盐胁迫下不同甘薯品种的转录组测序分析

doi:10.3724/SP.J.1006.2023.24143

摘要/Abstract

摘要：

为了获得甘薯耐盐转录组序列信息, 挖掘差异表达基因及其相关代谢途径, 本文以盐胁迫处理0 d、3 d和6 d的耐盐甘薯品种‘榕薯819’以及不耐盐甘薯品种‘榕薯910’的叶片为材料, 借助高通量测序技术进行转录组测序分析。结果表明, 2个品种共获得157,252条Unigenes, 平均组装长度为576 bp。其中有83,264条Unigenes在七大数据库中得到注释, 占总数的52.95%。NR注释分类结果显示, 在牵牛花(Ipomoea nil)中比对到同源序列的Unigenes最多, 共43,620条, 占总数的57.05%。Unigenes在KOG数据库中的注释主要富集在普通功能预测(8752个)、信号转导机制(5067个)以及翻译后修饰、蛋白转换、分子伴侣(4471个)中。差异表达分析显示, 在‘榕薯819’中, 盐处理3 d和6 d的样品差异表达基因数分别为323个和3752个, 共参与了33个GO功能分类项和302条KEGG代谢通路。在‘榕薯910’中, 差异表达基因数则分别为5554个和7395个, 共参与了50个GO功能分类项, 涉及了329条KEGG代谢通路。以部分差异表达基因的转录组数据为基础, 进行了表达量热图绘制。结果显示, 注释到淀粉和蔗糖代谢途径的7个差异表达β-葡萄糖苷酶基因均表现为在耐盐品种中上调, 在不耐盐品种中下调; 注释到Ca²⁺信号途径的7个类钙调素基因中, 有2个在耐盐品种中特异上调, 5个在不耐盐品种中特异下调。差异表达转录因子表达量热图显示, IbERF1仅在耐盐品种中特异表达, IbNAC3、IbNAC11、IbERF3和IbERF4仅在不耐盐品种中特异表达, 而IbNAC29在耐盐品种中下调表达, 在不耐盐品种中上调表达。综上分析, 甘薯耐盐转录组获得的Unigenes数量较大, 序列信息丰富, 盐胁迫下获得的差异表达基因及高丰度转录因子可能在甘薯抵御盐胁迫过程中发挥着重要作用。

关键词: 甘薯, 盐胁迫, 转录组, 高通量测序

Abstract:

The objective of this study is to obtain the salt tolerant transcriptome sequence information of sweet potato, mine and identify the differentially expressed genes and their related metabolic pathways. Rongshu 819 (salt-tolerant variety) and Rongshu 910 (salt-sensitive variety) under salt treatment for 0, 3, and 6 days were conducted for the transcriptome by high-throughput sequencing. The results showed that a total of 157,252 Unigenes with an average length of 576 bp were obtained from the two varieties. The 83,264 Unigenes, accounting for 52.95% of the total Unigenes, were annotated in the 7 functional databases. NR annotation revealed that sweet potato Unigenes had the most homologous sequences in Ipomoea nil with a total of 43,620 accounting for 57.05%. The annotation of Unigenes in the KOG database is mainly concentrated in general functional prediction only (8752), signal transformation mechanisms (5067), and post translation modification, protein transformation, molecular chaperones (4471). The qRT-PCR indicated that, in Rongshu 819, the number of differentially expressed genes in 3 days and 6 days of salt treatment was 3752 and 807, respectively, which classified into 33 GO functional categories and 302 KEGG metabolic pathways. In Rongshu 910, the number of differentially expressed genes in 3 days and 6 days of salt treatment was 5554 and 7395, respectively, which classified into 50 GO functional categories and 329 KEGG metabolic pathways. The heat map was drawn based on the transcriptome data of partial differentially expressed genes. The result showed that 7 differentially expressed β-Glucosidase genes annotated into starch and sucrose metabolic pathway were up-regulated in salt-tolerant variety while down-regulated in salt-sensitive variety. Seven calmodulin-like genes annotated into Ca²⁺ signaling pathway were specifically expressed in two varieties, among which 2 were specifically up-regulated in salt-tolerant variety and 5 were specifically down-regulated in salt-sensitive variety. The expression heat map of differentially expressed transcription factors indicated that IbERF1 was only specifically expressed in salt-tolerant varieties, IbNAC3, IbNAC11, IbERF3, and IbERF4 were only specifically expressed in salt-sensitive varieties, while IbNAC29 was down-regulated in salt-tolerant varieties and up-regulated in salt-sensitive varieties. In conclusion, the number of Unigenes obtained from transcriptome of sweet potato under salt stress was large and the sequence information was rich. The differentially expressed genes and high abundance transcription factors may play an important role in sweet potato response to salt stress.

Key words: sweet potato, salt stress, transcriptome, high-throughput sequencing

张小红, 彭琼, 鄢铮. 盐胁迫下不同甘薯品种的转录组测序分析[J]. 作物学报, 2023, 49(5): 1432-1444.

ZHANG Xiao-Hong, PENG Qiong, YAN Zheng. Transcriptome sequencing analysis of different sweet potato varieties under salt stress[J]. Acta Agronomica Sinica, 2023, 49(5): 1432-1444.

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项目 Item	单基因簇 Unigene	转录本 Transcript
序列总数 Total sequence number	157,252	211,688
所有序列长度之和 Total sequence length (bp)	90,649,057	160,878,660
平均长度 Average length (bp)	576	759
GC碱基的数量占比 Percent GC (%)	41.12	41.14
N50长度 N50 length (bp)	1064	1646
N90长度 N90 length (bp)	243	262

	注释数据库 Anno database							总计 Total
	COG	GO	KEGG	KOG	Pfam	Swissprot	NR	总计 Total
注释的Unigene数(条) Annotated number (Unigene)	20,446	32,635	44,445	42,285	38,863	53,196	76,583	83,264

差异分组 DEG set	差异表达基因数量 DEG number	上调数量 Number of the up-regulated DEGs	下调数量 Number of the down-regulated DEGs
R1-1_R1-2_R1-3_vs_R2-1_R2-2_R2-3	323	206	117
R1-1_R1-2_R1-3_vs_R3-1_R3-2_R3-3	3752	1926	1826
T1-1_T1-2_T1-3_vs_T2-1_T2-2_T2-3	5554	2122	3432
T1-1_T1-2_T1-3_vs_T3-1_T3-2_T3-3	7395	3353	4042
R1-1_R1-2_R1-3_vs_T1-1_T1-2_T1-3	9352	5129	4223
R2-1_R2-2_R2-3_vs_T2-1_T2-2_T2-3	7538	3338	4200
R3-1_R3-2_R3-3_vs_T3-1_T3-2_T3-3	9903	4709	5194