Transcriptome Analysis of Response to Heavy Metal Copper Stress in Setcreasea purpurea Root Tissue

doi:10.13560/j.cnki.biotech.bull.1985.2021-0664

Abstract

Abstract:

Setcreasea purpurea is a highly copper（Cu）tolerant and hyperaccumulator plant. It is the first time that RNA-Seq technology was applied to profile the transcriptome of it in this study. Candidate genes related to copper tolerance of S. purpurea were assembled based on de novo transcriptome analysis. A total of 82 471 high-quality unigenes with an N50 length of 2 299 bp were obtained through transcriptome profiling,which provided abundant data for future studies on S. purpurea. The sequencing data of the control group（CK）,300 mol/L stress group（CT1）,and 1 000 mol/L stress group（CT2）were deposited in the NCBI sequence read archive database under the accession number SAMN11265427. After comparing CT1 with CK,a total of 5 028 unigenes were significantly differentially expressed in the roots,accounting for 6.10% of all unigenes. Among them,the significantly up-regulated unigenes and down-regulated unigenes were 3 138 and 1 890,respectively. After comparing CT2 with CT1,a total of 6 813 unigenes were significantly differentially expressed in the roots,accounting for 8.26% of all unigenes. Among them,the significantly up-regulated unigenes and down-regulated unigenes were 2 555 and 4 258,respectively. The results were consistent with Illumina sequencing data based on the quantitative fluorescence analysis of 10 randomly selected genes by qRT-PCR,which confirmed the validity of differentially expressed gene data. The above experiment provides a theoretical basis for examining the molecular mechanism of copper tolerance under copper stress on the molecular level.

Key words: Setcreasea purpurea, root tissue, copper stress, transcriptome

PENG Guo-ying, HU Liang, HUANG Chao, YANG Kun, WAN Wei, HUANG Chang-gan. Transcriptome Analysis of Response to Heavy Metal Copper Stress in Setcreasea purpurea Root Tissue[J]. Biotechnology Bulletin, 2022, 38(2): 83-94.

Figures/Tables 14

References 38

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序列号Unigene ID	注释Annotated	序列Sequence（5'-3'）	Tm/℃	长度Length/bp
c1920_g1	磷酸化酶Phosphorylase	F：ATGTGGGCTCTGTCGTT R：TGCCTGCTGTGCTAATG	58/60	178
c48219_g1	羧酸酯酶12 Carboxylesterase 12	F：TTTGCGAGGTTGGGTAT R：AAGAGTGGCCGAGTTGA	60/60	191
c1055_g1	铁通透酶基因1 Fe transporter permease 1	F：TACCTGCCCGCCGTGTT R：TGATGACTGCCGCCTCC	60/59	154
c1246_g1	金属尼古丁胺转运蛋白9 Metal nicotine amine transporter 9	F：ATGTTAGAGTGAGATACCCTGT R：AATGGTTATGGCGTTGG	60/60	177
c1178_g1	磷酸酯酶2C Protein phosphatase 2C	F：ATTACCTACGAGGAGCG R：CCAACCTTATCCCACAG	58/60	164
c51710_g1	谷胱甘肽转移酶 Glutathione transferase	F：GAGCAAAGTAGGCATCG R：ACTAACGGCTTGAGGGT	59/60	158
c18811_g1	生长素结合蛋白 Auxin binding protein	F：GCACTGGGTCTGCCTGAT R：TGGAGTTCGCCGATGAG	56/60	146
c2112_g1	硝酸根转运蛋白 Nitrate transporter	F：CAAAGCCAACATAATACAAG R：TTGGGAGACTGAGAAGGT	60/58	168
c30939_g1	水通道蛋白 Aquaporin	F：ACCCTTCTGGCTTAGTG R：AATGATGGTGATGTGGC	57/60	121
c113_g1	假定蛋白21 Hypothetical protein 21	F：GGCTCTTTCTGGCTCGTA R：CAAGTTCATTGGCACCC	56/60	138

序列号Unigene ID	注释Annotated	序列Sequence（5'-3'）	Tm/℃	长度Length/bp
c1920_g1	磷酸化酶Phosphorylase	F：ATGTGGGCTCTGTCGTT R：TGCCTGCTGTGCTAATG	58/60	178
c48219_g1	羧酸酯酶12 Carboxylesterase 12	F：TTTGCGAGGTTGGGTAT R：AAGAGTGGCCGAGTTGA	60/60	191
c1055_g1	铁通透酶基因1 Fe transporter permease 1	F：TACCTGCCCGCCGTGTT R：TGATGACTGCCGCCTCC	60/59	154
c1246_g1	金属尼古丁胺转运蛋白9 Metal nicotine amine transporter 9	F：ATGTTAGAGTGAGATACCCTGT R：AATGGTTATGGCGTTGG	60/60	177
c1178_g1	磷酸酯酶2C Protein phosphatase 2C	F：ATTACCTACGAGGAGCG R：CCAACCTTATCCCACAG	58/60	164
c51710_g1	谷胱甘肽转移酶 Glutathione transferase	F：GAGCAAAGTAGGCATCG R：ACTAACGGCTTGAGGGT	59/60	158
c18811_g1	生长素结合蛋白 Auxin binding protein	F：GCACTGGGTCTGCCTGAT R：TGGAGTTCGCCGATGAG	56/60	146
c2112_g1	硝酸根转运蛋白 Nitrate transporter	F：CAAAGCCAACATAATACAAG R：TTGGGAGACTGAGAAGGT	60/58	168
c30939_g1	水通道蛋白 Aquaporin	F：ACCCTTCTGGCTTAGTG R：AATGATGGTGATGTGGC	57/60	121
c113_g1	假定蛋白21 Hypothetical protein 21	F：GGCTCTTTCTGGCTCGTA R：CAAGTTCATTGGCACCC	56/60	138

样本 Sample	原始数据 Raw reads/Mb	过滤数据 Clean reads /Mb	碱基总数 Total number of bases/Gb	Q20/%	Q30/%	过滤数据率 Clean reads ratio/%
CK-1	46.39	42.94	7.00	96.91	92.50	92.58
CK-2	44.77	41.86	6.76	96.86	92.44	93.51
CK-3	43.28	40.72	6.54	96.88	92.36	94.07
CT1-1	44.58	41.71	6.73	96.82	92.34	93.56
CT1-2	50.21	47.17	7.58	96.89	92.36	93.95
CT1-3	44.60	41.94	6.73	96.67	91.91	94.03
CT2-1	47.85	44.95	7.23	96.79	92.17	93.93
CT2-2	40.67	38.21	6.14	96.92	92.43	93.95
CT2-3	45.70	42.69	6.90	96.91	92.42	93.40

样本 Sample	原始数据 Raw reads/Mb	过滤数据 Clean reads /Mb	碱基总数 Total number of bases/Gb	Q20/%	Q30/%	过滤数据率 Clean reads ratio/%
CK-1	46.39	42.94	7.00	96.91	92.50	92.58
CK-2	44.77	41.86	6.76	96.86	92.44	93.51
CK-3	43.28	40.72	6.54	96.88	92.36	94.07
CT1-1	44.58	41.71	6.73	96.82	92.34	93.56
CT1-2	50.21	47.17	7.58	96.89	92.36	93.95
CT1-3	44.60	41.94	6.73	96.67	91.91	94.03
CT2-1	47.85	44.95	7.23	96.79	92.17	93.93
CT2-2	40.67	38.21	6.14	96.92	92.43	93.95
CT2-3	45.70	42.69	6.90	96.91	92.42	93.40

数据库 Database	注释基因的数量Number of annotated unigenes	注释基因的比例Percentage of annotated unigenes/%
NR	68 227	82.73
GO	23 236	28.17
KEGG	35 123	42.59
Pfam	27 806	33.72
eggNOG	67 602	81.97
Swissprot	52 994	64.26
In all database	8 422	10.21