Shen-chong Li, Qinli Shan, Rongpei Yu, A. N. Siddique, Xia Li, Chunmei Yang, Jiwei Ruan, Mingyang Li
{"title":"两个非洲菊品种的比较转录组分析揭示了其抗寒机制","authors":"Shen-chong Li, Qinli Shan, Rongpei Yu, A. N. Siddique, Xia Li, Chunmei Yang, Jiwei Ruan, Mingyang Li","doi":"10.21475/POJ.11.01.18.PNE874","DOIUrl":null,"url":null,"abstract":"Temperature is one of central factors that shape the distribution and growth pattern of Gerbera hybrida. The cultivars of this species have vast variation in the morphology and stress adaptation. In the current study, comparative transcriptome analysis of two haploid cultivars with discriminative phenotype, i.e., Gerbera hybrida Hongjixing and Gerbera hybrida Qiuri, was used to uncover differentially expressed functional unigenes using an Illumina Hiseq2000 sequencing platform. Through high-throughput cDNA sequencing (RNA-seq), we generated 99160 UniGenes from 19.09G primary reads with an average length of 978 bp and an N50 equaling 1620. It was filtered by Trimmomatic and assembled by Trinity. A total of 58127 transcripts were functional annotated by mapping to five protein databases by BLASTX, with topmost differently expressed unigenes (DEGs) directed to transcriptional regulation, secondary metabolism and stress response, etc. Cold treatment (-2°C) of haploid seedlings in intelligent cooled incubator had adverse effects on both cultivars, which was more serious in Qiuri which was exhibited by the lower chlorophyll fluorescence after cold treatment, compared to Hongjixing. This indicates the better cold tolerance of Hongjixing. The qRT-PCR result indicated that besides common pathways, novel pathways like latex biosynthesis potentially contributes to the better cold tolerance of Hongjixing. In view of the ubiquity of cold temperature, this study provided new insights into the mechanism dissection and guidance for cold stress condition.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"11 1","pages":"10-19"},"PeriodicalIF":0.0000,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"5","resultStr":"{\"title\":\"Comparative transcriptome analysis of two Gerbera hybrida cultivars revealed cold tolerance mechanism\",\"authors\":\"Shen-chong Li, Qinli Shan, Rongpei Yu, A. N. Siddique, Xia Li, Chunmei Yang, Jiwei Ruan, Mingyang Li\",\"doi\":\"10.21475/POJ.11.01.18.PNE874\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Temperature is one of central factors that shape the distribution and growth pattern of Gerbera hybrida. The cultivars of this species have vast variation in the morphology and stress adaptation. In the current study, comparative transcriptome analysis of two haploid cultivars with discriminative phenotype, i.e., Gerbera hybrida Hongjixing and Gerbera hybrida Qiuri, was used to uncover differentially expressed functional unigenes using an Illumina Hiseq2000 sequencing platform. Through high-throughput cDNA sequencing (RNA-seq), we generated 99160 UniGenes from 19.09G primary reads with an average length of 978 bp and an N50 equaling 1620. It was filtered by Trimmomatic and assembled by Trinity. A total of 58127 transcripts were functional annotated by mapping to five protein databases by BLASTX, with topmost differently expressed unigenes (DEGs) directed to transcriptional regulation, secondary metabolism and stress response, etc. Cold treatment (-2°C) of haploid seedlings in intelligent cooled incubator had adverse effects on both cultivars, which was more serious in Qiuri which was exhibited by the lower chlorophyll fluorescence after cold treatment, compared to Hongjixing. This indicates the better cold tolerance of Hongjixing. The qRT-PCR result indicated that besides common pathways, novel pathways like latex biosynthesis potentially contributes to the better cold tolerance of Hongjixing. In view of the ubiquity of cold temperature, this study provided new insights into the mechanism dissection and guidance for cold stress condition.\",\"PeriodicalId\":54602,\"journal\":{\"name\":\"Plant Omics\",\"volume\":\"11 1\",\"pages\":\"10-19\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2018-02-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"5\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Plant Omics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.21475/POJ.11.01.18.PNE874\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Agricultural and Biological Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Omics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.21475/POJ.11.01.18.PNE874","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
Comparative transcriptome analysis of two Gerbera hybrida cultivars revealed cold tolerance mechanism
Temperature is one of central factors that shape the distribution and growth pattern of Gerbera hybrida. The cultivars of this species have vast variation in the morphology and stress adaptation. In the current study, comparative transcriptome analysis of two haploid cultivars with discriminative phenotype, i.e., Gerbera hybrida Hongjixing and Gerbera hybrida Qiuri, was used to uncover differentially expressed functional unigenes using an Illumina Hiseq2000 sequencing platform. Through high-throughput cDNA sequencing (RNA-seq), we generated 99160 UniGenes from 19.09G primary reads with an average length of 978 bp and an N50 equaling 1620. It was filtered by Trimmomatic and assembled by Trinity. A total of 58127 transcripts were functional annotated by mapping to five protein databases by BLASTX, with topmost differently expressed unigenes (DEGs) directed to transcriptional regulation, secondary metabolism and stress response, etc. Cold treatment (-2°C) of haploid seedlings in intelligent cooled incubator had adverse effects on both cultivars, which was more serious in Qiuri which was exhibited by the lower chlorophyll fluorescence after cold treatment, compared to Hongjixing. This indicates the better cold tolerance of Hongjixing. The qRT-PCR result indicated that besides common pathways, novel pathways like latex biosynthesis potentially contributes to the better cold tolerance of Hongjixing. In view of the ubiquity of cold temperature, this study provided new insights into the mechanism dissection and guidance for cold stress condition.
期刊介绍:
Plant OMICS is an international, peer-reviewed publication that gathers and disseminates fundamental and applied knowledge in almost all area of molecular plant and animal biology, particularly OMICS-es including:
Coverage extends to the most corners of plant and animal biology, including molecular biology, genetics, functional and non-functional molecular breeding and physiology, developmental biology, and new technologies such as vaccines. This journal also covers the combination of many areas of molecular plant and animal biology. Plant Omics is also exteremely interested in molecular aspects of stress biology in plants and animals, including molecular physiology.