RNA-seq揭示碱性盐(NaHCO3)对细叶百合鳞茎基因表达的影响

doi:10.11924/j.issn.1000-6850.casb2020-0400

中国农学通报 ›› 2021, Vol. 37 ›› Issue (12): 64-71.doi: 10.11924/j.issn.1000-6850.casb2020-0400

所属专题：生物技术

RNA-seq揭示碱性盐(NaHCO₃)对细叶百合鳞茎基因表达的影响

李冠嵘(), 何好, 朱国庆, 陈诗雅, 徐阳, 金淑梅()

东北盐碱植被恢复与重建教育部重点实验室,东北林业大学生命科学学院,哈尔滨 150040

收稿日期:2020-08-25 修回日期:2020-11-16 出版日期:2021-04-25 发布日期:2021-05-13
通讯作者: 金淑梅
作者简介:李冠嵘,男,1997年出生,黑龙江哈尔滨人,学生,硕士,研究方向：分子植物育种研究。通信地址：150040 黑龙江省哈尔滨市南岗区和兴路26号东北林业大学,Tel：18746399076,E-mail： liguanrong01@163.com。
基金资助:
中央高校基本科研业务费专项资金资助“拟南芥抑制素AtPHB互作蛋白筛选及功能验证”(2572020DY18);黑龙江省自然科学基金联合引导项目“蒙古柳(Salix linearistipularis)耐盐相关基因prohibitin的挖掘及功能解析”(LH2019C011)

Salt-stress (NaHCO₃) Revealed by RNA-seq: Effect on Gene Expression in Lilium pumilum Bulb

Li Guanrong(), He Hao, Zhu Guoqing, Chen Shiya, Xu Yang, Jin Shumei()

Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040

Received:2020-08-25 Revised:2020-11-16 Online:2021-04-25 Published:2021-05-13
Contact: Jin Shumei

摘要/Abstract

摘要：

本研究旨在揭示细叶百合在盐碱逆境中的基因表达表达情况,为合理利用盐碱地和大面积种植百合提供理论基础。以一年生的细叶百合鳞茎为材料,经过20 mmol/L NaHCO₃处理24 h后,用Illumina HiSeqTM2000测序平台进行转录组测序。共测得56828个mRNA的注释信息,其中,55433个Unigene被注释到Nr数据库,26973条Unigene被注释到KOG数据库,23610条Unigene被注释到GO数据库,13142条Unigene被注释到KEGG数据库的五大类中。共鉴定出390个差异表达基因。选取了9个与盐碱胁迫密切相关的基因进行qPCR验证,9个基因的表达结果与转录组的结果基本趋于一致。通过细叶百合在碳酸盐(NaHCO₃)逆境下的转录组对比数据,提供了许多的基因表达通路和表达量的差异,为合理利用盐碱地和大面积种植百合提供理论基础。

关键词: 细叶百合, 鳞茎, NaHCO₃, 逆境, 转录组, 基因表达, 表达量, qPCR

Abstract:

The aim of this study is to reveal the gene expression of Lilium pumilum under saline-alkali stress, and to provide a theoretical basis for rational utilization of saline-alkali land and large-scale planting of Lilium pumilum. Using the bulb of annual Lilium pumilum as material, treated with 20 mmol/L NaHCO₃ for 24 h, the transcriptome was sequenced by Illumina HiSeqTM2000 sequencing platform. A total of 56828 mRNA annotation information was measured, among which 55433 Unigenes were annotated to NR database, 26973 Unigenes were annotated to KOG database, 23610 Unigenes were annotated to GO database, and 13142 Unigenes were annotated to five categories of KEGG database. 390 differentially expressed genes were identified. 9 genes closely related to saline-alkali stress were selected for qPCR verification, and the expression results of the 9 genes were basically consistent with the results of transcriptome. Through the transcriptome comparison data of Lilium pumilum under carbonate (NaHCO₃) stress, many gene expression pathways and expression differences were provided, which could lay a theoretical basis for rational utilization of saline-alkali land and large-scale planting of Lilium pumilum.

Key words: Lilium pumilum, bulb, NaHCO₃, saline-alkali stress, transcriptome, gene expression, expression level, qPCR

中图分类号:

S184

李冠嵘, 何好, 朱国庆, 陈诗雅, 徐阳, 金淑梅. RNA-seq揭示碱性盐(NaHCO₃)对细叶百合鳞茎基因表达的影响[J]. 中国农学通报, 2021, 37(12): 64-71.

Li Guanrong, He Hao, Zhu Guoqing, Chen Shiya, Xu Yang, Jin Shumei. Salt-stress (NaHCO₃) Revealed by RNA-seq: Effect on Gene Expression in Lilium pumilum Bulb[J]. Chinese Agricultural Science Bulletin, 2021, 37(12): 64-71.

图/表 10

参考文献 30

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基因编号	基因注释	引物F(5’-3’)	引物R(5’-3’)
TRINITY_DN4382 6_c0_g1_i2	BEL1-like homeodomain protein 3	AGTACCACAGCTGCAGACAC	ACAGATTTCTCAGGCAGGCC
TRINITY_DN4296 9_c0_g1_i1	Mini-chromsome maintenance	GGTTACGGGAGTCTCTGCTC	TCCGAATGCCCACTGAGTTT
TRINITY_DN3310 7_c0_g1_i1	luminal-binding protein 2	TGGTGTTATCGCTGGCTTGA	CTGCTGATATCCTGCCGTGT
TRINITY_DN4776 4_c0_g1_i2	sugar transporter ERD6	CTCCGGTGTGGTCTCTGTTG	ATAGCAAGCCATCCCACGAC
TRINITY_DN3883 3_c0_g1_i2	probable proline transporter 2	TCAACAGCTACCAGCCTCAG	GCTGCCATTCCTCGGAGATT
TRINITY_DN4372 8_c0_g1_i2	gibberellin-regulated protein 2	TCTCTCATGGCCAAGGCA	GCTTTAGGGTTGCAGTGT
TRINITY_DN4803 0_c0_g2_i3	ferric reduction oxidase 8	GAGCGGAAGAATGGGCAAAC	ACCGGATTTGAGAGAGTGGC
TRINITY_DN4277 8_c0_g1_i5	cucumber peeling cupredoxin	AGAAGCTGGCTGTCACTGTC	AGGAGTGTCAGCAGTGAAGC
TRINITY_DN3846 9_c0_g1_i3	peroxisome biogenesis protein 7	TCCGAGTCTCACGAGTCCAT	CAGTAGGCATGCTCCCGAAA

基因编号	基因注释	引物F(5’-3’)	引物R(5’-3’)
TRINITY_DN4382 6_c0_g1_i2	BEL1-like homeodomain protein 3	AGTACCACAGCTGCAGACAC	ACAGATTTCTCAGGCAGGCC
TRINITY_DN4296 9_c0_g1_i1	Mini-chromsome maintenance	GGTTACGGGAGTCTCTGCTC	TCCGAATGCCCACTGAGTTT
TRINITY_DN3310 7_c0_g1_i1	luminal-binding protein 2	TGGTGTTATCGCTGGCTTGA	CTGCTGATATCCTGCCGTGT
TRINITY_DN4776 4_c0_g1_i2	sugar transporter ERD6	CTCCGGTGTGGTCTCTGTTG	ATAGCAAGCCATCCCACGAC
TRINITY_DN3883 3_c0_g1_i2	probable proline transporter 2	TCAACAGCTACCAGCCTCAG	GCTGCCATTCCTCGGAGATT
TRINITY_DN4372 8_c0_g1_i2	gibberellin-regulated protein 2	TCTCTCATGGCCAAGGCA	GCTTTAGGGTTGCAGTGT
TRINITY_DN4803 0_c0_g2_i3	ferric reduction oxidase 8	GAGCGGAAGAATGGGCAAAC	ACCGGATTTGAGAGAGTGGC
TRINITY_DN4277 8_c0_g1_i5	cucumber peeling cupredoxin	AGAAGCTGGCTGTCACTGTC	AGGAGTGTCAGCAGTGAAGC
TRINITY_DN3846 9_c0_g1_i3	peroxisome biogenesis protein 7	TCCGAGTCTCACGAGTCCAT	CAGTAGGCATGCTCCCGAAA

样品	Read数	碱基数	GC含量	%≥Q30
CK1	40,321,512	5,967,250,186	49.76	90.44
CK2	37,657,206	5,575,627,054	50.61	89.35
Salt1	40,795,804	6,049,302,264	50.35	89.68
Salt2	40,741,664	6,053,455,981	49.82	89.90

样品	Read数	碱基数	GC含量	%≥Q30
CK1	40,321,512	5,967,250,186	49.76	90.44
CK2	37,657,206	5,575,627,054	50.61	89.35
Salt1	40,795,804	6,049,302,264	50.35	89.68
Salt2	40,741,664	6,053,455,981	49.82	89.90

长度	Unigene
Total Number	115061
Total length	70878295
Min Unigene length	201
Max Unigene length	14663
N50 length	939

RNA-seq揭示碱性盐(NaHCO₃)对细叶百合鳞茎基因表达的影响

Salt-stress (NaHCO₃) Revealed by RNA-seq: Effect on Gene Expression in Lilium pumilum Bulb

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