基于转录组测序分析的黄精种子休眠解除相关差异基因研究

doi:10.11924/j.issn.1000-6850.casb2020-0209

摘要/Abstract

摘要：

旨在获得黄精转录组数据库并挖掘参与其种子发育和休眠解除相关基因,以休眠解除前后的黄精种胚为试材,利用新一代高通量测序手段对供试样品进行转录组测序,并进行系统的生物信息学分析。黄精种子休眠解除前后样品中共得到79716个差异表达基因,上调的表达基因有60074个,下调的表达基因有19642个。休眠解除前后的黄精种胚中共有130284个差异表达基因被GO功能注释到生物进程、分子功能和细胞组分3个大类56个亚类,注释的差异表达基因与代谢过程、生物调控、细胞组分合成和酶催化活性等密切相关。KEGG代谢通路结果表明,共有65038个差异表达基因,涉及138个代谢通路,主要参与碳代谢、次生代谢产物的生物合成和多糖的代谢。基于KEGG数据库中注释结果,共发现15条与黄精种胚休眠解除相关的代谢通路。黄精种子发育与休眠解除过程,大量的种胚形态建成、多糖分解及蛋白质合成差异基因参与表达,并涉及到多个代谢途径的相互作用,构成复杂的休眠解除调控网络。

关键词: 黄精, 种胚, 高通量测序, 休眠, 转录组, 代谢通路, 差异基因

Abstract:

The purpose is to obtain the transcriptome database of Polygonatum sibiricum Red. and explore the genes involved in seed development and dormancy release. The embryos of Polygonatum sibiricum Red. before and after dormancy were used as materials, the transcriptome of the test samples was sequenced by a new generation of high-throughput sequencing method, and the bioinformatics analysis was carried out systematically. A total of 79716 differentially expressed genes were obtained from the samples before and after dormancy release of Polygonatum sibiricum Red. seeds, including 60074 upregulated expression genes and 19642 downregulated expression genes. There were 130284 differentially expressed genes annotated by go function into 56 subclasses of three categories: biological process, molecular function and cell component. The annotated differentially expressed genes were closely related to metabolic process, biological regulation, cell component synthesis and enzyme catalytic activity. The results of KEGG metabolic pathway showed that there were 65038 differentially expressed genes, involving 138 metabolic pathways, mainly involved in carbon metabolism, secondary metabolite biosynthesis and polysaccharide metabolism. Based on the annotation results in KEGG database, 15 metabolic pathways related to the dormancy release of Polygonatum sibiricum Red. embryo were found. In conclusion, during the process of seed development and dormancy release, a large number of different genes including the expression of embryo morphogenesis, polysaccharide decomposition and protein synthesis are expressed and involved in the interaction of multiple metabolic pathways, forming a complex regulatory network of dormancy release.

Key words: Polygonatum sibiricum Red., embryos, high-throughput sequencing method, dormancy, transcriptome, metabolic pathway, differential gene

中图分类号:

S567.239

罗丽娜, 向增旭. 基于转录组测序分析的黄精种子休眠解除相关差异基因研究[J]. 中国农学通报, 2021, 37(11): 1-8.

Luo Li’na, Xiang Zengxu. The Relative Difference Genes in the Process of Dormancy Release of Polygonatum sibiricum Red. Based on the Transcriptome Sequencing Analysis[J]. Chinese Agricultural Science Bulletin, 2021, 37(11): 1-8.

图/表 10

参考文献 15

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样本名	原始reads 数目/Mb	过滤后reads 总数/Mb	过滤后的碱基总数/Gb	Q20/ %	Q30/ %	有效碱基百分比/%	GC/ %
HJCKA	42.16	42.15	6.32	96.10	87.08	99.97 99.97	42.24
HJCKB	42.16	42.15	6.32	96.03	86.91	99.97 99.97	42.29
HJGA3A	42.16	42.15	6.32	95.87	86.53	99.97	44.58
HJGA3B	42.16	42.15	6.32	95.90	86.65	99.97	44.62

样本名	原始reads 数目/Mb	过滤后reads 总数/Mb	过滤后的碱基总数/Gb	Q20/ %	Q30/ %	有效碱基百分比/%	GC/ %
HJCKA	42.16	42.15	6.32	96.10	87.08	99.97 99.97	42.24
HJCKB	42.16	42.15	6.32	96.03	86.91	99.97 99.97	42.29
HJGA3A	42.16	42.15	6.32	95.87	86.53	99.97	44.58
HJGA3B	42.16	42.15	6.32	95.90	86.65	99.97	44.62

样品	总碱基数	总序列数	比对序列	比对效率/%	唯一比对序列	唯一序列效率/%
HJCKA	6322376100	42149174	32156338	76.29	10357434	32.21
HJCKB	6322189800	42147932	32278506	76.58	10412446	32.26
HJGA3A	6322164300	42147762	31334568	74.34	13344214	42.59
HJGA3B	6322212000	42148080	31262430	74.17	13239608	42.35
总计	25288942200	168592948	127031842	75.35	47353702	37.28

样品	总碱基数	总序列数	比对序列	比对效率/%	唯一比对序列	唯一序列效率/%
HJCKA	6322376100	42149174	32156338	76.29	10357434	32.21
HJCKB	6322189800	42147932	32278506	76.58	10412446	32.26
HJGA3A	6322164300	42147762	31334568	74.34	13344214	42.59
HJGA3B	6322212000	42148080	31262430	74.17	13239608	42.35
总计	25288942200	168592948	127031842	75.35	47353702	37.28

数据库	注释基因数	读长300≤Length<1000	读长Length≥1000
NR	4609	2301	2013
NT	4577	2706	1396
Swissprot	37558	2 3486	7570
KEGG	23775	14712	18685
KOG	38667	23949	7937
Pfam	22942	16199	17605
GO	16680	10691	4339
总计	38669	23950	7938