干旱胁迫下青稞全基因组可变剪切分析
|
摘要
为阐明青稞在旱胁迫下基因发生可变剪切的规律,本研究以抗旱的"喜拉16号"和旱敏感的"迪庆黑元桂"为试验材料,分别对对照和21%PEG浓度下处理的样本进行多时间点的全转录组测序。结果表明,利用Leaf Cutter软件在所有的样品中共检测到了22 181个可变剪切事件;通过PCA分析发现,可变剪切具有明显的品种间特异性;另外,通过与抗旱基因数据库比对分析发现,在干旱胁迫处理下2个类型品种间有多个抗旱相关的基因发生了显著的差异可变剪切,分别是HVUL1H16429 (AtrbohF)、HVUL1H12808 (HAB1)、HVUL4H58649 (ABF4)、HVUL4H35985 (AtrbohD)、HVUL7H07799 (LOS5)、HVUL3H43774 (CLCc)、HVUL3H23631(ABCG40)、HVUL1H16840(MYB60)和HVUL6H08236(AREB1);对2个品种各自在对照与旱胁迫条件下的差异可变剪切基因进行pathway分析,发现了抗旱品种的差异可变剪切基因参与了更多的pathway,并且鉴别出Fatty acid degradation、Inositol phosphate metabolism、alpha-Linolenic acid metabolism和Fatty acid metabolism这4条通路显著富集。为解析青稞抗旱分子机理与培育青稞抗旱新品种奠定了理论基础。
In order to study the pattern of variable shearing of genes in highland barley under drought stress,the drought-resistant‘Xila 16'and drought-sensitive‘Diqing Heiyuangui'were used as experimental materials. The samples processed at control and 21 % PEG concentrations were separately sequenced at multiple time points. The results showed that a total of 22 181 variable shearing events were detected in all samples by Leaf Cutter software,and it was also found by PCA analysis that the variable shearing has obvious specificity among varieties.In addition,by comparing with drought resistance gene database,there were significant differences in drought resistance related genes between the two varieties under drought stress: HVUL1 H16429( Atrboh F),HVUL1 H12808( HAB1),HVUL4 H58649( ABF4),HVUL4 H35985( Atrboh D),HVUL7 H07799( LOS5),HVUL3 H43774( CLCc),HVUL3 H23631( ABCG40),HVUL1 H16840( MYB60) and HVUL6 H08236( AREB1). Comparing the variable shearing genes between two varieties by KEGG analysis,the drought-resistant varieties were involved in more pathways,and four significant enrichment pathways were identified,which were fatty acid degradation,inositol phosphate metabolism,alpha-Linolenic acid metabolism and fatty acid metabolism pathways. The research lays a theoretical foundation for analyzing the molecular mechanism of drought resistance of highland barley and breeding new varieties.
In order to study the pattern of variable shearing of genes in highland barley under drought stress,the drought-resistant‘Xila 16'and drought-sensitive‘Diqing Heiyuangui'were used as experimental materials. The samples processed at control and 21 % PEG concentrations were separately sequenced at multiple time points. The results showed that a total of 22 181 variable shearing events were detected in all samples by Leaf Cutter software,and it was also found by PCA analysis that the variable shearing has obvious specificity among varieties.In addition,by comparing with drought resistance gene database,there were significant differences in drought resistance related genes between the two varieties under drought stress: HVUL1 H16429( Atrboh F),HVUL1 H12808( HAB1),HVUL4 H58649( ABF4),HVUL4 H35985( Atrboh D),HVUL7 H07799( LOS5),HVUL3 H43774( CLCc),HVUL3 H23631( ABCG40),HVUL1 H16840( MYB60) and HVUL6 H08236( AREB1). Comparing the variable shearing genes between two varieties by KEGG analysis,the drought-resistant varieties were involved in more pathways,and four significant enrichment pathways were identified,which were fatty acid degradation,inositol phosphate metabolism,alpha-Linolenic acid metabolism and fatty acid metabolism pathways. The research lays a theoretical foundation for analyzing the molecular mechanism of drought resistance of highland barley and breeding new varieties.
引文
[1]LIANG J,CHEN X,DENG G,et al. Dehydration induced transcriptomic responses in two Tibetan hulless barley(Hordeum vulgare var. nudum)accessions distinguished by drought tolerance[J].BMC genomics,2017,18(1):775.
[2]LI Y,KNOWLES D,HUMPHREY J,et al. Annotation-free quantification of RNA splicing using Leaf Cutter[J]. Nature Genetics,2018,50(1):151.
[3]TANG Y,ZENG X,WANG Y,et al. Transcriptomics analysis of hulless barley during grain development with a focus on starch biosynthesis[J]. Functional&Integrative Genomics,2017,17(1):107-117.
[4]WEI Z,ZENG X,QIN C,et al. Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley[J]. Frontiers in Plant Science,2016,7:1067.
[5]YUAN H,ZENG X,LING Z,et al. Transcriptome profiles reveal cold acclimation and freezing tolerance of susceptible and tolerant hulless barley genotypes[J]. Acta Physiologiae Plantarum,2017,39(12):275.
[6]王玉林,徐齐君,原红军,等. PEG模拟干旱胁迫处理对青稞幼苗生长和生理特性的影响[J].大麦与谷类科学,2018,35(1):6-12.
[7]TRAPNELL C,PACHTER L,SALZBERG S L. TopHat:discovering splice junctions with RNA-Seq[J]. Bioinformatics,2009,25(9):1105-1111.
[8]ALTER S,BADER K,SPANNAGL M,et al. DroughtDB:an expert-curated compilation of plant drought stress genes and their homologs in nine species[J]. Database,2015:046.
[9]ZHONG D,DU H,WANG Z,et al. Genotypic variation in fatty acid composition and unsaturation levels in bermudagrass associated with leaf dehydration tolerance[J]. Journal of the American Society for Horticultural Science,2011,136(1):35-40.
[10]EXCOFFON K,BOWERS J,SHARMA P. Alternative splicing of viral receptors:A review of the diverse morphologies and physiologies of adenoviral receptors[J]. Recent Research Developments in Virology,2014,9:1-24.
[11]HAMID F,MAKEYEV E. Emerging functions of alternative splicing coupled with nonsense-mediated decay[J]. Biochemical Society Transactions,2014,42(4):1168-1173.
[2]LI Y,KNOWLES D,HUMPHREY J,et al. Annotation-free quantification of RNA splicing using Leaf Cutter[J]. Nature Genetics,2018,50(1):151.
[3]TANG Y,ZENG X,WANG Y,et al. Transcriptomics analysis of hulless barley during grain development with a focus on starch biosynthesis[J]. Functional&Integrative Genomics,2017,17(1):107-117.
[4]WEI Z,ZENG X,QIN C,et al. Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley[J]. Frontiers in Plant Science,2016,7:1067.
[5]YUAN H,ZENG X,LING Z,et al. Transcriptome profiles reveal cold acclimation and freezing tolerance of susceptible and tolerant hulless barley genotypes[J]. Acta Physiologiae Plantarum,2017,39(12):275.
[6]王玉林,徐齐君,原红军,等. PEG模拟干旱胁迫处理对青稞幼苗生长和生理特性的影响[J].大麦与谷类科学,2018,35(1):6-12.
[7]TRAPNELL C,PACHTER L,SALZBERG S L. TopHat:discovering splice junctions with RNA-Seq[J]. Bioinformatics,2009,25(9):1105-1111.
[8]ALTER S,BADER K,SPANNAGL M,et al. DroughtDB:an expert-curated compilation of plant drought stress genes and their homologs in nine species[J]. Database,2015:046.
[9]ZHONG D,DU H,WANG Z,et al. Genotypic variation in fatty acid composition and unsaturation levels in bermudagrass associated with leaf dehydration tolerance[J]. Journal of the American Society for Horticultural Science,2011,136(1):35-40.
[10]EXCOFFON K,BOWERS J,SHARMA P. Alternative splicing of viral receptors:A review of the diverse morphologies and physiologies of adenoviral receptors[J]. Recent Research Developments in Virology,2014,9:1-24.
[11]HAMID F,MAKEYEV E. Emerging functions of alternative splicing coupled with nonsense-mediated decay[J]. Biochemical Society Transactions,2014,42(4):1168-1173.