不同刈割强度下羊草转录组研究

doi:10.11686/cyxb2017143

草业学报 ›› 2018, Vol. 27 ›› Issue (2): 105-116.DOI: 10.11686/cyxb2017143

不同刈割强度下羊草转录组研究

赵劲博^{1, 2}, 侯向阳^{1, 2, *}, 武自念^{1, 2}, 任卫波^{1, 2}, 胡宁宁^{1, 2}, 郭丰辉^{1, 2}, 马文静^{1, 2}

1.中国农业科学院草原研究所,内蒙古呼和浩特 010010;
2. 农业部草地生态与修复治理重点实验室,内蒙古呼和浩特 010010

收稿日期:2017-03-28 修回日期:2017-05-17 出版日期:2018-02-20 发布日期:2018-02-20
通讯作者: houxy16@126.com
作者简介:赵劲博(1992-),男,山西忻州人,在读硕士。E-mail:zhaojinbo116633@163.com
基金资助:
国家重点基础研究发展计划(973计划)(2014CB138806),国家自然基金(31502008)和中央级公益性科研院所基本科研业务费专项资金项目(1610332015002),公益性行业(农业)科研专项经费项目(201303060)和中国农业科学院科技创新工程协同创新(CAAS-XTCT2016001-2)资助

Transcriptome analysis of Leymus chinensis under different mowing intensities

ZHAO Jin-bo^{1, 2}, HOU Xiang-yang^{1, 2, *}, WU Zi-nian^{1, 2}, REN Wei-bo^{1, 2}, HU Ning-ning^{1, 2}, GUO Feng-hui^{1, 2}, MA Wen-jing^{1, 2}

1.Institute of Grassland Research of Chinese Academy of Agriculture Sciences, Hohhot 010010, China;
2.Key Laboratory of Grassland Ecology and Restoration of the Ministry of Agriculture, Huhhot 010010, China

Received:2017-03-28 Revised:2017-05-17 Online:2018-02-20 Published:2018-02-20

摘要/Abstract

摘要： 刈割是一种重要的草地管理措施,刈割留茬高度直接影响草地生产力及群落结构,在牧草生产中具有重要意义。为研究羊草在不同刈割强度下的转录响应,利用Illumina HiSeq-PE150高通量测序技术,对不同刈割留茬高度(0,2,4,8,12 cm)处理下羊草再生叶片进行了转录组测序。共得到139767803条读长(reads),41.94 Gb原始数据。经过过滤、质控与从头组装后,总共得到转录本270207条,总长度为191.6 Mb。通过与多种数据库比对得到48097条单基因簇(Unigene)注释结果。筛选出了所有刈割强度处理与不刈割对照组显著差异基因共2579条,经过生物信息分析,将其定位到碳水化合物代谢、损伤应答、过氧化氢分解、植物激素信号转导等功能与代谢通路。利用聚类方法得到了随着刈割强度增强,表达量规律变化的基因,分别富集到了过氧化物酶体、光合作用等代谢途径。对羊草在不同刈割高度下的转录组进行了研究,为草本植物分子生物学研究提供了宝贵的数据资源,对于解析羊草响应刈割的分子调控机制及相关基因挖掘具有重要指导意义。

Abstract: Mowing is an important part of grassland management. The height of stubble left after mowing directly influences grassland productivity and community structure, which have important implications for forage production. To investigate the transcriptional responses of Leymus chinensis under different mowing intensities, the transcriptome of the regenerative blades from L. chinensis mowed to different stubble heights (0, 2, 4, 8, and 12 cm) were sequenced using the Illumina HiSeq-PE150 high-throughput sequencing platform. In total, 139767803 reads and 41.94 Gb raw data were generated. After filtering, quality control, and de novo assembly, we obtained 270207 transcripts with a total length of 191.6 Mb. After comparisons with various databases, we obtained 48097 unigenes. We detected 2579 differentially expressed genes (DEGs) between the mowed group and the non-mowed control group. The DEGs were classified into several functional categories and metabolic pathways including carbohydrate metabolism, response to wounding, hydrogen peroxide catabolism, and plant hormone signal transduction. A cluster analysis was used to identify genes showing changes in transcript abundance with increasing mowing intensity. These genes were enriched in peroxisome, photosynthesis, and other metabolic pathways. Research on the transcriptome of L. chinensis under different mowing intensities provides valuable data resources for molecular research on herbaceous plants. Our findings will be useful for analyzing the molecular mechanism of mowing responses and for mining genes related high performance of L. chinensis after mowing.

赵劲博, 侯向阳, 武自念, 任卫波, 胡宁宁, 郭丰辉, 马文静. 不同刈割强度下羊草转录组研究[J]. 草业学报, 2018, 27(2): 105-116.

ZHAO Jin-bo, HOU Xiang-yang, WU Zi-nian, REN Wei-bo, HU Ning-ning, GUO Feng-hui, MA Wen-jing. Transcriptome analysis of Leymus chinensis under different mowing intensities[J]. Acta Prataculturae Sinica, 2018, 27(2): 105-116.

参考文献

[1] Li Y H.The divergence and convergence of Aneurolepidium chinese steppe and Stip grandis steppe under the grazing influence in Xilin river valley, Inner Mongolia. Chinese Journal of Plant Ecology, 1988, 12(3): 189-196.
李永宏. 内蒙古锡林河流域羊草草原和大针茅草原在放牧影响下的分异和趋同. 植物生态学报, 1988, 12(3): 189-196.
[2] Zhao H.The Study of Nutrition Value of The Leymus chinensis for Dairy Cattle and Assiociative Effects of Feeds. Daqing: Heilongjiang Bayi Agricultural University, 2008.
赵鹤. 羊草对奶牛营养价值及其日粮组合效应的研究. 大庆: 黑龙江八一农垦大学, 2008.
[3] Ferraro D O, Oesterheld M.Effect of defoliation on grass growth. A quantitative review. Oikos, 2002, 98(1): 125-133.
[4] Davidson J L, Milthorpe F L.Leaf growth in dactylis glomerate following defoliation. Annals of Botany, 1966, 30(2): 173-184.
[5] Wang Z F, Wang D J, Yu H Z, et al. Effects of cutting time and stubble height on hay yield and quality of Leymus chinensis meadow. Pratacultural Science, 2016, (2): 276-282.
王志锋, 王多伽, 于洪柱, 等. 刈割时间与留茬高度对羊草草甸草产量和品质的影响. 草业科学, 2016, (2): 276-282.
[6] Zhong Y K, Bao Q H.The effects of different mowing intensity on natural grassland. Grassland of China, 1999, (5): 15-18.
仲延凯, 包青海. 不同刈割强度对天然割草地的影响. 中国草地, 1999, (5): 15-18.
[7] Han L, Guo Y J, Han J G, et al. A study on the diversity and aboveground biomass in a Leymus chinensis meadow steppe community under different cutting intensities. Acta Prataculturae Sinica, 2010, 19(3): 70-75.
韩龙, 郭彦军, 韩建国, 等. 不同刈割强度下羊草草甸草原生物量与植物群落多样性研究. 草业学报, 2010, 19(3): 70-75.
[8] Conesa A, Madrigal P, Tarazona S, et al. A survey of best practices for RNA-seq data analysis. Genome Biology, 2016, 17(1): 181.
[9] Hou X Y.Advances and prospects of grassland plant basic biology research. China Basic Science, 2016, 18(2): 67-76.
侯向阳. 草原植物基础生物学研究进展与展望. 中国基础科学, 2016, 18(2): 67-76.
[10] Chen S, Cai Y, Zhang L, et al. Transcriptome analysis reveals common and distinct mechanisms for sheepgrass (Leymus chinensis) responses to defoliation compared to mechanical wounding. Plos One, 2014, 9(2): e89495.
[11] Huang X, Peng X, Zhang L, et al. Bovine serum albumin in saliva mediates grazing response in Leymus chinensis revealed by RNA sequencing. BMC Genomics, 2014, 15(1): 1126.
[12] Grabherr M G, Haas B J, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 2011, 29(7): 644-652.
[13] Haas B J, Papanicolaou A, Yassour M, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 2013, 8(8): 1494-1512.
[14] Altschul S F, Gish W, Miller W, et al. Basic local alignment search tool. Journal of Molecular Biology, 1990, 215(3): 403-410.
[15] Punta M, Coggill P C, Eberhardt R Y, et al. The Pfam protein families database. Nucleic Acids Research, 2012, 36: 263-266.
[16] Kanehisa M, Goto S, Sato Y, et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research, 2012, 40: D109-D114.
[17] Wu C H, Apweiler R, Bairoch A, et al. The universal protein resource (UniProt): an expanding universe of protein information. Nucleic Acids Research, 2006, 34: D187-D191.
[18] Ye J.WEGO: a web tool for plotting GO annotations. Nucleic Acids Research, 2006, 34(Web Server issue): W293-W297.
[19] Young M D, Wakefield M J, Smyth G K, et al. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology, 2010, 11(2): R14.
[20] Xie C, Mao X, Huang J, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research, 2011, 39(Web Server issue): W316-W322.
[21] Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 2009, 10(3): R25.
[22] Li B, Dewey C N, Li B, et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 2011, 12(1): 323.
[23] Wang L, Feng Z, Wang X, et al. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics (Oxford, England), 2010, 26(1): 136-138.
[24] Ernst J, Barjoseph Z.STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics, 2006, 7(7): 1-11.
[25] Sun Y, Wang F, Wang N, et al. Transcriptome exploration in Leymus chinensis under saline-alkaline treatment using 454 pyrosequencing. Plos One, 2013, 8(1): e53632.
[26] Zhao P, Liu P, Yuan G, et al. New insights on drought stress response by global investigation of gene expression changes in sheepgrass (Leymus chinensis). Frontiers in Plant Science, 2016, 7(147): 954.
[27] Devoto A, Ellis C.Expression profiling reveals COI1 to be a key regulator of genes involved in wound- and methyl jasmonate-induced secondary metabolism, defence, and hormone interactions. Plant Molecular Biology, 2005, 58(4): 497-513.
[28] Turner J G, Ellis C, Devoto A.The jasmonate signal pathway. Plant Cell, 2002, 14(Suppl 1): S153-S164.
[29] Zhou W.Molecular Mechanism of Jasmonate-regulated Plant Defense Controled by JAV1. Beijing: Tsinghua University, 2013.
周武. JAV1调控茉莉素介导的植物抗性反应的分子机理研究. 北京: 清华大学, 2013.
[30] Yan J, Zhang C, Gu M, et al. The Arabidopsis CORONATINE INSENSITIVE1 protein is a jasmonate receptor. Plant Cell, 2009, 21(8): 2220.
[31] Adams E, Turner J.Illuminating COI1: a component of the Arabidopsis jasomonate receptor complex also interacts with ethylene signaling. Plant Signaling & Behavior, 2010, 5(12): 1682-1684.
[32] Thines B, Katsir L, Melotto M, et al. JAZ repressor proteins are targets of the SCF(COI1) complex during jasmonate signalling. Nature, 2007, 448(7154): 661-665.
[33] Chen X Y, Tang Z C.Plant Physiology and Moleculer Biology. Beijing: Higher Education Press, 2012: 553-554.
陈晓亚, 汤章城. 植物生理与分子生物学. 北京: 高等教育出版社, 2012: 553-554.
[34] Ma Y, Szostkiewicz I, Korte A, et al. Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science, 2009, 324(5930): 1064.
[35] Park S Y, Fung P, Nishimura N, et al. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science, 2009, 324(5930): 1068-1071.
[36] Gonzalez-Guzman M, Pizzio G A, Antoni R, et al. Arabidopsis PYR/PYL/RCAR receptors play a major role in quantitative regulation of stomatal aperture and transcriptional response to abscisic acid. The Plant Cell, 2012, 24(6): 2483-2496.
[37] Schweighofer, Alois, Hirt, et al. Plant PP2C phosphatases: emerging functions in stress signaling. Trends in Plant Science, 2004, 9(5): 236.
[38] Jia L, Liu M M, Zhang H Q, et al. Antioxidant defense system responses of Artemisia frigida to mechanical damage. Journal of Zhejiang A & F University, 2016, 33(3): 462-470.
贾丽, 刘盟盟, 张洪芹, 等. 冷蒿抗氧化防御系统对机械损伤的响应. 浙江农林大学学报, 2016, 33(3): 462-470.
[39] Domergue F, Vishwanath S J, Joubès J, et al. Three Arabidopsis fatty acyl-coenzyme A reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition. Plant Physiology, 2010, 153(4): 1539-1554.
[40] Koo A J K, Cooke T F, Howe G A. Cytochrome P450 CYP94B3 mediates catabolism and inactivation of the plant hormone jasmonoyl-L-isoleucine. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(22): 9298.
[41] Yan Y, Stolz S, Chételat A, et al. A downstream mediator in the growth repression limb of the jasmonate pathway. Plant Cell, 2007, 19(8): 2470-2483.
[42] Walley J W, Coughlan S, Hudson M E, et al. Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. Plos Genetics, 2007, 3(10): 1800-1812.
[43] Chen F,D’Auria J C,Tholl D, et al. An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. Plant Journal, 2003, 36(5): 577-588.

不同刈割强度下羊草转录组研究

Transcriptome analysis of Leymus chinensis under different mowing intensities

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