P | GE01538 | AGCCTCTTGCCATTGCC | CACCACCTGGGTATCGC |
NMDCN0000J7O | GE02901 | CCCTCCGCCAGAACAAT | TCCACCGACACGATGATG |
NMDCN0000J7M | GE00281 | GCGCTACAACGGCTACC | GCCAGGCAGAGGAACAC |
NMDCN0000J7L | GE01342 | TGCCGTGACGACTGCTT | GCGTATTGTTGGCCTTGT |
NMDCN0000J7K | GE04032 | AACAACTACCAGGTGGGACT | GGTGAGCTGCACGGATT |
NMDCN0000J7J | GE01848 | CGCCTATCCGTCCAAGC | AGCACCGTGTAGCCGTC |
NMDCN0000J7I | GE02981 | CGCCGTCCCTCCCGTTT | GCCAGGATCGTCCCCAG |
NMDCN0000J7H | GE01751 | GTCAACCTCTGGGGCTACA | AACTCGTACACGAAGGTCTTG |
NMDCN0000J7G | GE01955 | GAACCTGGAAGTCATCATCG | CCTTGGTCTTGTTGTCGG |
NMDCN0000Q79 | GE04262 | GGCTGGCTGGGTCATAC | ATTGTAGATTTCGCCGTTG |
NMDCN0000Q7A | GE02797 | CACAAGACTGTTTCTGTTCCAAG | GCACGTATGTCCGTCACCT |
NMDCN0000Q7B | GE00664 | CGTCCCGTATCGCCGTCA | GCGTGATGCCCGTGAGC |
NMDCN0000Q7C | GE01086 | GCTGCTGTCGGAAATGG | TTGTTGGTGCGGAAGTTAC |
rpoB | - | GCGACAGCGTGCTCAAAGTG | GGCCTTCGTTGGTGCGTTTCT |
Table 1 Primers used for validation qPCR of transcriptome data
基因ID Gene ID | 本地数据库基因ID Local database gene ID | 正向引物(5'~3') Forward primer | 反向引物(5'~3') Reverse primer |
---|---|---|---|
NMDCN0000J7Q | GE00642 | GCGTGACCGCCATCCAG | CCTTGCGGGCGATGATG |
NMDCN0000J7N | GE00282 | AACAACTACCAGGTGGGACT | GGTGAGCTGCACGGATT |
NMDCN0000J7P | GE01538 | AGCCTCTTGCCATTGCC | CACCACCTGGGTATCGC |
NMDCN0000J7O | GE02901 | CCCTCCGCCAGAACAAT | TCCACCGACACGATGATG |
NMDCN0000J7M | GE00281 | GCGCTACAACGGCTACC | GCCAGGCAGAGGAACAC |
NMDCN0000J7L | GE01342 | TGCCGTGACGACTGCTT | GCGTATTGTTGGCCTTGT |
NMDCN0000J7K | GE04032 | AACAACTACCAGGTGGGACT | GGTGAGCTGCACGGATT |
NMDCN0000J7J | GE01848 | CGCCTATCCGTCCAAGC | AGCACCGTGTAGCCGTC |
NMDCN0000J7I | GE02981 | CGCCGTCCCTCCCGTTT | GCCAGGATCGTCCCCAG |
NMDCN0000J7H | GE01751 | GTCAACCTCTGGGGCTACA | AACTCGTACACGAAGGTCTTG |
NMDCN0000J7G | GE01955 | GAACCTGGAAGTCATCATCG | CCTTGGTCTTGTTGTCGG |
NMDCN0000Q79 | GE04262 | GGCTGGCTGGGTCATAC | ATTGTAGATTTCGCCGTTG |
NMDCN0000Q7A | GE02797 | CACAAGACTGTTTCTGTTCCAAG | GCACGTATGTCCGTCACCT |
NMDCN0000Q7B | GE00664 | CGTCCCGTATCGCCGTCA | GCGTGATGCCCGTGAGC |
NMDCN0000Q7C | GE01086 | GCTGCTGTCGGAAATGG | TTGTTGGTGCGGAAGTTAC |
rpoB | - | GCGACAGCGTGCTCAAAGTG | GGCCTTCGTTGGTGCGTTTCT |
样品名 Sample | Reads总数 Total reads | 碱基总数 Bases(bp) | N (%) | Q20 (%) | Q30 (%) |
---|---|---|---|---|---|
CK1 | 29 540 900 | 4 460 675 900 | 0.04 | 96.90 | 92.01 |
CK2 | 31 451 022 | 4 749 104 322 | 0.04 | 96.80 | 91.82 |
CK3 | 27 676 892 | 4 179 210 692 | 0.02 | 97.09 | 92.40 |
T1 | 29 357 120 | 4 432 925 120 | 0.02 | 96.93 | 92.02 |
T2 | 27 027 648 | 4 081 174 848 | 0.01 | 96.99 | 92.14 |
T3 | 27 104 738 | 4 092 815 438 | 0.02 | 97.04 | 92.24 |
Table 2 Base mass statistics of the transcript of Acidovorax citrulli FC440 under copper stress
样品名 Sample | Reads总数 Total reads | 碱基总数 Bases(bp) | N (%) | Q20 (%) | Q30 (%) |
---|---|---|---|---|---|
CK1 | 29 540 900 | 4 460 675 900 | 0.04 | 96.90 | 92.01 |
CK2 | 31 451 022 | 4 749 104 322 | 0.04 | 96.80 | 91.82 |
CK3 | 27 676 892 | 4 179 210 692 | 0.02 | 97.09 | 92.40 |
T1 | 29 357 120 | 4 432 925 120 | 0.02 | 96.93 | 92.02 |
T2 | 27 027 648 | 4 081 174 848 | 0.01 | 96.99 | 92.14 |
T3 | 27 104 738 | 4 092 815 438 | 0.02 | 97.04 | 92.24 |
样品名 Sample | 可用读取 Useful Reads | 总映射读取 Total Mapped Reads | 占比 Proportion (%) | 单映射读取 Uniquely Mapped Reads | 占比 Proportion (%) | 多映射读取 Multiple Mapped Reads | 占比 Proportion (%) |
---|---|---|---|---|---|---|---|
CK1 | 29 395 754 | 29 311 584 | 99.71 | 28 350 407 | 96.72 | 961 177 | 3.28 |
CK2 | 31 279 164 | 31 182 372 | 99.69 | 30 036 408 | 96.32 | 1 145 964 | 3.68 |
CK3 | 27 553 118 | 27 468 703 | 99.69 | 26 767 147 | 97.45 | 701 556 | 2.55 |
T1 | 29 214 302 | 29 096 642 | 99.60 | 28 357 073 | 97.46 | 739 569 | 2.54 |
T2 | 26 898 484 | 26 777 059 | 99.55 | 26 086 501 | 97.42 | 690 558 | 2.58 |
T3 | 26 987 212 | 26 892 876 | 99.65 | 26 195 932 | 97.41 | 696 944 | 2.59 |
Table 3 Reference genome comparison of Acidovorax citrulli FC440
样品名 Sample | 可用读取 Useful Reads | 总映射读取 Total Mapped Reads | 占比 Proportion (%) | 单映射读取 Uniquely Mapped Reads | 占比 Proportion (%) | 多映射读取 Multiple Mapped Reads | 占比 Proportion (%) |
---|---|---|---|---|---|---|---|
CK1 | 29 395 754 | 29 311 584 | 99.71 | 28 350 407 | 96.72 | 961 177 | 3.28 |
CK2 | 31 279 164 | 31 182 372 | 99.69 | 30 036 408 | 96.32 | 1 145 964 | 3.68 |
CK3 | 27 553 118 | 27 468 703 | 99.69 | 26 767 147 | 97.45 | 701 556 | 2.55 |
T1 | 29 214 302 | 29 096 642 | 99.60 | 28 357 073 | 97.46 | 739 569 | 2.54 |
T2 | 26 898 484 | 26 777 059 | 99.55 | 26 086 501 | 97.42 | 690 558 | 2.58 |
T3 | 26 987 212 | 26 892 876 | 99.65 | 26 195 932 | 97.41 | 696 944 | 2.59 |
Fig.3 Clustering heat map of differentially expressed genes between samples of Acidovorax citrulli FC440 under copper stress Note: Horizontal represents the gene, each column is a sample, red represents the high expressed gene, green represents the low expressed gene
Fig.7 The KEGG pathway significantly enriched bubble diagram Note: The ordinate is KEGG Pathway entry;The horizontal axis is Richfactor.The size of the dots in the figure indicates the number of differential genes annotated to this pathway, and the color indicates the significant FDR value of this pathway
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