De novo assembly and characterization of germinating lettuce seed transcriptome using Illumina paired-end sequencing.
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 μM 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.
Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Shu-Jun
SJ
Liu
Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
Shun-Hua
SH
Song
Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Wei-Qing
WQ
Wang
Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China. Electronic address: sqsong@ibcas.ac.cn.
Song-Quan
SQ
Song
D005030:Ethylenes / Q000378:metabolism; D018525:Germination; D018545:Lactuca / Q000196:embryology*; D012639:Seeds / Q000254:growth & development*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D059467:Transcriptome
D005030:Ethylenes; C036216:ethylene
Germination thermoinhibition; Illumina paired-end sequencing; Lettuce seed; Sodium nitroprusside; Transcriptome