牛耳朵与黄花牛耳朵比较转录组学分析
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摘要
牛耳朵和黄花牛耳朵在岩溶环境的适应性上区别显著。为研究它们在岩溶环境中分子适应机制的差异及相关基因,本实验对它们的叶片转录组进行了测序,通过比较转录组分析,筛选两个物种中的直系同源基因,检测正选择基因,寻找可能参与适应岩溶环境的基因。结果表明,牛耳朵与黄花牛耳朵的N50值分别为795和819,在牛耳朵中测序得到了157 728个unigene,黄花牛耳朵为156 965个。为了解两个物种unigene的功能信息,将其与公共数据库进行BLAST同源比对;用OrthoMCL筛选两个物种间的直系同源基因,经过严格的数据筛选后,共得到了1 898对直系同源基因,并计算其Ka、Ks及Ka/Ks值,利用公式T=K/2r估算两个物种的分化时间约为0.86±0.72百万年前(Mya)。在两个物种中有152对直系同源基因受到了强烈的正选择作用,对其进行GO、KEGG功能富集分析及基因功能注释,得到了与岩溶环境适应有关的19对功能基因。对两个物种的进化分析不仅估算了大概的分化时间,而且还发现了在岩溶环境中差异适应的相关基因。
The adaptability of Primulina eburnea and Primulina lutea in karst environment is significantly different.In order to study the difference of molecular adaptation mechanism in karst environment and related genes, the leaf transcriptomes of P. eburnea and P. lutea were sequenced. The orthologous genes of two plants were screened by comparing transcriptome analysis, and the positive selected genes were detected to find out genes that may be involved in adapting to karst environment. The results showed that N50 values of P. eburnea and P. lutea were 795 and 819, respectively, and 157 728 unigenes were obtained in P. eburnea as well as 156 965 unigenes were obtained in P. lutea. Unigenes of two plants were compared with the public database to annotate their gene function by BLAST. The orthologous genes of two plants were screened by OrthoMCL, and 1 898 pairs of orthologs were identified after strict data screening. Then, Ka, Ks and Ka/Ks values were calculated and the differentiation time of two plants was approximately 0.86±0.72 mya(million years ago) by using the formula T=K/2 r. 152 pairs of orthologous genes were under strongly positive selection in P. eburnea and P. lutea. 19 pairs of functional genes related to the adaptation in karst environment were obtained in orthologous genes by GO, KEGG functional enrichment analysis and gene function annotation. The evolutionary analysis of P. eburnea and P. lutea not only estimated the approximate differentiation time, but also found the gene related to the differential adaptation in karst environment.
The adaptability of Primulina eburnea and Primulina lutea in karst environment is significantly different.In order to study the difference of molecular adaptation mechanism in karst environment and related genes, the leaf transcriptomes of P. eburnea and P. lutea were sequenced. The orthologous genes of two plants were screened by comparing transcriptome analysis, and the positive selected genes were detected to find out genes that may be involved in adapting to karst environment. The results showed that N50 values of P. eburnea and P. lutea were 795 and 819, respectively, and 157 728 unigenes were obtained in P. eburnea as well as 156 965 unigenes were obtained in P. lutea. Unigenes of two plants were compared with the public database to annotate their gene function by BLAST. The orthologous genes of two plants were screened by OrthoMCL, and 1 898 pairs of orthologs were identified after strict data screening. Then, Ka, Ks and Ka/Ks values were calculated and the differentiation time of two plants was approximately 0.86±0.72 mya(million years ago) by using the formula T=K/2 r. 152 pairs of orthologous genes were under strongly positive selection in P. eburnea and P. lutea. 19 pairs of functional genes related to the adaptation in karst environment were obtained in orthologous genes by GO, KEGG functional enrichment analysis and gene function annotation. The evolutionary analysis of P. eburnea and P. lutea not only estimated the approximate differentiation time, but also found the gene related to the differential adaptation in karst environment.
引文
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Blanc G.,and Wolfe K.H.,2004,Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes,Plant Cell,16(7):1667-1678
Chen Q.,Tang H.R.,Dong X.L.,Hou Y.X.,Luo Y.,Jiang Y.,and Huang Q.Y.,2009,Progress in the study of plant Myb transcription factors,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),28(2):365-372(陈清,汤浩茹,董晓莉,侯艳霞,罗娅,蒋艳,黄琼瑶,2009,植物Myb转录因子的研究进展,基因组学与应用生物学,28(2):365-372)
Chen W.J.,Wen Y.X.,Chen Y.Y.,Huang Y.L.,and Li D.P.,2010,Phenylethanoid glycosides and their cytotoxicity of Chirita eburnea Hance,Zhongchengyao(Chinese Traditional Patent Medicine),32(6):1000-1003(陈文娟,文永新,陈月圆,黄永林,李典鹏,2010,牛耳朵苯乙醇苷类化学成分及其细胞毒活性研究,中成药,32(6):1000-1003)
Cowan I.R.,1977,Stomatal behavior and environment,Advances in Botanical Research,190:117-228
Gao Y.,Tian L.,and Qin S.,2008,Positive selection in plant evolution,Zhuwu Xuebao(Chinese Bulletin of Botany),25(4):401-406(高远,田李,秦松,2008,植物进化中的正选择作用,植物学报,25(4):401-406)
Grabherr M.G.,Haas B.J.,Yassour M.,Levin J.Z.,Thompson D.A.,Amit I.,Adiconis X.,Fan L.,Raychowdhury R.,Zeng Q.,Chen Z.,Mauceli E.,Hacohen N.,Gnirke A.,Rhind N.,di Palma F.,Birren B.W.,Nusbaum C.,Lindblad-Toh K.,Friedman N.,and Regev A.,2011,Full-length transcriptome assembly from RNA-Seq data without a reference genome,Nat.Biotechnol.,29(7):644-652
Graur D.,and Li W.H.,eds.,2000,Fundamentals of molecular evolution(2nd ed.),Sinauer Associates Inc.,Sunderland,M.A.,pp.100-200
Gusinde M.,Matus J.T.,Francia P.,Rusconi F.,Ca觡ón P.,Medina C.,Conti L.,Cominelli E.,Tonelli C.,and Arce-Johnson P.,2011,T he grapevine guard cell-related vvmyb60 transcription factor is involved in the regulation of stomatal activity and is differentially expressed in response to ABAand osmotic stress,BMC Plant Biol.,11(1):142
Jia Y.,Liu M.L.,Yue M.,Zhao Z.,Zhao G.F.,and Li Z.H.,2017,Comparative transcriptome analysis reveals adaptive evolution of Notopterygium incisum and Notopterygium franchetii,two high-alpine herbal species endemic to china,Molecules,22(7):1158
Kane N.C.,Barker M.S.,Zhan S.H.,and Rieseberg L.H.,2011,Molecular evolution across the Asteraceae.micro-and macroevolutionary processes,Mol.Biol.Evol.,28(12):3225-3235
Kanehisa M.,Araki M.,Goto S.,Hattori M.,Hirakawa M.,Itoh M.,Katayama T.,Kawashima S.,Okuda S.,Tokimatsu T.,and Yamanishi Y.,2008,KEGG for linking genomes to life and the environment,Nucleic Acids Res.,36(D):480-484
Koch M.A.,Haubold B.,and Mitchell-Olds T.,2000,Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis,Arabis,and related genera(Brassicaceae),Mol.Biol.Evol.,17(10):1483-1498
Li L.,Stoeckert C.J.,and Roos D.S.,2003,OrthoMCL:identification of ortholog groups for eukaryotic genomes,Genome Res.,13(9):2178-2189
Liu Y.,and Wei Y.G.,2004,Chirita lutea a new species of Gesneriaceae from Guangxi,China,Zhiwu Kexue Xuebao(Journal of Wuhan Botanical Research),22(5):391-393(刘演,韦毅刚,2004,中国广西唇柱苣苔属(苦苣苔科)一新种-黄花牛耳朵,植物科学学报,22(5):391-393)
Lynch M.,and Conery J.S.,2000,The evolutionary fate and consequences of duplicate genes,Science,290(5494):1151-1155
Ning Y.S.,Wang G.L.,and Xie Q.,2011,E3 ubiquitin ligase-mediated drought responses in plants,Zhiwu Xuebao(Bulletin of Botany),46(6):606-616(宁约瑟,王国梁,谢旗,2011,泛素连接酶e3介导的植物干旱胁迫反应,植物学报,46(6):606-616)
Qi Y.,Xu Z.S.,Li P.S.,Chen M.,Li L.C.,and Ma Y.Z.,2013,Research progress on molecular mechanism and application of HSP70 in plants,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),14(3):507-511(齐妍,徐兆师,李盼松,陈明,李连城,马有志,2013,植物热激蛋白70的分子作用机理及其利用研究进展,植物遗传资源学报,14(3):507-511)
Qin Y.,Wang M.,Tian Y.,He W.,Han L.,and Xia G.,2012,Over-expression of TaMYB33 encoding a novel wheat M-YB transcription factor increases salt and drought tolerance in Arabidopsis,Mol.Biol.Rep.,39(6):7183-7192
Rogel M.R.,Jaitovich A.,and Ridge K.M.,2010,The role of the ubiquitin proteasome pathway in keratin intermediate filament protein degradation,Proc.Am.Thorac.Soc.,7(1):71-76
Sang Y.,Yan F.,and Ren X.,2015,The role and mechanism of crl4 e3 ubiquitin ligase in cancer and its potential therapy implications,Oncotarget,6(40):42590-42602
Shan H.,Chen S.,Jiang J.,Chen F.,Chen Y.,Gu C.,Li P.,Song A.,Zhu X.,Gao H.,Zhou G.,Li T.,and Yang X.,2012,H-eterologous expression of the chrysanthemum R2R3-MYBtranscription factor Cm MYB2 enhances drought and salinity tolerance,increases hypersensitivity to ABA and delays flowering in Arabidopsis thaliana,Mol.Biotechnol.,51(2):160-173
Shang F.,and Taylor A.,2012,Roles for the ubiquitin-proteasome pathway in protein quality control and signaling in the retina.implications in the pathogenesis of age-related macular degeneration,Mol.Aspects Med.,33(4):446-466
Tang N.,and Chen X.B.,2014,Research of MYB transcription factors in plant and abiotic stress response,Shengwuxue Z-azhi(Journal of Biology),31(3):74-78(唐宁,陈信波,2014,植物MYB转录因子与非生物胁迫响应研究,生物学杂志,31(3):74-78)
Tang S.C.,Pu G.Z.,Pan Y.M.,Zou R.,and Wei C.Q.,2009,Pol lination biology of Chirita lutea in China(Gesneriaceae),R-edai Yaredai Zhiwu Xuebao(Journal of Tropical and Subtropical Botany),17(4):328-333(唐赛春,蒲高忠,潘玉梅,邹蓉,韦春强,2009,黄花牛耳朵(苦苣苔科)的传粉生物学,热带亚热带植物学报,17(4):328-333)
Wang M.Q.,and Zhang D.Y.,2015,Research advance of heat shock protein 70 gene family and its biological functions in plant,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(2):421-428(王明强,张道远,2015,植物热激蛋白70基因家族及其生物学功能研究进展,基因组学与应用生物学,34(2):421-428)
Wang X.Q.,Bai Z.F.,Liu Y.,and Xiao P.G.,2011,Microscopic and chemical identification of Chirita eburnean and Chirita lutea,Zhongguo Shiyan Fangjixue Zazhi(Chinese Journal of Experimental Traditional Medical Formulae),(14):99-101(王晓琴,白贞芳,刘勇,肖培根,2011,牛耳朵和黄花牛耳朵的显微和化学鉴别,中国实验方剂学杂志,(14):99-101)
Wang Y.,and Hey J.,2010,Estimating divergence parameters with small samples from a large number of loci,Genetics,184(2):363-379
Wen F.,2008,Studies on investigation and introduction of wild ornamental resources of Gesneriaceae in Guangxi,Dissertation for Ph.D.,Beijing Forestry University,Supervisor:Zhang Q.X.,pp.1-18(温放,2008,广西苦苣苔科观赏植物资源调查与引种研究,博士学位论文,北京林业大学,导师:张启翔,pp.1-18)
Wu G.,2011,The mechanism of typical plants adaptative to calcium rich environment in karst area of southwest China,Dissertation for Ph.D.,Huazhong University of Science and Technology,Supervisors:Yu L.J.,and Li M.T.,pp.453-454(吴耿,2011,西南岩溶地区典型植物适应岩溶高钙环境的机制,博士学位论文,华中科技大学,导师:余龙江,栗茂腾,pp.453-454)
Xu K.H.,Zhang Y.T.,Zhang Y.,Wang B.,Wang F.W.,and Li H.Y.,2018,Research advances on the F-box gene family in plants,Shengwu Jishu Tongbao(Biotechnology Bulletin),34(1):26-32(许克恒,张云彤,张莹,王彬,王法微,李海燕,2018,植物F-box基因家族的研究进展,生物技术通报,34(1):26-32)
Xu Y.,Li L.X.,Yu X.M.,and Liu D.Q.,2015,The functions of F-box protein in plant resistance to stress,Zhiwu Shengli Xuebao(Plant Physiology Journal),51(7):1003-1008(许媛,李铃仙,于秀梅,刘大群,2015,F-box蛋白在植物抗逆境胁迫中的功能,植物生理学报,51(7):1003-1008)
Yan H.X.,Guan S.K.,Deng J.L.,He J.Z.,Huang C.Y.,and Bu Z.Y.,2018,Adventitious bud induction and plant regeneration of detached leaves from Primulina lutea,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(1):211-216(闫海霞,关世凯,邓杰玲,何荆洲,黄昌艳,卜朝阳,2018,黄花牛耳朵离体叶片不定芽的诱导及植株再生,分子植物育种,16(1):211-216)
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Young M.D.,Wakefield M.J.,Smyth G.K.,and Oshlack A.,2010,Gene ontology analysis for RNA-seq:accounting for selection bias,Genome Biol.,11(2):14
Zhang L.,Yan H.F.,Wu W.,Yu H.,and Ge X.J.,2013,Comparative transcriptome analysis and marker development of two closely related primrose species(Primula poissonii,and Primula wilsonii),BMC Genomics,14(1):329
Zhang X.L.,Yang L.H.,and Kang M.,2017,Post-pollination reproductive isolation of sympatric populations of Primulina eburnea and P.mabaensis(Gesneriaceae),Shengwu Duoyangxing(Biodiversity Science),25(6):615-620(张小龙,杨丽华,康明,2017,牛耳朵和马坝报春苣苔同域种群授粉后的生殖隔离,生物多样性,25(6):615-620)
Zheng B.X.,Xu Q.Q.,and Shen Y.P.,2002,The relationship between climate change and quaternary glacial cycles on the Qinghai-Tibetan Plateau:review and speculation,Quaternary International,97(1):93-101
Blanc G.,and Wolfe K.H.,2004,Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes,Plant Cell,16(7):1667-1678
Chen Q.,Tang H.R.,Dong X.L.,Hou Y.X.,Luo Y.,Jiang Y.,and Huang Q.Y.,2009,Progress in the study of plant Myb transcription factors,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),28(2):365-372(陈清,汤浩茹,董晓莉,侯艳霞,罗娅,蒋艳,黄琼瑶,2009,植物Myb转录因子的研究进展,基因组学与应用生物学,28(2):365-372)
Chen W.J.,Wen Y.X.,Chen Y.Y.,Huang Y.L.,and Li D.P.,2010,Phenylethanoid glycosides and their cytotoxicity of Chirita eburnea Hance,Zhongchengyao(Chinese Traditional Patent Medicine),32(6):1000-1003(陈文娟,文永新,陈月圆,黄永林,李典鹏,2010,牛耳朵苯乙醇苷类化学成分及其细胞毒活性研究,中成药,32(6):1000-1003)
Cowan I.R.,1977,Stomatal behavior and environment,Advances in Botanical Research,190:117-228
Gao Y.,Tian L.,and Qin S.,2008,Positive selection in plant evolution,Zhuwu Xuebao(Chinese Bulletin of Botany),25(4):401-406(高远,田李,秦松,2008,植物进化中的正选择作用,植物学报,25(4):401-406)
Grabherr M.G.,Haas B.J.,Yassour M.,Levin J.Z.,Thompson D.A.,Amit I.,Adiconis X.,Fan L.,Raychowdhury R.,Zeng Q.,Chen Z.,Mauceli E.,Hacohen N.,Gnirke A.,Rhind N.,di Palma F.,Birren B.W.,Nusbaum C.,Lindblad-Toh K.,Friedman N.,and Regev A.,2011,Full-length transcriptome assembly from RNA-Seq data without a reference genome,Nat.Biotechnol.,29(7):644-652
Graur D.,and Li W.H.,eds.,2000,Fundamentals of molecular evolution(2nd ed.),Sinauer Associates Inc.,Sunderland,M.A.,pp.100-200
Gusinde M.,Matus J.T.,Francia P.,Rusconi F.,Ca觡ón P.,Medina C.,Conti L.,Cominelli E.,Tonelli C.,and Arce-Johnson P.,2011,T he grapevine guard cell-related vvmyb60 transcription factor is involved in the regulation of stomatal activity and is differentially expressed in response to ABAand osmotic stress,BMC Plant Biol.,11(1):142
Jia Y.,Liu M.L.,Yue M.,Zhao Z.,Zhao G.F.,and Li Z.H.,2017,Comparative transcriptome analysis reveals adaptive evolution of Notopterygium incisum and Notopterygium franchetii,two high-alpine herbal species endemic to china,Molecules,22(7):1158
Kane N.C.,Barker M.S.,Zhan S.H.,and Rieseberg L.H.,2011,Molecular evolution across the Asteraceae.micro-and macroevolutionary processes,Mol.Biol.Evol.,28(12):3225-3235
Kanehisa M.,Araki M.,Goto S.,Hattori M.,Hirakawa M.,Itoh M.,Katayama T.,Kawashima S.,Okuda S.,Tokimatsu T.,and Yamanishi Y.,2008,KEGG for linking genomes to life and the environment,Nucleic Acids Res.,36(D):480-484
Koch M.A.,Haubold B.,and Mitchell-Olds T.,2000,Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis,Arabis,and related genera(Brassicaceae),Mol.Biol.Evol.,17(10):1483-1498
Li L.,Stoeckert C.J.,and Roos D.S.,2003,OrthoMCL:identification of ortholog groups for eukaryotic genomes,Genome Res.,13(9):2178-2189
Liu Y.,and Wei Y.G.,2004,Chirita lutea a new species of Gesneriaceae from Guangxi,China,Zhiwu Kexue Xuebao(Journal of Wuhan Botanical Research),22(5):391-393(刘演,韦毅刚,2004,中国广西唇柱苣苔属(苦苣苔科)一新种-黄花牛耳朵,植物科学学报,22(5):391-393)
Lynch M.,and Conery J.S.,2000,The evolutionary fate and consequences of duplicate genes,Science,290(5494):1151-1155
Ning Y.S.,Wang G.L.,and Xie Q.,2011,E3 ubiquitin ligase-mediated drought responses in plants,Zhiwu Xuebao(Bulletin of Botany),46(6):606-616(宁约瑟,王国梁,谢旗,2011,泛素连接酶e3介导的植物干旱胁迫反应,植物学报,46(6):606-616)
Qi Y.,Xu Z.S.,Li P.S.,Chen M.,Li L.C.,and Ma Y.Z.,2013,Research progress on molecular mechanism and application of HSP70 in plants,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),14(3):507-511(齐妍,徐兆师,李盼松,陈明,李连城,马有志,2013,植物热激蛋白70的分子作用机理及其利用研究进展,植物遗传资源学报,14(3):507-511)
Qin Y.,Wang M.,Tian Y.,He W.,Han L.,and Xia G.,2012,Over-expression of TaMYB33 encoding a novel wheat M-YB transcription factor increases salt and drought tolerance in Arabidopsis,Mol.Biol.Rep.,39(6):7183-7192
Rogel M.R.,Jaitovich A.,and Ridge K.M.,2010,The role of the ubiquitin proteasome pathway in keratin intermediate filament protein degradation,Proc.Am.Thorac.Soc.,7(1):71-76
Sang Y.,Yan F.,and Ren X.,2015,The role and mechanism of crl4 e3 ubiquitin ligase in cancer and its potential therapy implications,Oncotarget,6(40):42590-42602
Shan H.,Chen S.,Jiang J.,Chen F.,Chen Y.,Gu C.,Li P.,Song A.,Zhu X.,Gao H.,Zhou G.,Li T.,and Yang X.,2012,H-eterologous expression of the chrysanthemum R2R3-MYBtranscription factor Cm MYB2 enhances drought and salinity tolerance,increases hypersensitivity to ABA and delays flowering in Arabidopsis thaliana,Mol.Biotechnol.,51(2):160-173
Shang F.,and Taylor A.,2012,Roles for the ubiquitin-proteasome pathway in protein quality control and signaling in the retina.implications in the pathogenesis of age-related macular degeneration,Mol.Aspects Med.,33(4):446-466
Tang N.,and Chen X.B.,2014,Research of MYB transcription factors in plant and abiotic stress response,Shengwuxue Z-azhi(Journal of Biology),31(3):74-78(唐宁,陈信波,2014,植物MYB转录因子与非生物胁迫响应研究,生物学杂志,31(3):74-78)
Tang S.C.,Pu G.Z.,Pan Y.M.,Zou R.,and Wei C.Q.,2009,Pol lination biology of Chirita lutea in China(Gesneriaceae),R-edai Yaredai Zhiwu Xuebao(Journal of Tropical and Subtropical Botany),17(4):328-333(唐赛春,蒲高忠,潘玉梅,邹蓉,韦春强,2009,黄花牛耳朵(苦苣苔科)的传粉生物学,热带亚热带植物学报,17(4):328-333)
Wang M.Q.,and Zhang D.Y.,2015,Research advance of heat shock protein 70 gene family and its biological functions in plant,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(2):421-428(王明强,张道远,2015,植物热激蛋白70基因家族及其生物学功能研究进展,基因组学与应用生物学,34(2):421-428)
Wang X.Q.,Bai Z.F.,Liu Y.,and Xiao P.G.,2011,Microscopic and chemical identification of Chirita eburnean and Chirita lutea,Zhongguo Shiyan Fangjixue Zazhi(Chinese Journal of Experimental Traditional Medical Formulae),(14):99-101(王晓琴,白贞芳,刘勇,肖培根,2011,牛耳朵和黄花牛耳朵的显微和化学鉴别,中国实验方剂学杂志,(14):99-101)
Wang Y.,and Hey J.,2010,Estimating divergence parameters with small samples from a large number of loci,Genetics,184(2):363-379
Wen F.,2008,Studies on investigation and introduction of wild ornamental resources of Gesneriaceae in Guangxi,Dissertation for Ph.D.,Beijing Forestry University,Supervisor:Zhang Q.X.,pp.1-18(温放,2008,广西苦苣苔科观赏植物资源调查与引种研究,博士学位论文,北京林业大学,导师:张启翔,pp.1-18)
Wu G.,2011,The mechanism of typical plants adaptative to calcium rich environment in karst area of southwest China,Dissertation for Ph.D.,Huazhong University of Science and Technology,Supervisors:Yu L.J.,and Li M.T.,pp.453-454(吴耿,2011,西南岩溶地区典型植物适应岩溶高钙环境的机制,博士学位论文,华中科技大学,导师:余龙江,栗茂腾,pp.453-454)
Xu K.H.,Zhang Y.T.,Zhang Y.,Wang B.,Wang F.W.,and Li H.Y.,2018,Research advances on the F-box gene family in plants,Shengwu Jishu Tongbao(Biotechnology Bulletin),34(1):26-32(许克恒,张云彤,张莹,王彬,王法微,李海燕,2018,植物F-box基因家族的研究进展,生物技术通报,34(1):26-32)
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