title: Comparative transcriptome profiling of Pyropia yezoensis (Ueda) M.S. Hwang & H.G. Choi in response to temperature stresses.
abstract: BACKGROUND
  Pyropia yezoensis is a model organism often used to investigate the mechanisms underlying stress tolerance in intertidal zones. The digital gene expression (DGE) approach was used to characterize a genome-wide comparative analysis of differentially expressed genes (DEGs) that influence the physiological, developmental or biochemical processes in samples subjected to 4 treatments: high-temperature stress (HT), chilling stress (CS), freezing stress (FS) and normal temperature (NT).
  
  
  RESULTS
  Equal amounts of total RNAs collected from 8 samples (two biological replicates per treatment) were sequenced using the Illumina/Solexa platform. Compared with NT, a total of 2202, 1334 and 592 differentially expressed unigenes were detected in HT, CS and FS respectively. Clustering analysis suggested P. yezoensis acclimates to low and high-temperature stress condition using different mechanisms: In heat stress, the unigenes related to replication and repair of DNA and protein processing in endoplasmic reticulum were active; however at low temperature stresses, unigenes related to carbohydrate metabolism and energy metabolism were active. Analysis of gene differential expression showed that four categories of DEGs functioning as temperature sensors were found, including heat shock proteins, H2A, histone deacetylase complex and transcription factors. Heat stress caused chloroplast genes down-regulated and unigenes encoding metacaspases up-regulated, which is an important regulator of PCD. Cold stress caused an increase in the expression of FAD to improve the proportion of polyunsaturated fatty acids. An up-regulated unigene encoding farnesyl pyrophosphate synthase was found in cold stress, indicating that the plant hormone ABA also played an important role in responding to temperature stress in P. yezoensis.
  
  
  CONCLUSIONS
  The variation of amount of unigenes and different gene expression pattern under different temperature stresses indicated the complicated and diverse regulation mechanism in response to temperature stress in P. yezoensis. Several common metabolism pathways were found both in P. yezoensis and in higher plants, such as FAD in low-temperature stress and HSP in heat stress. Meanwhile, many chloroplast genes and unigene related to the synthesis of abscisic acid were detected, revealing its unique temperature-regulation mechanism in this intertidal species. This sequencing dataset and analysis may serve as a valuable resource to study the mechanisms involved in abiotic stress tolerance in intertidal seaweeds.
authors.affiliation: Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. sunpei0819@163.com.
authors.forename: Peipei
authors.initials: P
authors.lastname: Sun
authors.affiliation: Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. yxmao@ouc.edu.cn.
authors.forename: Yunxiang
authors.initials: Y
authors.lastname: Mao
authors.affiliation: Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China. Liguiyang410@126.com.
authors.forename: Guiyang
authors.initials: G
authors.lastname: Li
authors.affiliation: Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. caominjiayou@163.com.
authors.forename: Min
authors.initials: M
authors.lastname: Cao
authors.affiliation: Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. fnkong@ouc.edu.cn.
authors.forename: Fanna
authors.initials: F
authors.lastname: Kong
authors.affiliation: Institute of Plant Resources, Dalian Nationalities University, Dalian, 116600, China. Liwang@dlnu.edu.cn.
authors.forename: Li
authors.initials: L
authors.lastname: Wang
authors.affiliation: Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. fenghen360@126.com.
authors.forename: Guiqi
authors.initials: G
authors.lastname: Bi
mesh_terms: D002736:Chloroplasts / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D005231:Fatty Acids, Unsaturated / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D006360:Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism; D006655:Histone Deacetylases / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000032:analysis / Q000302:isolation & purification; D000461:Rhodophyta / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics*; D013696:Temperature; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D005231:Fatty Acids, Unsaturated; D006360:Heat-Shock Proteins; D010940:Plant Proteins; D014157:Transcription Factors; D012313:RNA; D006655:Histone Deacetylases