Transcriptional Analysis Of Switchgrass Under Cadmium Stress And Analysis Of CCCH Gene Family

Switchgrass(Panicum virgatum L.)is a warm-season C4 perennial grass origined from North America used for grazing,soil-water conservation and ecological construction.In recent years,switchgrass have attracted much attetion as a new kind of biomass energy plants.Studies showed that switchgrass could adapt to adverse growing conditions,such as heavy metal pollution,salinity,drought,low temperature and poor land.According to the present situation of our country,use the marginal soil to plant switchgrass could achieve win-win of phytoremediation and land use.In this study,we established the transcriptome data information of switchgrass seedling root under cadmium stress by using high-throughput sequencing technology and carried on the preliminary analysis swithgrass gene expression profile under cadmium stress;meanwhile,we studied the CCCH zinc finger proteins of switchgras,discussed the origin and evolution of allotetraploid,and dug up the participation genes related to abiotic stress(such as ABA,drought,low temperature,salinity,etc).The specific results are as following:1.The transcriptome data informations of lowland switchgrass Alamo roots at control(0h),6 h and 24 h were established by Illumina Hiseq 2500 platform.We obtained 9 samples in total 63 Gb data.After aligned to the reference genome of switchgrass,compared with control,3164 differnetially expressed genes were detected at 6 h which 1882 of them were up-regulated and 1282 of them were down-regulated,2207 differnetially expressed genes were detected at 24 h which 1388 of them were up-regulated and 819 of them were down-regulated.Results showed that the differential expressed genes at 24 h was far less than 6 h,speculated that the peak period of gene expression should not longer than 24 h.2.Function annotation and classification found that differential expression genes might be directly related to cadmium stress,stress factor genes and transcription factor genes.The Gene Ontology(GO)was analyzed at 6 h and 24 h,most of the differential expression genes were involved in three ontology:Metabolic process,Celluar process,Response to stimulus,Establishment and Establishment of localization at Biological Process;Catalytic activity,Binding and Transporter activity at Molecular Function;Cell,Cell part and Organelle at Cellular Component;Differential expression genes mostly involved in pathways such as phenylalanine metabolic phenylpropane synthesis pathways when analyzed the pathways at 6 h and 24 h under cadmium stress.Responsion to cadmium stress of switchgrass is a process co-regulated by mutiple genes and multiple biological processes;3.We found total 103 switchgrass CCCH genes by using HMM and built a homologous genes phylogenetic tree and seprated them into 21 sub-families.Members in same sub-family shared same gene structure and protein structure proved the reliable of the phylogenetic tree.By analysis of chromesomal locations and evolutionary pressures speculated that gene amplification and functional diversity of switchgrass CCCH genes might be caused by tandem copies and diversity selection;4.We found the 14 sub-family might be related to ABA and abiotic stress such as drought,low temperature and salinity stress after built the CCCH orthologous genes phylogenetic tree.qRT-PCR was used to predict genes in 14 sub-family and we found that these genes had a different changes in the expression under ABA and abiotic stress.