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

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

Abstract

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

CLC Number:

S184

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.

Figures/Tables 10

References 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

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

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