槟榔花果转录组数据组装及基因功能注释
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摘要
为了挖掘参与槟榔主要次生代谢产物生物合成与积累的关键酶基因,并明确其组织特异性,本研究以‘热研1号’槟榔雄花、雌花、种子、果肉为试验材料,用Illumina HiSeq TM 2000分别进行转录组测序,共获得265 505 184个Clean reads片段,组装后与Nr、KOG、KEGG、Swiss-Prot四大数据库进行比对,共有78 798个Unigenes被四大数据库注释,其中NR共注释35 467个Unigenes,对比后发现槟榔与油棕、海枣等具有一定的相似性;Swiss-prot共注释23 722个Unigenes;KOG共注释20 499个Unigenes,根据功能将槟榔转录组中的Unigene分为26类;KEGG共注释20 499个Unigenes,有10 009个Unigenes被四大数据库同时注释。槟榔转录组数据库的建立,可以有效地为解决槟榔次生代谢调控方面研究空白及活性成分合成和积累的代谢途径尚未明确的问题给予强大数据支持。该研究所得结果有助于槟榔药用成分的大量生产,为槟榔药用价值的开发利用提供依据。
In order to find the key enzyme genes involved in the biosynthesis and physiological processes of the main secondary metabolites of Areca catechu, and to clarify their expression level and tissue specificity, this study used 'Reyan No.1' Areca as the material to sequence the areca sample transcriptome with Illumina HiSeqTM2000.A total of 265 505 184 Clean reads fragments were obtained. After assembly, the areca transcriptome All-Unigene was annotated to the Nr, KOG, KEGG, and Swiss-Prot databases, and the number of Unigenes annotated in each database was counted. A total of 78 798 Unigenes were used in the four databases. 35 467 Unigenes were annotated to NR database. After comparison, it is found that areca has similarity with Elaeis guineensis and Phoenix dactylifera. A total of 23 722 Unigenes were annotated to Swiss-prot database; 20 499 Unigenes were annotated to KOG database. According to the function of the areca transcriptome, Unigenes is divided into 26 categories; 20 499 Unigenes were annotated to KEGG pathway, and 10 009 Unigenes are simultaneously annotated by four major databases. The establishment of the Areca catechu transcriptome database can effectively provide strong data support for solving the problems of the blank research on the regulation of Areca catechu secondary metabolism and the unclear metabolic pathways of the synthesis and accumulation of active components. The results of this study are helpful to the mass production of the medicinal components of areca nut and provide the basis for the exploitation and utilization of the medicinal value of Areca catechu.
In order to find the key enzyme genes involved in the biosynthesis and physiological processes of the main secondary metabolites of Areca catechu, and to clarify their expression level and tissue specificity, this study used 'Reyan No.1' Areca as the material to sequence the areca sample transcriptome with Illumina HiSeqTM2000.A total of 265 505 184 Clean reads fragments were obtained. After assembly, the areca transcriptome All-Unigene was annotated to the Nr, KOG, KEGG, and Swiss-Prot databases, and the number of Unigenes annotated in each database was counted. A total of 78 798 Unigenes were used in the four databases. 35 467 Unigenes were annotated to NR database. After comparison, it is found that areca has similarity with Elaeis guineensis and Phoenix dactylifera. A total of 23 722 Unigenes were annotated to Swiss-prot database; 20 499 Unigenes were annotated to KOG database. According to the function of the areca transcriptome, Unigenes is divided into 26 categories; 20 499 Unigenes were annotated to KEGG pathway, and 10 009 Unigenes are simultaneously annotated by four major databases. The establishment of the Areca catechu transcriptome database can effectively provide strong data support for solving the problems of the blank research on the regulation of Areca catechu secondary metabolism and the unclear metabolic pathways of the synthesis and accumulation of active components. The results of this study are helpful to the mass production of the medicinal components of areca nut and provide the basis for the exploitation and utilization of the medicinal value of Areca catechu.
引文
Chen H.,Wu Y.G.,Yang Y.Z.,Pang Z.Z.,Zhang J.F.,and Yu J.,2018,Transcriptome data assembly and gene function annotation of young and mature leaves from Pogostemon cablin,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(7):2139-2154(陈赫,吴友根,杨豫章,庞真真,张军锋,于靖,2018,广藿香幼叶与成熟叶片转录组数据组装及基因功能注释,分子植物育种,16(7):2139-2154)
Foley S.W.,Vandivier L.E.,Kuksa P.P.,and Gregory B.D.,2015,Transcriptome-wide measurement of plant RNA secondary structure,Curr.Opin.Plant Biol.,27:36-43
Li T.Z.,Du H.Y.,Liu H.M.,Wuyun T.N.,Wang L.,and Ye S.J.,2012,Transcriptome data assembly and gene function annotation of Eucommia mature fruits and young fruits,Zhongnan Linye Keji Daxue Xuebao(Journal of Central South U-niversity of Forestry&Technology),32(10):9-17(李铁柱,杜红岩,刘慧敏,乌云塔娜,王淋,叶生晶,2012,杜仲幼果和成熟果实转录组数据组装及基因功能注释,中南林业科技大学学报,32(10):9-17)
Liu D.L.,Wang X.Y.,Yang B.,and Zhang H.,2013,Review of pharmacological effects and toxicological information of Arecae Semen,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),38(14):2273-2275(刘东林,王小莹,杨冰,张晗,2013,槟榔药理毒理研究进展,中国中药杂志,38(14):2273-2275)
Liu L.,Zhao H.,Ran M.Z.,Du B.G.,Shao Q.Q.,Wu X.L.,Jia B.H.,and Zha Y.,2017,Transcriptome data assembly and gene function annotation of flowers and leaves of Ocimum basilicum,Zhongcaoyao(Chinese Traditional and Herbal Drugs),48(17):3612-3618(刘雷,赵欢,冉茂中,杜保国,邵镪钎,伍希来,贾白慧,查英,2017,罗勒花和叶的转录组数据组装及基因功能注释,中草药,48(17):3612-3618)
Qi Y.X.,Liu Y.B.,and Rong W.H.,2011,RNA-Seq and its applications:a new technology for transcriptomics,Yichuan(Hereditas),33(11):1191-1202(祁云霞,刘永斌,荣威恒,2011,转录组研究新技术:RNA-Seq及其应用,遗传,33(11):1191-1202)
Ren F.J.,Wang W.Q.,and Tang L.X.,2010,A survey of the studies on Areca catechu L.,Zhongguo Nongxue Tongbao(Chinese Agricultural Science Bulletin),26(19):397-400(任军方,王文泉,唐龙祥,2010,槟榔的研究概况,中国农学通报,26(19):397-400)
Wang H.,Wang Y.W.,Wang D.L.,Zhang S.H.,Hu X.F.,Lu S.Y.,and Gong X.M.,2018,De novo assembly and functional annotation of transcriptome data of Rhododendron pulchurum cv.Baifeng 4 leaf,Zhejiang Nongye Xuebao(Acta Agriculturae Zhejiangensis),30(7):1149-1159(王华,汪王微,王冬良,张石虎,胡新芳,卢诗雨,龚雪梅,2018,杜鹃花叶片转录组测序数据组装及功能注释,浙江农业学报,30(7):1149-1159)
Wang Y.S.,Wen G.Q.,and Nie F.,2017,High throughput sequencing and bio-information analysis of transcriptome of lingonberry spires,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(9):3871-3881(王云生,文光琴,聂飞,2017,红豆越橘幼叶转录组高通量测序及生物信息学分析,基因组学与应用生物学,36(9):3871-3881)
Zhang S.P.,Jin J.,Hu B.X.,Wu Y.Y.,Yan Q.,Zeng W.Y.,Zheng Y.L.,Zhang X.F.,and Chen P.,2015,Transcriptome profiling and analysis of Panax japonicus var.major,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),40(11):2084-2089(张绍鹏,金健,胡炳雄,吴亚运,闫祺,曾万勇,郑用琏,张西峰,陈平,2015,珍稀药用植物珠子参的转录组测序及分析,中国中药杂志,40(11):2084-2089)
Zhang X.,Tang M.H.,Chen M.,Li C.Y.,and Liu H.F.,2017,Sequencing analysis of transcriptome of Vitis amurensis during different periods of coloration,Guoshu Xuebao(Journal of Fruit Science),34(7):781-789(张雪,唐铭浩,陈蒙,李春艳,刘海峰,2017,山葡萄不同着色时期果皮转录组测序分析,果树学报,34(7):781-789)
Zhao Z.Y.,Wang S.Y.,Guo F.G.,Yin D.M.,Zhu X.H.,and Du Y.X.,2017,RNA-sequencing and tts application in medicinal plants,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(2):820-825(赵振宇,王仕玉,郭凤根,尹冬梅,朱旭海,杜玉霞,2017,转录组测序及其在药用植物上的应用,基因组学与应用生物学,36(2):820-825)
Zou L.Q.,Kuang X.J.,Li Y.,and Sun C.,2016,Advance in transcriptomic studies of ginseng species,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),41(22):4138-4143(邹丽秋,匡雪君,李滢,孙超,2016,人参属药用植物转录组研究进展,中国中药杂志,41(22):4138-4143)
Foley S.W.,Vandivier L.E.,Kuksa P.P.,and Gregory B.D.,2015,Transcriptome-wide measurement of plant RNA secondary structure,Curr.Opin.Plant Biol.,27:36-43
Li T.Z.,Du H.Y.,Liu H.M.,Wuyun T.N.,Wang L.,and Ye S.J.,2012,Transcriptome data assembly and gene function annotation of Eucommia mature fruits and young fruits,Zhongnan Linye Keji Daxue Xuebao(Journal of Central South U-niversity of Forestry&Technology),32(10):9-17(李铁柱,杜红岩,刘慧敏,乌云塔娜,王淋,叶生晶,2012,杜仲幼果和成熟果实转录组数据组装及基因功能注释,中南林业科技大学学报,32(10):9-17)
Liu D.L.,Wang X.Y.,Yang B.,and Zhang H.,2013,Review of pharmacological effects and toxicological information of Arecae Semen,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),38(14):2273-2275(刘东林,王小莹,杨冰,张晗,2013,槟榔药理毒理研究进展,中国中药杂志,38(14):2273-2275)
Liu L.,Zhao H.,Ran M.Z.,Du B.G.,Shao Q.Q.,Wu X.L.,Jia B.H.,and Zha Y.,2017,Transcriptome data assembly and gene function annotation of flowers and leaves of Ocimum basilicum,Zhongcaoyao(Chinese Traditional and Herbal Drugs),48(17):3612-3618(刘雷,赵欢,冉茂中,杜保国,邵镪钎,伍希来,贾白慧,查英,2017,罗勒花和叶的转录组数据组装及基因功能注释,中草药,48(17):3612-3618)
Qi Y.X.,Liu Y.B.,and Rong W.H.,2011,RNA-Seq and its applications:a new technology for transcriptomics,Yichuan(Hereditas),33(11):1191-1202(祁云霞,刘永斌,荣威恒,2011,转录组研究新技术:RNA-Seq及其应用,遗传,33(11):1191-1202)
Ren F.J.,Wang W.Q.,and Tang L.X.,2010,A survey of the studies on Areca catechu L.,Zhongguo Nongxue Tongbao(Chinese Agricultural Science Bulletin),26(19):397-400(任军方,王文泉,唐龙祥,2010,槟榔的研究概况,中国农学通报,26(19):397-400)
Wang H.,Wang Y.W.,Wang D.L.,Zhang S.H.,Hu X.F.,Lu S.Y.,and Gong X.M.,2018,De novo assembly and functional annotation of transcriptome data of Rhododendron pulchurum cv.Baifeng 4 leaf,Zhejiang Nongye Xuebao(Acta Agriculturae Zhejiangensis),30(7):1149-1159(王华,汪王微,王冬良,张石虎,胡新芳,卢诗雨,龚雪梅,2018,杜鹃花叶片转录组测序数据组装及功能注释,浙江农业学报,30(7):1149-1159)
Wang Y.S.,Wen G.Q.,and Nie F.,2017,High throughput sequencing and bio-information analysis of transcriptome of lingonberry spires,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(9):3871-3881(王云生,文光琴,聂飞,2017,红豆越橘幼叶转录组高通量测序及生物信息学分析,基因组学与应用生物学,36(9):3871-3881)
Zhang S.P.,Jin J.,Hu B.X.,Wu Y.Y.,Yan Q.,Zeng W.Y.,Zheng Y.L.,Zhang X.F.,and Chen P.,2015,Transcriptome profiling and analysis of Panax japonicus var.major,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),40(11):2084-2089(张绍鹏,金健,胡炳雄,吴亚运,闫祺,曾万勇,郑用琏,张西峰,陈平,2015,珍稀药用植物珠子参的转录组测序及分析,中国中药杂志,40(11):2084-2089)
Zhang X.,Tang M.H.,Chen M.,Li C.Y.,and Liu H.F.,2017,Sequencing analysis of transcriptome of Vitis amurensis during different periods of coloration,Guoshu Xuebao(Journal of Fruit Science),34(7):781-789(张雪,唐铭浩,陈蒙,李春艳,刘海峰,2017,山葡萄不同着色时期果皮转录组测序分析,果树学报,34(7):781-789)
Zhao Z.Y.,Wang S.Y.,Guo F.G.,Yin D.M.,Zhu X.H.,and Du Y.X.,2017,RNA-sequencing and tts application in medicinal plants,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(2):820-825(赵振宇,王仕玉,郭凤根,尹冬梅,朱旭海,杜玉霞,2017,转录组测序及其在药用植物上的应用,基因组学与应用生物学,36(2):820-825)
Zou L.Q.,Kuang X.J.,Li Y.,and Sun C.,2016,Advance in transcriptomic studies of ginseng species,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),41(22):4138-4143(邹丽秋,匡雪君,李滢,孙超,2016,人参属药用植物转录组研究进展,中国中药杂志,41(22):4138-4143)