Comparative Transcriptomic Analysis During Seed Stratification Of Paris Polyphylla Var.yunnanensis

Paris polyphylla var.yunnanensis is a well-known chinese medicine with remarkable effect on clearing heat detoxify and reducing swelling pain.Because of its favorable social and economic benefit,the market demand is increasing.Under natural conditions,Paris polyphylla var.yunnanensis.is mainly propagated by seed.However,its germination rate was low and dormancy time was very long because of morphological and physiological after-ripening trait.This paper studied the molecular mechanisms of seed donnancy remaintanance and release of Paris polyphylla var.yunnanensis through comparative transcriptiomics.The main results are as follows:1.Five tissues(untreated mature Seed,Seed;S-Str,stratified seed at 20 C for 45 days;S Ger,germinated seed after warm stritification;Root and StL)were sequenced using high throughput sequencing technology Illumina HiseqTM2000 platform.6.67 G,6.46 G,7.55 G,7.21 G and 9.41 G of reads for the above five tissues were obtained,respectively.Their clean reads were pooled and assembled by Trinity software into 311,401 transcripts with an average length of 610bp.We got 234,331 Unigenes with the average length of 541bp.The transcriptional sequences of obtained Unigenes were used as reference sequences for subsequent analysis.2.Of 234,331 Unigene,96,709(41.27%)were annotated in at least one of NR,NT,COG,Swissprot,KEGG and GO databases.The clean reads of five samples were mapped back onto the transcriptome reference sequences obtained by Trinity,and the total number of mapped reads was 40,522,138,accounting for 75.95%.For S Str the mapped reads were 39,904,854,accounting for 77.16%;for S Ger,45,056,134,accounting for 74,570%;for StL,57,186,162,accounting for 76.00%and for the root,42,723,086,accounting for 74.02%.3.595 candidate genes involved in the biosynthesis and degradation of ABA,GA and other hormones were identified via homologous comparison with know hormone-metabolism genes of Arabidopsis thaliana,of which 124 unigenes showed tissue-differential expression among 5 samples.Similarily,2,678 genes were identified homolougs to Arabidiopsis,of which 507 putative TF unigenes showed tissue-differential expression among 5 samples.Via literature search on NCBI Pubmed,we found that the roles of 530 genes in seed germination and dormancy have been characterized.Via homologous protein sequences and differential expression analysis,a total of 326 Unigenes possibly involved in P.polyphylla seed dormancy and germination were differentially expressed among five samples.These results provided the genes resources to study molecular mechanisms underlying morphological and physiological after-ripening processes in Paris polyphylla var.yunnanensisis dormant seeds.