不同光暗周期下野牛草相连克隆分株间生物节律同步化研究
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摘要
生物钟作为植物的内源性调节机制，驱动植物体的生命活动与昼夜交替相互协调，维持近24h的节律性振荡，进而增强其适应性和生存能力。因此，生物钟的生理与分子调控机制成为近年来的研究热点之一。野牛草（Buchloe dactyloides (Nutt.)Engelm.）作为匍匐茎型克隆植物，其相连克隆分株间通过节间子连接，实现水分，矿质元素及光合产物的传递和共享。本文在研究不同光暗周期下野牛草分株活性氧清除系统及内源激素日变化规律的基础上，通过转录组测序鉴定了野牛草的节律表达基因，并从转录水平解析其表达模式，最终明确不同光暗周期下野牛草相连克隆分株间节律协调机制。主要结论如下：
(1)野牛草植株活性氧清除系统活性和内源激素含量都具有节律性变化规律，野牛草相连分株在不同光暗周期下其活性氧清除系统的节律性变化与内源激素含量的节律性变化均趋于同步。本研究以野牛草分株为材料，在光/暗周期（12h光照/12h黑暗）和暗/光暗周期（12h黑暗/12h光照）条件下，野牛草断开分株中超氧化物歧化酶（SOD），过氧化物酶（POD），过氧化氢酶（CAT），抗坏血酸过氧化物酶（APX）的活性以及丙二醛（MDA）的含量节律性变化趋势基本相反，而野牛草相连分株中SOD，POD，CAT，APX活性以及MDA含量的节律性变化趋于同步；同时，在上述两种光照条件下，野牛草断开分株中生长素(IAA)、赤霉素(GA)、脱落酸(ABA)、玉米素核苷(ZR)含量的节律性变化趋势基本相反，野牛草相连分株在不同光暗周期下的IAA、GA、ABA、及ZR含量的节律性变化趋于同步。
(2)从野牛草日变化转录组中鉴定了121个节律转录本，分别代表已知的16个节律基因。本研究对一个光/暗周期内（ZT0至ZT0′，4h间隔）的7份野牛草植株样本进行转录组测序，得到平均约5G的高质量数据。通过对7份转录组数据进行从头拼接（De novo），共组装产生196,010条转录本，转录本的平均长度和N50分别为1302bp和2116bp。野牛草转录组与公共蛋白数据BLASTx显示，分别有129,554（66.1％），93,386（47.6％），40,904（20.87％）和50,592（25.81％）条转录本分别注释到Nr，Swiss-Prot，GO和COG蛋白数据库，且GO分类表明绝大多数转录本与结合功能、代谢过程、催化活性等功能相关；KEGG分析显示，共有127818（65.2%）条转录本参与到127条不同的代谢通路，其中起重要调控作用的信号通路为氧化磷酸化，糖酵解/糖异生，植物激素信号转导等；将野牛草转录组数据与拟南芥TAIR数据库比对，共有25,881（13.2%）条转录本与拟南芥基因相似，其中包括121个节律转录本，分别代表了CCA1（生物钟相关蛋白1），LHY（晚期下胚轴蛋白），GI（GIGANTEA），ZTL（Zeitlupe），PHYA（光敏色素A），PHYB（光敏色素B），CRY2（隐花色素2），COP1（光形态建成蛋白1），CHS（查尔酮合成酶）；PIF3（光敏色素互作因子3），HY5（下胚轴伸长蛋白5），CDF1（Cycling dof factor1），UVR8（紫外线B受体蛋白8），PAP1（光敏色素关联蛋白1），CKIIα（酪蛋白激酶2α多肽）和CKIIβ（酪蛋白激酶2β多肽）等16个节律基因。
(3)野牛草节律转录本的表达呈现节律性变化，野牛草相连分株在不同光暗周期下节律转录本的节律性表达存在同步化趋势。利用qRT-PCR对不同的处理条件下（16h光照/8h黑暗，8h光照/16h黑暗，24h光照，24h黑暗，以及盐，干旱，冷，热等）51份野牛草样品中的10个候选内参基因的表达量进行了分析，对内参基因的表达稳定性分析（GeNorm，NormFinder和Bestkeeper）表明，β-ACT，DNAJ和PP2A是不同光暗周期下野牛草样品中表达最稳定的内参基因，而GAPDH，β-ACTIN，DNAJ和PP2A是不同逆境条件下最合适的内参基因；根据野牛草转录组测序结果，选取节律转录本CCA1，LHY，GI，PHYA，CKIIα，CKIIβ等，利用qRT-PCR对RNA-seq中这几个转录本的表达量进行验证，结果发现，6个节律转录本的qRT-PCR数据和RNA-seq结果基本吻合，且各自呈现不同趋势的节律性变化，只是在表达量上略有差异。其中，LHY与CCA1的表达呈现近余弦的变化趋势，两个调节基因CKIIα/β的表达呈现近正弦的变化趋势，GI的表达也呈现近正弦的变化趋势，PHYA的表达呈现“倒V形”的变化趋势。此外，野牛草断开分株中HY5的表达在光/暗周期下呈现节律性变化，而其在暗/光暗周期下的表达呈现紊乱模式，同时，野牛草相连分株中HY5在不同光暗周期下其节律性表达趋于同步。
综上所述，野牛草植株活性氧清除系统的活性变化、内源激素的含量变化以及节律转录本的表达都具有节律性，野牛草相连克隆分株活性氧清除系统的节律性变化、内源激素含量的节律性变化与节律转录本的节律性表达在不同光暗周期下有同步化的趋势。
As an endogenous regulatory mechanisms of plants, circadian clock coordinatesday-nightcycle and life activities of plants to maintain nearly24h rhythmic oscillation, thus enhancing itsadaptability and survivability. Thus, physiological and molecular mechanisms of the circadianclock become one of the research focus in recent years. As stolon clonal plants, Buchloedactyloides (Nutt.) Engelm. connected ramets, which is connected by setsuko, sharing andtransmitting water, mineral elements and photosynthetic products. In this paper, Buchloedactyloides (Nutt.) Engelm. ramets were used as the experiment material, diurnal variation ofreactive oxygen scavenging system and endogenous hormones of Buchloe dactyloides (Nutt.)Engelm. were tested under differences photoperiod,based on the transcriptome sequencingofBuchloe dactyloides (Nutt.) Engelm., the circadian rhythm transcripts were identified, andexpression patterns of circadian rhythm transcripts were tested, finally, coordinationmechanisms between Buchloe dactyloides (Nutt.) Engelm. connected ramets under differencephotoperiod. The main conclusions are as follows:
(1) Reactive oxygen species scavenging system activity and endogenous hormone contentof Buchloe dactyloides (Nutt.) Engelm. both have a circadian rhythm variation, and reactiveoxygen species scavenging system activity and endogenous hormone content of Buchloedactyloides (Nutt.) Engelm.connected ramets tend to synchronize under differencesphotoperiod. In this study, superoxide superoxide dismutase (SOD), peroxidase (POD),catalase (CAT), ascorbate peroxidase (APX) activity and malondialdehyde (MDA) contentinBuchloe dactyloides (Nutt.) Engelm. disconnected ramets had a opposite variation trend inthe light/dark cycle (12h light/12h dark) and dark/light cycle (12h dark/12h light) conditions,however, varation of SOD, POD, CAT, APX activity and MDA content inBuchloe dactyloides(Nutt.) Engelm.connected ramets tend to synchronize; In addition, auxin (IAA), gibberellic acid (GA), abscisic acid (ABA), zeatin nuclear glycosides (ZR) content changes of Buchloedactyloides (Nutt.) Engelm. have a circadian rhythm variation, and IAA, GA, ABA, ZR contentchanges of Buchloe dactyloides (Nutt.) Engelm. connected ramets tend to synchronize underdifferences photoperiods.
(2)121transcripts were identified from Buchloe dactyloides (Nutt.) Engelm. circadianrhythm transcriptome, which represented16known circadian rhythm genes. In this study,seven samples of Buchloe dactyloides (Nutt.) Engelm. transcriptome in a light/dark cycle (ZT0to ZT0',4h interval) were sequencing, and a high-quality data was obtainedwith an average ofabout5G.7transcriptomesdatas were assembledde novo, and196,010transcripts wereobtained in total, the average length and N50were1302bp and2116bp, respectively.BLASTx were conducted betweenBuchloe dactyloides (Nutt.) Engelm. transcriptome andpublic protein data, there were129,554(66.1%),93,386(47.6%),40,904(20.87%) and50,592(25.81%)of the transcripts were annotated to Nr, Swiss-Prot, GO and COG proteindatabase, respectively.and GO classification indicates that majority of transcripts belong tobinding function, metabolic processes, and other functions related to the catalytic activitycategories; KEGG analysis showed a total of127,818(65.2%) of127transcripts which wasinvolved in different metabolic pathways, from which signaling pathway is important for theregulation of oxidative phosphorylation, glycolysis/gluconeogenesis, plant hormone signaltransduction; BLASTN was conducted betweenBuchloe dactyloides (Nutt.) Engelm.transcriptome and TAIR database, a total of25,881(13.2%) of the transcripts were similar withArabidopsis genes, including121circadian rhythm transcripts, representing CCA1(Circadianclock-associated protein1), LHY (Late next hypocotyl protein), GI (GIGANTEA), ZTL(Zeitlupe), PHYA (Phytochrome a), PHYB (Phytochrome B), CRY2(cryptochrome2), COP1(Constitutivelyphotomorphogenic protein1), CHS (Chalcone synthase); PIF3(Phytochromeinteracting factor3), HY5(hypocotyl elongation protein5), CDF1(Cycling dof factor1),UVR8(UV-B receptor protein8), PAP1(Phytochrome-associated protein1), CKIIα (Caseinkinase2α) and CKIIβ (Casein kinase2β) etc.16circadian rhythm genes.
(3) Buchloe dactyloides (Nutt.) Engelm. circadian rhythm transcripts showed rhythmicexpression patterns,expression levels of Buchloe dactyloides (Nutt.) Engelm. connectedrametscircadian rhythm transcripts tend to synchronize under different light/dark cycles.qRT-PCRwas used to test expression levels of ten candidate reference genes in51Buchloe dactyloides(Nutt.) Engelm. samples under different processing conditions (16h light/8h dark,8h light/16hdark,24h light,24h dark, as well as salt, drought, cold, heat, etc.).Stability of ten candidatereference genes were analyzed by three softwares(GeNorm, NormFinder and Bestkeeper). Theresults indicate that, β-ACT, DNAJ and PP2Awere the most stable reference gene underdifferent photoperiod samples, and GAPDH, β-ACTIN, DNAJ and PP2Awere the most suitableunder different stress conditions; According Buchloe dactyloides (Nutt.) Engelm.transcriptomesequencing results, the expression levels of circadian rhythm transcripts CCA1, LHY, GI, PHYA,CKIIα, CKIIβwere evaluated using qRT-PCR and RNA-seq, the result indicated that had aconsistent circadian rhythm changes of transcripts between qRT-PCR data and RNA-seq results,and each presents different variation trends, but a slight differenceson expression levels.Among them, the expression of LHY and CCA1presents a trend closed to cosine curve, and theexpression of two regulatory genes CKIIα/β rendered a nearly sinusoidal curve trend, theexpression of GI also showed a change in nearly sinusoidal trend, PHYA presents "inverted V-shaped" expression trends. In addition, HY5expression ofBuchloedactyloides (Nutt.) Engelm.disconnected ramets showed rhythmic changes in light/dark cycle, whreas its expression wasdisorder in the dark/light cycle, while the expression levels ofHY5in Buchloe dactyloides (Nutt.)Engelm.connected ramets tends to be rhythmic expression synchronic.in a different light/darkcycles.
In summary, the activity of reactive oxygen scavenging system, changesof endogenoushormone levels and expression of circdian rhythmic transcripts of Buchloe dactyloides (Nutt.)Engelm. plants have circadian rhythmic, and changes ofreactive oxygen scavenging system,changes of endogenous hormone levels and the expression levels of circadian rhythm transcripts of Buchloe dactyloides (Nutt.) Engelm. connectedramets are all synchronized underdifferent light/dark cycles.
(1)野牛草植株活性氧清除系统活性和内源激素含量都具有节律性变化规律，野牛草相连分株在不同光暗周期下其活性氧清除系统的节律性变化与内源激素含量的节律性变化均趋于同步。本研究以野牛草分株为材料，在光/暗周期（12h光照/12h黑暗）和暗/光暗周期（12h黑暗/12h光照）条件下，野牛草断开分株中超氧化物歧化酶（SOD），过氧化物酶（POD），过氧化氢酶（CAT），抗坏血酸过氧化物酶（APX）的活性以及丙二醛（MDA）的含量节律性变化趋势基本相反，而野牛草相连分株中SOD，POD，CAT，APX活性以及MDA含量的节律性变化趋于同步；同时，在上述两种光照条件下，野牛草断开分株中生长素(IAA)、赤霉素(GA)、脱落酸(ABA)、玉米素核苷(ZR)含量的节律性变化趋势基本相反，野牛草相连分株在不同光暗周期下的IAA、GA、ABA、及ZR含量的节律性变化趋于同步。
(2)从野牛草日变化转录组中鉴定了121个节律转录本，分别代表已知的16个节律基因。本研究对一个光/暗周期内（ZT0至ZT0′，4h间隔）的7份野牛草植株样本进行转录组测序，得到平均约5G的高质量数据。通过对7份转录组数据进行从头拼接（De novo），共组装产生196,010条转录本，转录本的平均长度和N50分别为1302bp和2116bp。野牛草转录组与公共蛋白数据BLASTx显示，分别有129,554（66.1％），93,386（47.6％），40,904（20.87％）和50,592（25.81％）条转录本分别注释到Nr，Swiss-Prot，GO和COG蛋白数据库，且GO分类表明绝大多数转录本与结合功能、代谢过程、催化活性等功能相关；KEGG分析显示，共有127818（65.2%）条转录本参与到127条不同的代谢通路，其中起重要调控作用的信号通路为氧化磷酸化，糖酵解/糖异生，植物激素信号转导等；将野牛草转录组数据与拟南芥TAIR数据库比对，共有25,881（13.2%）条转录本与拟南芥基因相似，其中包括121个节律转录本，分别代表了CCA1（生物钟相关蛋白1），LHY（晚期下胚轴蛋白），GI（GIGANTEA），ZTL（Zeitlupe），PHYA（光敏色素A），PHYB（光敏色素B），CRY2（隐花色素2），COP1（光形态建成蛋白1），CHS（查尔酮合成酶）；PIF3（光敏色素互作因子3），HY5（下胚轴伸长蛋白5），CDF1（Cycling dof factor1），UVR8（紫外线B受体蛋白8），PAP1（光敏色素关联蛋白1），CKIIα（酪蛋白激酶2α多肽）和CKIIβ（酪蛋白激酶2β多肽）等16个节律基因。
(3)野牛草节律转录本的表达呈现节律性变化，野牛草相连分株在不同光暗周期下节律转录本的节律性表达存在同步化趋势。利用qRT-PCR对不同的处理条件下（16h光照/8h黑暗，8h光照/16h黑暗，24h光照，24h黑暗，以及盐，干旱，冷，热等）51份野牛草样品中的10个候选内参基因的表达量进行了分析，对内参基因的表达稳定性分析（GeNorm，NormFinder和Bestkeeper）表明，β-ACT，DNAJ和PP2A是不同光暗周期下野牛草样品中表达最稳定的内参基因，而GAPDH，β-ACTIN，DNAJ和PP2A是不同逆境条件下最合适的内参基因；根据野牛草转录组测序结果，选取节律转录本CCA1，LHY，GI，PHYA，CKIIα，CKIIβ等，利用qRT-PCR对RNA-seq中这几个转录本的表达量进行验证，结果发现，6个节律转录本的qRT-PCR数据和RNA-seq结果基本吻合，且各自呈现不同趋势的节律性变化，只是在表达量上略有差异。其中，LHY与CCA1的表达呈现近余弦的变化趋势，两个调节基因CKIIα/β的表达呈现近正弦的变化趋势，GI的表达也呈现近正弦的变化趋势，PHYA的表达呈现“倒V形”的变化趋势。此外，野牛草断开分株中HY5的表达在光/暗周期下呈现节律性变化，而其在暗/光暗周期下的表达呈现紊乱模式，同时，野牛草相连分株中HY5在不同光暗周期下其节律性表达趋于同步。
综上所述，野牛草植株活性氧清除系统的活性变化、内源激素的含量变化以及节律转录本的表达都具有节律性，野牛草相连克隆分株活性氧清除系统的节律性变化、内源激素含量的节律性变化与节律转录本的节律性表达在不同光暗周期下有同步化的趋势。
As an endogenous regulatory mechanisms of plants, circadian clock coordinatesday-nightcycle and life activities of plants to maintain nearly24h rhythmic oscillation, thus enhancing itsadaptability and survivability. Thus, physiological and molecular mechanisms of the circadianclock become one of the research focus in recent years. As stolon clonal plants, Buchloedactyloides (Nutt.) Engelm. connected ramets, which is connected by setsuko, sharing andtransmitting water, mineral elements and photosynthetic products. In this paper, Buchloedactyloides (Nutt.) Engelm. ramets were used as the experiment material, diurnal variation ofreactive oxygen scavenging system and endogenous hormones of Buchloe dactyloides (Nutt.)Engelm. were tested under differences photoperiod,based on the transcriptome sequencingofBuchloe dactyloides (Nutt.) Engelm., the circadian rhythm transcripts were identified, andexpression patterns of circadian rhythm transcripts were tested, finally, coordinationmechanisms between Buchloe dactyloides (Nutt.) Engelm. connected ramets under differencephotoperiod. The main conclusions are as follows:
(1) Reactive oxygen species scavenging system activity and endogenous hormone contentof Buchloe dactyloides (Nutt.) Engelm. both have a circadian rhythm variation, and reactiveoxygen species scavenging system activity and endogenous hormone content of Buchloedactyloides (Nutt.) Engelm.connected ramets tend to synchronize under differencesphotoperiod. In this study, superoxide superoxide dismutase (SOD), peroxidase (POD),catalase (CAT), ascorbate peroxidase (APX) activity and malondialdehyde (MDA) contentinBuchloe dactyloides (Nutt.) Engelm. disconnected ramets had a opposite variation trend inthe light/dark cycle (12h light/12h dark) and dark/light cycle (12h dark/12h light) conditions,however, varation of SOD, POD, CAT, APX activity and MDA content inBuchloe dactyloides(Nutt.) Engelm.connected ramets tend to synchronize; In addition, auxin (IAA), gibberellic acid (GA), abscisic acid (ABA), zeatin nuclear glycosides (ZR) content changes of Buchloedactyloides (Nutt.) Engelm. have a circadian rhythm variation, and IAA, GA, ABA, ZR contentchanges of Buchloe dactyloides (Nutt.) Engelm. connected ramets tend to synchronize underdifferences photoperiods.
(2)121transcripts were identified from Buchloe dactyloides (Nutt.) Engelm. circadianrhythm transcriptome, which represented16known circadian rhythm genes. In this study,seven samples of Buchloe dactyloides (Nutt.) Engelm. transcriptome in a light/dark cycle (ZT0to ZT0',4h interval) were sequencing, and a high-quality data was obtainedwith an average ofabout5G.7transcriptomesdatas were assembledde novo, and196,010transcripts wereobtained in total, the average length and N50were1302bp and2116bp, respectively.BLASTx were conducted betweenBuchloe dactyloides (Nutt.) Engelm. transcriptome andpublic protein data, there were129,554(66.1%),93,386(47.6%),40,904(20.87%) and50,592(25.81%)of the transcripts were annotated to Nr, Swiss-Prot, GO and COG proteindatabase, respectively.and GO classification indicates that majority of transcripts belong tobinding function, metabolic processes, and other functions related to the catalytic activitycategories; KEGG analysis showed a total of127,818(65.2%) of127transcripts which wasinvolved in different metabolic pathways, from which signaling pathway is important for theregulation of oxidative phosphorylation, glycolysis/gluconeogenesis, plant hormone signaltransduction; BLASTN was conducted betweenBuchloe dactyloides (Nutt.) Engelm.transcriptome and TAIR database, a total of25,881(13.2%) of the transcripts were similar withArabidopsis genes, including121circadian rhythm transcripts, representing CCA1(Circadianclock-associated protein1), LHY (Late next hypocotyl protein), GI (GIGANTEA), ZTL(Zeitlupe), PHYA (Phytochrome a), PHYB (Phytochrome B), CRY2(cryptochrome2), COP1(Constitutivelyphotomorphogenic protein1), CHS (Chalcone synthase); PIF3(Phytochromeinteracting factor3), HY5(hypocotyl elongation protein5), CDF1(Cycling dof factor1),UVR8(UV-B receptor protein8), PAP1(Phytochrome-associated protein1), CKIIα (Caseinkinase2α) and CKIIβ (Casein kinase2β) etc.16circadian rhythm genes.
(3) Buchloe dactyloides (Nutt.) Engelm. circadian rhythm transcripts showed rhythmicexpression patterns,expression levels of Buchloe dactyloides (Nutt.) Engelm. connectedrametscircadian rhythm transcripts tend to synchronize under different light/dark cycles.qRT-PCRwas used to test expression levels of ten candidate reference genes in51Buchloe dactyloides(Nutt.) Engelm. samples under different processing conditions (16h light/8h dark,8h light/16hdark,24h light,24h dark, as well as salt, drought, cold, heat, etc.).Stability of ten candidatereference genes were analyzed by three softwares(GeNorm, NormFinder and Bestkeeper). Theresults indicate that, β-ACT, DNAJ and PP2Awere the most stable reference gene underdifferent photoperiod samples, and GAPDH, β-ACTIN, DNAJ and PP2Awere the most suitableunder different stress conditions; According Buchloe dactyloides (Nutt.) Engelm.transcriptomesequencing results, the expression levels of circadian rhythm transcripts CCA1, LHY, GI, PHYA,CKIIα, CKIIβwere evaluated using qRT-PCR and RNA-seq, the result indicated that had aconsistent circadian rhythm changes of transcripts between qRT-PCR data and RNA-seq results,and each presents different variation trends, but a slight differenceson expression levels.Among them, the expression of LHY and CCA1presents a trend closed to cosine curve, and theexpression of two regulatory genes CKIIα/β rendered a nearly sinusoidal curve trend, theexpression of GI also showed a change in nearly sinusoidal trend, PHYA presents "inverted V-shaped" expression trends. In addition, HY5expression ofBuchloedactyloides (Nutt.) Engelm.disconnected ramets showed rhythmic changes in light/dark cycle, whreas its expression wasdisorder in the dark/light cycle, while the expression levels ofHY5in Buchloe dactyloides (Nutt.)Engelm.connected ramets tends to be rhythmic expression synchronic.in a different light/darkcycles.
In summary, the activity of reactive oxygen scavenging system, changesof endogenoushormone levels and expression of circdian rhythmic transcripts of Buchloe dactyloides (Nutt.)Engelm. plants have circadian rhythmic, and changes ofreactive oxygen scavenging system,changes of endogenous hormone levels and the expression levels of circadian rhythm transcripts of Buchloe dactyloides (Nutt.) Engelm. connectedramets are all synchronized underdifferent light/dark cycles.
引文
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