De novo assembly and characterization of germinating lettuce seed transcriptome using Illumina paired-end sequencing

doi:10.1016/j.plaphy.2015.07.020

	De novo assembly and characterization of germinating lettuce seed transcriptome using Illumina paired-end sequencing
	Liu, Shu-Jun ; Song, Shun-Hua ; Wang, Wei-Qing ; Song, Song-Quan
	2015
发表期刊	PLANT PHYSIOLOGY AND BIOCHEMISTRY
ISSN	0981-9428
卷号	96 页码:154-162
摘要	At supraoptimal temperature, germination of lettuce (Lactuca sativa L.) seeds exhibits a typical germination thermoinhibition, which can be alleviated by sodium nitroprusside (SNP) in a nitric oxide-dependent manner. However, the molecular mechanism of seed germination thermoinhibition and its alleviation by SNP are poorly understood. In the present study, the lettuce seeds imbibed at optimal temperature in water or at supraoptimal temperature with or without 100 mu M SNP for different periods of time were used as experimental materials, the total RNA was extracted and sequenced, we gained 147,271,347 raw reads using Illumina paired-end sequencing technique and assembled the transcriptome of germinating lettuce seeds. A total of 51,792 unigenes with a mean length of 849 nucleotides were obtained. Of these unigenes, a total of 29,542 unigenes were annotated by sequence similarity searching in four databases, NCBI non-redundant protein database, SwissProt protein database, euKaryotic Ortholog Groups database, and NCBI nucleotide database. Among the annotated unigenes, 22,276 unigenes were assigned to Gene Ontology database. When all the annotated unigenes were searched against the Kyoto Encyclopedia of Genes and Genomes Pathway database, a total of 8,810 unigenes were mapped to 5 main categories including 260 pathways. We first obtained a lot of unigenes encoding proteins involved in abscisic acid (ABA) signaling in lettuce, including 11 ABA receptors, 94 protein phosphatase 2Cs and 16 sucrose non-fermenting 1-related protein kinases. These results will help us to better understand the molecular mechanism of seed germination, thermoinhibition of seed germination and its alleviation by SNP. (C) 2015 Elsevier Masson SAS. All rights reserved.
关键词	Germination thermoinhibition Illumina paired-end sequencing Lettuce seed Sodium nitroprusside Transcriptome
学科领域	Plant Sciences
DOI	10.1016/j.plaphy.2015.07.020
收录类别	SCI
语种	英语
WOS关键词	ABSCISIC-ACID ; POSITIVE REGULATOR ; PROTEOMIC ANALYSIS ; MESSENGER-RNAS ; DORMANCY ; THERMOINHIBITION ; GIBBERELLIN ; TEMPERATURE ; NITRATE ; BIOSYNTHESIS
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000364880500018
出版者	ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER
文献子类	Article
出版地	ISSY-LES-MOULINEAUX
EISSN	1873-2690
资助机构	National Natural Science Foundation of China [31200232, 31171624]
作者邮箱	sqsong@ibcas.ac.cn
引用统计	被引频次：10[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/25633
专题	中科院北方资源植物重点实验室
作者单位	1.[Liu, Shu-Jun 2.Wang, Wei-Qing 3.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 4.Being Acad Agr & Forestry Sci, Beijing Vegetable Res Ctr, Beijing 100097, Peoples R China
推荐引用方式 GB/T 7714	Liu, Shu-Jun,Song, Shun-Hua,Wang, Wei-Qing,et al. De novo assembly and characterization of germinating lettuce seed transcriptome using Illumina paired-end sequencing[J]. PLANT PHYSIOLOGY AND BIOCHEMISTRY,2015,96:154-162.
APA	Liu, Shu-Jun,Song, Shun-Hua,Wang, Wei-Qing,&Song, Song-Quan.(2015).De novo assembly and characterization of germinating lettuce seed transcriptome using Illumina paired-end sequencing.PLANT PHYSIOLOGY AND BIOCHEMISTRY,96,154-162.
MLA	Liu, Shu-Jun,et al."De novo assembly and characterization of germinating lettuce seed transcriptome using Illumina paired-end sequencing".PLANT PHYSIOLOGY AND BIOCHEMISTRY 96(2015):154-162.

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