木薯中开花相关miRNA对phasiRNA的调控
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摘要
木薯是一种重要的能源和淀粉作物。为探索木薯开花相关miRNAs对phasiRNA的调控,揭示此类phasiRNA在开花过程中的功能。本研究利用RNA-seq技术对木薯品种"华南八号"花序和幼叶进行转录组和s RNA测序分析,筛选出11类开花相关的miRNAs及其对应的PHAS位点序列,表达分析发现开花相关miRNA与其对应的PHAS位点基因表达水平存在一定差异。结果表明木薯开花相关miRNAs在对phasiRNA的调控过程中,不但直接影响了开花,还广泛参与了木薯其它生长发育过程。本研究为木薯开花调控机制的后续深入探索提供依据,并有助于解决海南以外主产区木薯无法正常开花结实并进行杂交育种的问题。
Cassava(Manihot esculenta Crantz) is an important energy and starch crop. To explore the regulation of phasiRNA by miRNA related to flowering in cassava, and to reveal the function of these phasiRNA during flowering process. In this study, a strategy using RNA-seq was performed for transcriptome and s RNA sequencing and data analysis with "SC8" inflorescence and young leaf as material, then the 11 flowering-related miRNAs and their corresponding PHAS loci sequences were screened. Expression analysis showed that miRNAs related to flowering and their corresponding PHAS loci genes expressed differentially. This results showed miRNAs related to flowering not only affect the bloom, but also widely participate in other growth and development processes in cassava. This study provided foundation for further research of cassava flowering regulation mechanism, and also contributed to solving the question that cassava could not flower and fruit for crossbreeding in the main production area except for Hainan province.
Cassava(Manihot esculenta Crantz) is an important energy and starch crop. To explore the regulation of phasiRNA by miRNA related to flowering in cassava, and to reveal the function of these phasiRNA during flowering process. In this study, a strategy using RNA-seq was performed for transcriptome and s RNA sequencing and data analysis with "SC8" inflorescence and young leaf as material, then the 11 flowering-related miRNAs and their corresponding PHAS loci sequences were screened. Expression analysis showed that miRNAs related to flowering and their corresponding PHAS loci genes expressed differentially. This results showed miRNAs related to flowering not only affect the bloom, but also widely participate in other growth and development processes in cassava. This study provided foundation for further research of cassava flowering regulation mechanism, and also contributed to solving the question that cassava could not flower and fruit for crossbreeding in the main production area except for Hainan province.
引文
Arikit S.,Xia R.,Kakrana A.,Huang K.,Zhai J.X.,Yan Z.,Vald-és-López O.,Prince S.,Musket T.A.,Nguyen H.T.,Stacey G.,and Meyers B.C.,2014,An atlas of soybean small RNAs identifies phased si RNAs from hundreds of coding genes,Plant Cell,26(12):4584-4601
Borges F.,and Martienssen R.A.,2015,The expanding world of small RNAs in plants,Nat.Rev.Mol.Cell Biol.,16:727-741
Cartolano M.,Castillo R.,Efremova N.,Kuckenberg M.,Zethof J.,Gerats T.,Schwarz-Sommer Z.,and Vandenbussche M.,2007,A conserved microRNA module exerts homeotic control over Petunia hybrid and Antirrhinum majus floral organ identity,Nat.Genet.,39(7):901-905
Chapman E.J.,and Estelle M.,2009,Mechanism of auxin-regulated gene expression in plants,Annu.Rev.Genet.,43(1):265-285
Chen H.M.,Chen L.T.,Patel K.,Li Y.H.,Baulcombe D.C.,and Wu S.H.,2010,22-nucleotide RNAs trigger secondary si R-NA biogenesis in plants,Proc.Natl.Acad.Sci.USA,107(34):15269-15274
Cheng Y.,Xu Y.,Pan X.Q.,Feng Y.,and Li Y.Z.,2017,Activities of related enzymes associated with high starch accumulation in cassava tuberous roots,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(1):376-381(程艳娥,徐勇,潘晓芹,冯燕,李有志,2017,木薯块根淀粉高累积的相关酶的活性特征,基因组学与应用生物学,36(1):376-381)
Crawford B.C.W.,Nath U.,Carpenter R.,and Coen E.S.,2004,CINNCINNATA controls both cell differentiation and growth in petal lobes and leaves of Antirrhinum,Plant Physiol.,135(1):244-253
Ding A.M.,Qu X.,Li L.,and Sun Y.H.,2014,The progress of PPR protein family in plants,Zhongguo Nongxue Tongbao(Chinese Agricultural Science Bulletin),30(9):218-224(丁安明,屈旭,李凌,孙玉合,2014,植物PPR蛋白家族研究进展,中国农学通报,30(9):218-224)
Efroni I.,Blum E.,Goldshmidt A.,and Eshed Y.,2008,A protracted and dynamic maturation schedule underlies Arabidopsis leaf development,Plant Cell,20(9):2293-2306
Fan Y.R.,Yang J.Y.,Mathioni S.M.,Yu J.S.,Shen J.Q.,Yang X.F.,Wang L.,Zhang Q.H.,Cai Z.X.,Xu C.G.,Li X.H.,Xiao J.H.,Meyers B.C.,and Zhang Q.F.,2016,PMS1T,producing phased small-interfering RNAs,regulates photoperiodsensitive male sterility in rice,Proc.Natl.Acad.Sci.USA,113(52):15144-15149
Gou J.Y.,Felippes F.F.,Liu C.J.,Weigel D.,and Wang J.W.,2011,Negative regulation of anthocyanin biosynthesis in Arabidopsis by mi R156-targeted SPL transcription factor,Plant Cell,23(4):1512-1522
Hsieh L.C.,Lin S.I.,Shih A.C.C.,Chen J.W.,Lin W.Y.,Tseng C.Y.,Li W.H.,and Chiou T.J.,2009,Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing,Plant Physiol.,151(4):2120-2132
Huang H.,and Xu Q.J.,2012,Progress in research of MicroRNAregulation on angiosperm flower development,Zhiwu Shengli Xuebao(Plant Physiology Journal),48(10):929-940(黄赫,徐启江,2012,MicroRNA调控被子植物花发育的研究进展,植物生理学报,48(10):929-940)
Huang T.,López-Giráldez F.,Townsend J.P.,and Irish V.F.,2012,RBE controls microRNA164 expression to effect floral organogenesis,Development,139(12):2161-2169
Husbands A.Y.,Chitwood D.H.,Plavskin Y.,and Timmermans M.C.P.,2009,Signals and prepatterns:new insights into organ polarity in plants,Genes Dev.,23(17):1986-1997
Khatabi B.,Arikit S.,Xia R.,Winter S.,Oumar D.,Mongomake K.,Meyers B.C.,and Fondong V.N.,2016,High-resolution identification and abundance profiling of cassava(Manihot esculenta Crantz)microRNAs,BMC Genomics,17(1):85
Kim J.,Jung J.H.,Reyes J.L.,Kim Y.S.,Kim S.Y.,Chung K.S.,Kim J.A.,Lee M.,Lee Y.,Kim V.N.,Chua N.H.,and Park C.M.,2005,microRNA-directed cleavage of ATHB15 m R-NA regulates vascular development in Arabidopsis in florescence stems,Plant J.,42(1):84-94
Lauter N.,Kampani A.,Carlson S.,Goebel M.,and Moose S.P.,2005,microRNA172 down-regulates glossy15 to promote vegetative phase change in maize,Proc.Natl.Acad.Sci.U-SA,102(26):9412-9417
Luo D.,Carpenter R.,Copsey L.,Vincent C.,and Coen E.,1999,Control of organ asymmetry in flowers of Antirrhinum,Cell,99(4):367-376
Mallory A.C.,Bartel D.P.,and Bartel B.,2005,microRNA-directed regulation of Arabidopsis AUXIN RESPONSE FAC-TOR17 is essential for proper development and modulates expression of early auxin response genes,Plant Cell,17(3):1360-1375
Mallory A.C.,Reinhart B.J.,Jones-Rhoades M.W.,Tang G.L.,Zamore P.D.,Barton M.K.,and Barte D.P.,2004,microR-NA control of PHABULOSA in leaf development:importance of pairing to the microRNA 5'region,EMBO J.,23(16):3356-3364
Millar A.A.,and Gubler F.,2005,The Arabidopsis GAMYB-like genes,MYB33 and MYB65,are microRNA-regulated genes that redundantly facilitate anther development,Plant Cell,17(3):705-721
Mockaitis K.,and Estelle M.,2008,Auxin receptors and plant development:a new signaling paradigm,Annu.Rev.Cell Dev.Biol.,24(24):55-80
Prochnik S.,Marri P.R.,Desany B.,Rabinowicz P.D.,Kodira C.,Mohiuddin M.,Rodriguez F.,Fauquet C.,Tohme J.,Harkins T.,Rokhsar D.S.,and Rounsley S.,2012,The cassava genome:current progress,future directions,Trop Plant Biol.,5(1):88-94
Quintero A.,Pérez-Quintero A.L.,and López C.,2013,Identification of ta-siRNAs and cis-nat-siRNAs in cassava and their roles in response to cassava bacterial blight,Genom.Proteom.Bioinf.,11(3):172-181
Jun Y.,Gu Y.Y.,Jia X.Y.,Kang W.J.,Pan S.J.,Tang X.Q.,Chen X.M.,and Tang G.L.,2012,Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis,Plant Cell,24(2):415-427
Wu F.,Chen Y.,Tian X.,Zhu X.,and Jin W.,2017,Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum,Sci.Rep.,7(1):3019
Wu G.,Park M.Y.,Conway S.R.,Wang J.W.,Weigel D.,and Poethig R.S.,2009,The sequential action of mi R156 and mi R-172 regulates developmental timing in Arabidopsis,Cell,138(4):750-759
Wu G.,and Poethig R.S.,2006,Temporal regulation of shoot development in Arabidopsis thaliana by mi R156 and its target SPL3,Development,133(18):3539-3547
Wu M.F.,Tian Q.,and Reed J.W.,2006,Arabidopsis microRNA-167 controls patterns of ARF6 and ARF8 expression,and regulates both female and male reproduction,Development,133(21):4211-4218
Xia J.,Zeng C.,Chen Z.,Zhang K.,Chen X.,Zhou Y.,Song S.,Lu C.,Yang R.,Yang Z.,Zhou J.,Peng H.,Wang W.,Peng M.,and Zhang W.,2014,Endogenous small-noncoding R-NAs and their roles in chilling response and stress acclimation in cassava,BMC Genomics,15(1):634
Yang L.,Xu M.,Koo Y.,He J.,and Poethig R.S.,2013,Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of mi R156A and mi R156C,E-life,2(2):e00260
Zhai J.,Jeong D.H.,De P.E.,Park S.,Rosen B.D.,Li Y.,González A.J.,Yan Z.,Kitto S.L.,Grusak M.A.,Jackson S.A.,Stacey G.,Cook D.R.,Green P.J.,Sherrier D.J.,and Meyers B.C.,2011,microRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased,trans-acting si RNAs,Genes Dev.,25(23):2540-2553
Zhang C.,Li G.,Wang J.,and Fang J.,2012,Identification of trans-acting si RNAs and their regulatory cascades in grapevine,Bioinformatics,28(20):2561-2568
Zhang C.,Li G.,Zhu S.,Zhang S.,and Fang J.,2014,tasiRNAdb:a database of ta-siRNA regulatory pathways,Bioinformatics,30(7):1045-1046
Zheng Y.,Wang Y.,Wu J.,Ding B.,and Fei Z.,2015,A dynamic evolutionary and functional landscape of plant phased small interfering RNAs,BMC Biol.,13(1):32
Borges F.,and Martienssen R.A.,2015,The expanding world of small RNAs in plants,Nat.Rev.Mol.Cell Biol.,16:727-741
Cartolano M.,Castillo R.,Efremova N.,Kuckenberg M.,Zethof J.,Gerats T.,Schwarz-Sommer Z.,and Vandenbussche M.,2007,A conserved microRNA module exerts homeotic control over Petunia hybrid and Antirrhinum majus floral organ identity,Nat.Genet.,39(7):901-905
Chapman E.J.,and Estelle M.,2009,Mechanism of auxin-regulated gene expression in plants,Annu.Rev.Genet.,43(1):265-285
Chen H.M.,Chen L.T.,Patel K.,Li Y.H.,Baulcombe D.C.,and Wu S.H.,2010,22-nucleotide RNAs trigger secondary si R-NA biogenesis in plants,Proc.Natl.Acad.Sci.USA,107(34):15269-15274
Cheng Y.,Xu Y.,Pan X.Q.,Feng Y.,and Li Y.Z.,2017,Activities of related enzymes associated with high starch accumulation in cassava tuberous roots,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(1):376-381(程艳娥,徐勇,潘晓芹,冯燕,李有志,2017,木薯块根淀粉高累积的相关酶的活性特征,基因组学与应用生物学,36(1):376-381)
Crawford B.C.W.,Nath U.,Carpenter R.,and Coen E.S.,2004,CINNCINNATA controls both cell differentiation and growth in petal lobes and leaves of Antirrhinum,Plant Physiol.,135(1):244-253
Ding A.M.,Qu X.,Li L.,and Sun Y.H.,2014,The progress of PPR protein family in plants,Zhongguo Nongxue Tongbao(Chinese Agricultural Science Bulletin),30(9):218-224(丁安明,屈旭,李凌,孙玉合,2014,植物PPR蛋白家族研究进展,中国农学通报,30(9):218-224)
Efroni I.,Blum E.,Goldshmidt A.,and Eshed Y.,2008,A protracted and dynamic maturation schedule underlies Arabidopsis leaf development,Plant Cell,20(9):2293-2306
Fan Y.R.,Yang J.Y.,Mathioni S.M.,Yu J.S.,Shen J.Q.,Yang X.F.,Wang L.,Zhang Q.H.,Cai Z.X.,Xu C.G.,Li X.H.,Xiao J.H.,Meyers B.C.,and Zhang Q.F.,2016,PMS1T,producing phased small-interfering RNAs,regulates photoperiodsensitive male sterility in rice,Proc.Natl.Acad.Sci.USA,113(52):15144-15149
Gou J.Y.,Felippes F.F.,Liu C.J.,Weigel D.,and Wang J.W.,2011,Negative regulation of anthocyanin biosynthesis in Arabidopsis by mi R156-targeted SPL transcription factor,Plant Cell,23(4):1512-1522
Hsieh L.C.,Lin S.I.,Shih A.C.C.,Chen J.W.,Lin W.Y.,Tseng C.Y.,Li W.H.,and Chiou T.J.,2009,Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing,Plant Physiol.,151(4):2120-2132
Huang H.,and Xu Q.J.,2012,Progress in research of MicroRNAregulation on angiosperm flower development,Zhiwu Shengli Xuebao(Plant Physiology Journal),48(10):929-940(黄赫,徐启江,2012,MicroRNA调控被子植物花发育的研究进展,植物生理学报,48(10):929-940)
Huang T.,López-Giráldez F.,Townsend J.P.,and Irish V.F.,2012,RBE controls microRNA164 expression to effect floral organogenesis,Development,139(12):2161-2169
Husbands A.Y.,Chitwood D.H.,Plavskin Y.,and Timmermans M.C.P.,2009,Signals and prepatterns:new insights into organ polarity in plants,Genes Dev.,23(17):1986-1997
Khatabi B.,Arikit S.,Xia R.,Winter S.,Oumar D.,Mongomake K.,Meyers B.C.,and Fondong V.N.,2016,High-resolution identification and abundance profiling of cassava(Manihot esculenta Crantz)microRNAs,BMC Genomics,17(1):85
Kim J.,Jung J.H.,Reyes J.L.,Kim Y.S.,Kim S.Y.,Chung K.S.,Kim J.A.,Lee M.,Lee Y.,Kim V.N.,Chua N.H.,and Park C.M.,2005,microRNA-directed cleavage of ATHB15 m R-NA regulates vascular development in Arabidopsis in florescence stems,Plant J.,42(1):84-94
Lauter N.,Kampani A.,Carlson S.,Goebel M.,and Moose S.P.,2005,microRNA172 down-regulates glossy15 to promote vegetative phase change in maize,Proc.Natl.Acad.Sci.U-SA,102(26):9412-9417
Luo D.,Carpenter R.,Copsey L.,Vincent C.,and Coen E.,1999,Control of organ asymmetry in flowers of Antirrhinum,Cell,99(4):367-376
Mallory A.C.,Bartel D.P.,and Bartel B.,2005,microRNA-directed regulation of Arabidopsis AUXIN RESPONSE FAC-TOR17 is essential for proper development and modulates expression of early auxin response genes,Plant Cell,17(3):1360-1375
Mallory A.C.,Reinhart B.J.,Jones-Rhoades M.W.,Tang G.L.,Zamore P.D.,Barton M.K.,and Barte D.P.,2004,microR-NA control of PHABULOSA in leaf development:importance of pairing to the microRNA 5'region,EMBO J.,23(16):3356-3364
Millar A.A.,and Gubler F.,2005,The Arabidopsis GAMYB-like genes,MYB33 and MYB65,are microRNA-regulated genes that redundantly facilitate anther development,Plant Cell,17(3):705-721
Mockaitis K.,and Estelle M.,2008,Auxin receptors and plant development:a new signaling paradigm,Annu.Rev.Cell Dev.Biol.,24(24):55-80
Prochnik S.,Marri P.R.,Desany B.,Rabinowicz P.D.,Kodira C.,Mohiuddin M.,Rodriguez F.,Fauquet C.,Tohme J.,Harkins T.,Rokhsar D.S.,and Rounsley S.,2012,The cassava genome:current progress,future directions,Trop Plant Biol.,5(1):88-94
Quintero A.,Pérez-Quintero A.L.,and López C.,2013,Identification of ta-siRNAs and cis-nat-siRNAs in cassava and their roles in response to cassava bacterial blight,Genom.Proteom.Bioinf.,11(3):172-181
Jun Y.,Gu Y.Y.,Jia X.Y.,Kang W.J.,Pan S.J.,Tang X.Q.,Chen X.M.,and Tang G.L.,2012,Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis,Plant Cell,24(2):415-427
Wu F.,Chen Y.,Tian X.,Zhu X.,and Jin W.,2017,Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum,Sci.Rep.,7(1):3019
Wu G.,Park M.Y.,Conway S.R.,Wang J.W.,Weigel D.,and Poethig R.S.,2009,The sequential action of mi R156 and mi R-172 regulates developmental timing in Arabidopsis,Cell,138(4):750-759
Wu G.,and Poethig R.S.,2006,Temporal regulation of shoot development in Arabidopsis thaliana by mi R156 and its target SPL3,Development,133(18):3539-3547
Wu M.F.,Tian Q.,and Reed J.W.,2006,Arabidopsis microRNA-167 controls patterns of ARF6 and ARF8 expression,and regulates both female and male reproduction,Development,133(21):4211-4218
Xia J.,Zeng C.,Chen Z.,Zhang K.,Chen X.,Zhou Y.,Song S.,Lu C.,Yang R.,Yang Z.,Zhou J.,Peng H.,Wang W.,Peng M.,and Zhang W.,2014,Endogenous small-noncoding R-NAs and their roles in chilling response and stress acclimation in cassava,BMC Genomics,15(1):634
Yang L.,Xu M.,Koo Y.,He J.,and Poethig R.S.,2013,Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of mi R156A and mi R156C,E-life,2(2):e00260
Zhai J.,Jeong D.H.,De P.E.,Park S.,Rosen B.D.,Li Y.,González A.J.,Yan Z.,Kitto S.L.,Grusak M.A.,Jackson S.A.,Stacey G.,Cook D.R.,Green P.J.,Sherrier D.J.,and Meyers B.C.,2011,microRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased,trans-acting si RNAs,Genes Dev.,25(23):2540-2553
Zhang C.,Li G.,Wang J.,and Fang J.,2012,Identification of trans-acting si RNAs and their regulatory cascades in grapevine,Bioinformatics,28(20):2561-2568
Zhang C.,Li G.,Zhu S.,Zhang S.,and Fang J.,2014,tasiRNAdb:a database of ta-siRNA regulatory pathways,Bioinformatics,30(7):1045-1046
Zheng Y.,Wang Y.,Wu J.,Ding B.,and Fei Z.,2015,A dynamic evolutionary and functional landscape of plant phased small interfering RNAs,BMC Biol.,13(1):32