摘""要:甘蔗鞭黑粉菌(Sporisorium"scitamineum)是引起甘蔗鞭黑穗?。╯ugarcane"smut)的重要病原菌,侵染甘蔗后通常誘導(dǎo)頂端分生組織產(chǎn)生灰黑色“黑鞭”,在部分甘蔗品種(系)中能誘導(dǎo)植株提前開花,但其作用機制仍不明確。為了探究甘蔗響應(yīng)鞭黑粉菌侵染的開花相關(guān)基因及其表達(dá)模式,本研究以同期健康和感染鞭黑粉菌的桂糖42甘蔗品種為實驗材料進(jìn)行轉(zhuǎn)錄組測序分析,共篩選出了3276個顯著差異表達(dá)基因,其中1677個基因上調(diào)表達(dá)(Plt;0.05),1599個基因下調(diào)表達(dá)(Plt;0.05)。GO富集分析發(fā)現(xiàn)差異表達(dá)基因主要集中在生物合成過程、核糖體、核糖核蛋白復(fù)合體、核糖體結(jié)構(gòu)成分等小類中。KEGG富集結(jié)果顯示差異表達(dá)基因主要集中在氨基酸的生物合成、嘌呤代謝、碳代謝、吞噬作用等代謝通路。篩選到30個與開花途徑相關(guān)的差異表達(dá)基因,并對其中的FT1、PIE1、GID1、GA20ox-1、GA20ox-2等基因進(jìn)行了qRT-PCR驗證,qRT-PCR結(jié)果與轉(zhuǎn)錄組測序結(jié)果基本一致,驗證了轉(zhuǎn)錄組測序結(jié)果的可靠性。本研究結(jié)果為解析甘蔗鞭黑粉菌誘導(dǎo)甘蔗提前開花表型的分子機理提供了重要的候選基因,對甘蔗的育種也有重要的參考價值。
關(guān)鍵詞:甘蔗;甘蔗鞭黑粉菌;轉(zhuǎn)錄組;開花相關(guān)基因中圖分類號:S566.1""""""文獻(xiàn)標(biāo)志碼:A
Identification"of"Early"Flowering"Related"Genes"of"Sugarcane"in"Response"to"Sporisorium"scitamineum"Infection"Based"on"RNA-Seq
WANG"Zhiyuan1,2,"LIANG"Hongcui2,"CAI"Jianhe3,"CHEN"Baoshan1,2,4*,"XU"Xiongbiao1,2,4*
1."Guangxi"Key"Laboratory"of"Sugarcane"Biology,"Nanning,"Guangxi"530004,"China;"2."College"of"Agriculture,"Guangxi"University,"Nanning,"Guangxi"530004,"China;"3."Plant"Protection"Research"Institute,"Guangxi"Academy"of"Agricultural"Sciences,"Nanning,"Guangxi"530007,"China;"4."State"Key"Laboratory"for"Conservation"and"Utilization"of"Subtropical"Agro-bioresources,"Nanning,"Guangxi"530004,"China
Abstract:"Sporisorium"scitamineum,"the"pathogen"of"destructive"disease"smut,"usually"causes"abnormal"growth"of"meristematic"tissue"and"forms"a"“black"whip”"in"meristem"tissues."In"some"cases,"it"induces"formation"of"flowering"structures"in"some"sugarcane"cultivars"(genotypes),"but"the"exact"mechanism"remains"unclear."In"order"to"explore"flowering"related"genes"and"the"expression"patterns"in"sugarcane"in"response"to"infection"by"S."scitamineum,"the"healthy"and"S."scitamineum"infected"‘guitang42’"sugarcane"cultivar"samples"were"analyzed"by"transcriptome"sequencing."A"total"of"3276"differentially"expressed"genes"(DEGs)"were"identified,"of"which"1677"genes"were"up-regulated"(Plt;0.05)"and"1599"genes"down-regulated"(Plt;0.05)."The"DEGs"were"mostly"enriched"in"the"biosynthesis"process,"ribosome,"ribonucleoprotein"complex,"ribosome"structural"components,"etc."according"to"GO"enrichment"analysis."The"KEGG"analysis"showed"that"the"DEGs"were"mostly"enriched"in"amino"acid"biosynthesis,"purine"metabolism,"carbon"metabolism,"phagocytosis,"and"other"metabolic"pathways."Also,"out"of"30"DEGs"were"identified"to"be"associated"with"flowering,"and"the"representative"genes"such"as"FT1,"PIE1,"GID1,"GA20ox-1,"GA20ox-2"were"validated"by"qRT-PCR."The"qRT-PCR"results"were"consistent"with"the"transcriptomic"data,"confirming"the"dependability"of"the"transcriptome"sequencing"results."The"findings"would"present"essential"candidate"genes"for"revealing"the"mechanism"of"early"flowering"of"sugarcane"plants"caused"by"S."scitamineum,"and"lay"the"foundation"for"disease"resistance"breeding.
Keywords:"sugarcane;"Sporisorium"scitamineum;"transcriptome;"flowering-related"genes
DOI:"10.3969/j.issn.1000-2561.2024.06.002
甘蔗(Saccharum"spp.)是世界上最大的商業(yè)作物,在全球超120個國家和地區(qū)廣泛種植。甘蔗是主要的制糖原料,世界上大約80%的糖來源于甘蔗[1],我國90%的食糖也來源于蔗糖[2]。甘蔗黑穗病(sugarcane"smut)是世界范圍內(nèi)為害甘蔗最為嚴(yán)重的病害之一,可造成甘蔗產(chǎn)量和品質(zhì)的嚴(yán)重?fù)p失[3-4]。其病原菌為甘蔗鞭黑粉菌(Spori sorium"scitamineum),通過生長初期的蔗株幼芽頂端實現(xiàn)侵染[5]。蔗株被侵染后表現(xiàn)出分蘗增多、蔗葉淡綠細(xì)長、頂葉尖挺、蔗莖細(xì)小和節(jié)疏等癥狀[6-7]。隨著鞭黑粉菌的不斷蔓延,在梢頭逐漸形成由植物組織和真菌組成的不分支、方向朝下向內(nèi)卷曲的鞭狀物,俗稱“黑鞭”[7]。除上述常見癥狀外,甘蔗鞭黑粉菌侵染與甘蔗開花密切相關(guān),顏梅新等[8]通過孢子懸浮液接種試驗,發(fā)現(xiàn)甘蔗鞭黑粉菌能誘導(dǎo)桂柳05-136甘蔗品種提前開花。
開花是被子植物生活史中的重要組成部分,影響植物對不同環(huán)境的適應(yīng)、營養(yǎng)發(fā)育、生物量積累和谷物產(chǎn)量等[9-10]。開花是一個由5種基因通路組成的復(fù)雜網(wǎng)絡(luò)協(xié)調(diào)調(diào)控的生物學(xué)過程,包括光周期、春化、自主、赤霉素和年齡[9,"11-14]。此外,土壤營養(yǎng)、供水及溫度等因素也可以抑制、促進(jìn)或破壞開花過程[15-17]。開花整合基因FT(FLOWERING"LOCUSnbsp;T)和SOC1(SUPPR ESSOR"OF"OVEREXPRESSION"OF"CONSTANS"1),將上述這些復(fù)雜的調(diào)節(jié)因子整合后進(jìn)一步傳遞到下游的花分生組織基因(floral"meristem"identity"gene)中,從而啟動開花[12]。甘蔗的開花同樣受到許多因素,如晝長、晝夜溫度、濕度、甘蔗的生理成熟度,養(yǎng)分有效性,以及緯度等的影響[18]。目前,關(guān)于甘蔗開花相關(guān)基因的研究相對較少,對于甘蔗鞭黑粉誘導(dǎo)甘蔗提前開花的研究更是未見報道。
甘蔗開花與產(chǎn)量是一個矛盾的過程,一方面生殖生長導(dǎo)致糖分向花序運輸,降低了蔗莖中蔗糖的積累;另一方面,甘蔗親本誘導(dǎo)開花難且花期不遇成為影響甘蔗雜交育種和新親本創(chuàng)制的重要“瓶頸”。如何精準(zhǔn)調(diào)控甘蔗的開花過程是平衡甘蔗產(chǎn)量和育種的重點和難點,具有重要的生產(chǎn)實際意義。本研究基于RNA-Seq測序技術(shù),對甘蔗鞭黑粉菌侵染前、后2個時期的甘蔗葉片進(jìn)行測序分析,挖掘并篩選與甘蔗開花相關(guān)的差異表達(dá)基因,為甘蔗開花調(diào)控和育種提供理論基礎(chǔ)。
1.1""材料
本研究所用甘蔗品種桂糖42號取自廣西亞熱帶農(nóng)科新城及廣西大學(xué)甘蔗試驗基地,分別選取被甘蔗鞭黑粉菌侵染但“黑鞭”尚未抽出的甘蔗+1葉為試驗材料,以同齡期健康甘蔗植株+1葉為對照,各采集3株葉片樣本均勻混合,置于–80"℃超低溫冰箱保存。
1.2""方法
1.2.1""RNA提取及質(zhì)量檢測""對照組和試驗組甘蔗葉片組織總RNA由北京諾禾致源科技股份有限公司提取,以Nanodrop分光光度計檢測RNA純度,采用Agilent"2100核酸分析儀對提取的總RNA進(jìn)行質(zhì)量檢測。
1.2.2""文庫構(gòu)建及測序""對質(zhì)量檢測合格的甘蔗葉片總RNA,利用Oligo(dT)磁珠富集含poly(A)尾的mRNA,然后加入NEB"Fragmentation"Buffer將mRNA打斷成短片段,以mRNA為模板合成cDNA第一鏈,然后加入緩沖液、dNTPs和DNA"Polymerase"Ⅰ合成cDNA第二鏈,隨后對雙鏈cDNA進(jìn)行純化、末端修復(fù)、加尾并連接測序接頭,最后進(jìn)行片段大小選擇和PCR富集,獲得cDNA文庫。文庫檢測合格后進(jìn)行Illumina"NovaSeq"6000平臺測序。
1.2.3""測序數(shù)據(jù)處理與分析""測序得到的原始圖像數(shù)據(jù)文件經(jīng)CASAVA堿基識別(base"calling)分析轉(zhuǎn)化為原始測序序列(original"sequence)。對原始數(shù)據(jù)(raw"reads)進(jìn)行過濾,去除帶接頭和N比率大于10%及低質(zhì)量的reads,得到高質(zhì)量序列(clean"reads)。將clean"reads與甘蔗參考基因組數(shù)據(jù)庫(https://sugarcane-genome.cirad.fr/)進(jìn)行比對和分類注釋。
1.2.4""差異表達(dá)基因篩選""對測序得到的原始reads進(jìn)行評估,經(jīng)TMM標(biāo)準(zhǔn)化處理后,獲得對照組和試驗組的基因表達(dá)量。應(yīng)用edgeR軟件進(jìn)行樣本間差異分析,得到P值后進(jìn)行多重假設(shè)檢驗校正,通過控制PDR值,并以|log2"(Fold"Change)|≥1和P≤0.05為標(biāo)準(zhǔn)對差異表達(dá)基因進(jìn)行篩選。
1.2.5""差異表達(dá)基因本位數(shù)據(jù)庫(GO)和Pathway顯著性富集(KEGG)分析""基于Gene"Ontology"(GO),分別從分子功能(molecular"function,"MF)、生物過程(biological"process,"BP)和細(xì)胞組分(cellular"component,"CC)3個方面對差異表達(dá)基因進(jìn)行GO注釋?;贙EGG數(shù)據(jù)庫,應(yīng)用超幾何檢驗,找出與整個基因組背景相比,在差異表達(dá)基因中顯著性富集的Pathway,采用Fisher進(jìn)行精確檢驗,通過Bonferroni校正法進(jìn)行校正,得到差異基因顯著富集的GO功能和代謝通路,從中篩選顯著差異表達(dá)基因進(jìn)行重點分析。
1.2.6""qRT-PCR驗證""為驗證轉(zhuǎn)錄組數(shù)據(jù)的可靠性,利用qRT-PCR對部分差異表達(dá)基因進(jìn)行驗證。利用HiScript"III"RT"SuperMix"for"qPCR(+gDNA"wiper)試劑盒(Vazyme,"Cat."R323-01)合成cDNA第一鏈,采用ChamQ"Universal"SYBR"qPCR"Master"Mix試劑盒(Vazyme,"Cat."Q711-02)檢測基因的表達(dá)量,以GAPDH基因作為內(nèi)參,用SnapGene軟件設(shè)計qRT-PCR引物(表1)。反應(yīng)體系為:cDNA模板(cDNA原液稀釋10倍)2"μL,10"μmol/L正、反向引物各0.4"μL,2×ChamQ"Universal"SYBR"qPCR"Master"Mix"10"μL,加入Nuclease-free"water至總體積為20"μL,在Light Cycler"96實時熒光定量PCR儀(Roche)上進(jìn)行qRT-PCR反應(yīng)。熒光定量PCR反應(yīng)程序為:95"℃預(yù)變性30"s;95"℃變性"10"s,60"℃退火延伸30"s,循環(huán)40次。所有試驗均設(shè)置3次生物學(xué)重復(fù)和3次實驗重復(fù)。運用2–ΔΔCT法進(jìn)行數(shù)據(jù)處理。
2.1""測序數(shù)據(jù)質(zhì)控結(jié)果分析
試驗組(Smut"+1leaf)和對照組(Control"+"1leaf)的原始數(shù)據(jù)raw"reads數(shù)分別為45"626"696條和46"125"906條,經(jīng)過濾得到clean"reads數(shù)分別為42"937"438條和44"276"602條,測序cDNA讀取量分別為6.44"Gb和6.64"Gb,Q20分別為98.05%和96.7%,Q30分別為94.17%和91.19"%,GC含量分別為50.48%和52.72"%。說明測序質(zhì)量較高,滿足后續(xù)生物信息學(xué)分析要求。
2.2""差異表達(dá)基因篩選
將對照組與試驗組的測序數(shù)據(jù)進(jìn)行比對分析,結(jié)果如圖1所示,共有3276個基因差異表達(dá),其中1677個基因顯著上調(diào)表達(dá)(Plt;0.05),1599個基因顯著下調(diào)表達(dá)(Plt;0.05)。
2.3""差異表達(dá)基因的GO功能注釋和KEGG分析
GO功能分析表明,差異表達(dá)基因被富集到生物過程、細(xì)胞組分和分子功能等3大類和785小類中,其中生物過程390個,細(xì)胞組分107個,分子功能288個。生物過程中有28個小類顯著富集,細(xì)胞組分中有7個小類顯著富集,分子功能中有16個小類顯著富集。選取3個大類中富集程度高和差異基因占比大的小類作圖(圖2),其中生物過程主要富集在酰胺生物合成過程(amide"biosynthetic"process)、翻譯(translation)、肽生物合成過程(peptide"biosynthetic"process)、細(xì)胞酰胺代謝過程(cellular"amidenbsp;metabolic"process)、肽代謝過程(peptide"metabolic"process);細(xì)胞組份主要富集在核糖體(ribosome)、核糖核蛋白復(fù)合體(ribonucleoprotein"complex)、非膜結(jié)合細(xì)胞器(non-membrane-bounded"organelle)、胞內(nèi)非膜結(jié)合細(xì)胞器(intracellular"non-membrane-bounded"organelle)、細(xì)胞質(zhì)部分(cytoplasmic"part);分子功能主要富集在核糖體的結(jié)構(gòu)成分(structural"constituent"of"ribosome)、結(jié)構(gòu)分子活性(structural"molecule"activity)及rRNA結(jié)合(rRNA"binding)等。
利用KEGG數(shù)據(jù)庫對篩選到的差異表達(dá)基因進(jìn)行功能分類和pathway注釋,結(jié)果顯示(表2):甘蔗鞭黑粉菌侵染前后的差異表達(dá)基因定位到了118個代謝通路中,顯著富集到了30個代謝通路中,如氨基酸的生物合成(biosynthesis"of"amino"acids)、嘌呤代謝(purine"metabolism)、碳代謝(carbon"metabolism)、吞噬作用(phagosome)、甘油磷脂代謝(glycerophospholipid"metabolism)等。
2.4""開花相關(guān)基因的差異表達(dá)分析
從轉(zhuǎn)錄組數(shù)據(jù)中篩選到30個與開花途徑相關(guān)的差異表達(dá)基因,其中包括開花整合子(floral"integrations)基因1個;花分生組織決定基因(floral"meristem"identity"genes)6個;光周期(photoperiod)途徑相關(guān)基因16個;春化途徑相關(guān)基因1個;赤霉素途徑相關(guān)基因6個(表3)。
2.5""開花相關(guān)基因的qRT-PCR驗證
選取GID1、FT1、PIE1、GA20ox-1、GA20ox-2等5個與植物開花途徑相關(guān)基因進(jìn)行qRT-PCR驗證(圖3),結(jié)果顯示,與健康對照相比,甘蔗鞭黑粉菌侵染的甘蔗+1葉片中FT1、GA20ox-1、GA20ox-2基因顯著上調(diào)表達(dá),而GID1和PIE1基因顯著下調(diào)表達(dá)。雖然這3個基因的轉(zhuǎn)錄組測序結(jié)果和qRT-PCR結(jié)果在基因差異表達(dá)倍數(shù)并非完全一致,但是二者之間反映出的差異表達(dá)變化趨勢是一致的,說明轉(zhuǎn)錄組數(shù)據(jù)的可靠性。
開花是植物由營養(yǎng)生長向生殖生長轉(zhuǎn)變的重要階段,在植物生活史中扮演著非常重要的作用。甘蔗開花的精準(zhǔn)高效調(diào)控對于蔗莖產(chǎn)量和遺傳育種具有重要意義。本研究通過轉(zhuǎn)錄組測序分析,
篩選出3276個差異表達(dá)基因,其中1677個基因上調(diào)表達(dá),1599個基因下調(diào)表達(dá)。結(jié)合植物開花調(diào)控途徑對差異表達(dá)基因進(jìn)一步分析,篩選出30個與開花途徑相關(guān)的差異表達(dá)基因。FLOWE RING"LOCUS"T(FT)成花基因作為下游開花整合基因,可以整合多個調(diào)控途徑中的花發(fā)育信號分子,促進(jìn)開花相關(guān)基因的表達(dá),促進(jìn)植物開花[19]。然而,過表達(dá)甘蔗ScFT1基因可抑制擬南芥開花[20]。本研究轉(zhuǎn)錄組測序分析發(fā)現(xiàn)在甘蔗鞭粉菌
侵染后ScFT1基因呈顯著上調(diào)表達(dá),同時qRT-"PCR也驗證了這一結(jié)果。推測甘蔗鞭粉菌侵染后誘導(dǎo)甘蔗提前開花的現(xiàn)象,可能是通過影響上游的開花途徑導(dǎo)致的。
赤霉素(gibberellins,"GAs)是一類重要的植物激素,在調(diào)節(jié)植物生長和抵抗生物和非生物脅迫中具有重要作用[21-22]。在赤霉素信號通路中,GA受體GIBBERELLIN"INSENSITIVE"DWARF1(GID1)感知GA信號后,與下游DELLA蛋白N-端DELLA/TVHYNP結(jié)構(gòu)域互作,促進(jìn)DELLA經(jīng)SCFGID2/SLY1泛素/26S蛋白酶體途徑降解[23-24],正向調(diào)控植株莖伸長、花和果實發(fā)育、葉片擴(kuò)張及種子萌發(fā)等生物學(xué)過程[25-27]。Gibberellin"20"oxidase(GA20ox)是赤霉素合成過程中的一類重要的限速酶,GA20ox及Gibberellin"3"oxidase"(GA3ox)通過一系列催化反應(yīng),將赤霉素前期GA12轉(zhuǎn)化為具有生物活性的GA1和GA4[28-30]。GA20ox-2被認(rèn)為是一個“綠色革命”基因,其突變導(dǎo)致水稻的矮桿化,從而大大提高了產(chǎn)量[31]。本研究發(fā)現(xiàn)與對照相比,甘蔗鞭黑粉菌侵染的甘蔗+1葉中ScGA20ox-1、ScGA20ox-2基因均呈現(xiàn)顯著上調(diào)表達(dá),而ScGID1基因呈顯著下調(diào)表達(dá),這與GID1正向調(diào)控開花的結(jié)果不一致[25-26]。此外,酵母雙雜交(yeast"two"hybrid,"Y2H)和雙分子熒光互補實驗(BiFC)研究發(fā)現(xiàn),ScGID1能與ScGA20ox2在體外和體內(nèi)發(fā)生互作(數(shù)據(jù)待發(fā)表)。推測甘蔗鞭黑粉菌侵染一方面下調(diào)ScGID1表達(dá),另一方面促進(jìn)上游ScGA20ox等赤霉素合成相關(guān)基因的表達(dá),干擾了ScGID1與ScGA20ox的相互作用,從而誘導(dǎo)甘蔗早花的表型。
不依賴光周期的早花基因PHOTOPERIOD"INDEPENDENT"EARLY"FLOWERING1(PIE1)能負(fù)調(diào)控擬南芥開花過程,PIE1突變能抑制FLOWERING"LOCUS"C(FLC)介導(dǎo)的遲花表型,并誘導(dǎo)非FLC依賴的早花表型[32]。本研究發(fā)現(xiàn)在甘蔗鞭黑粉菌侵染的甘蔗+1葉中ScPIE1基因轉(zhuǎn)錄水平極顯著下調(diào)表達(dá),推測甘蔗鞭黑粉菌誘導(dǎo)甘蔗早花現(xiàn)象可能與ScPIE1基因的表達(dá)下調(diào)有關(guān)。
在擬南芥中CONSTANS-Like(COL)基因是光周期誘導(dǎo)開花途徑中的關(guān)鍵轉(zhuǎn)錄因子[33],研究發(fā)現(xiàn)AtCOL4是長日照和短日照的開花抑制因子,COL4過表達(dá)導(dǎo)致開花延遲[34];而過表達(dá)AtCOL5可誘導(dǎo)短日照擬南芥開花[35];COL9通過抑制Ehd1(early"heading"date"1)基因延遲水稻的開花時間[36];COL16基因在水稻中通過上調(diào)開花阻礙基因Ghd7(grain"number,"plant"height"and"heading"date"7)來抑制開花[37]。本研究發(fā)現(xiàn)ScCOL4和ScCOL16顯著下調(diào)表達(dá),而COL4和COL16在其他作物中存在抑制開花的現(xiàn)象,推測甘蔗鞭黑粉菌可能通過下調(diào)這2個基因的表達(dá)從而誘導(dǎo)甘蔗早花。而COL5和COL9在甘蔗中的表達(dá)模式和功能可能與其他作物存在一定的差異。
乙烯響應(yīng)因子(ethylene-responsive"transcription"factor"RAP)RAP2-3、RAP2-4、RAP2-7等屬于AP2/ERF類轉(zhuǎn)錄因子,參與植物花發(fā)育、果實成熟、種子發(fā)育和萌發(fā)以及響應(yīng)逆境脅迫的過程[38]。APETALA2(AP2)基因在擬南芥中直接或間接調(diào)控花發(fā)育過程中其他基因的表達(dá),如FT[39]和SOC1基因[40],進(jìn)而抑制植物開花。本研究發(fā)現(xiàn)RAP2-11、RAP2-3、RAP2-4基因表達(dá)下調(diào),推測這3個基因可能響應(yīng)了甘蔗鞭黑粉菌的侵染,進(jìn)而誘導(dǎo)甘蔗早花現(xiàn)象。
CRY2(cryptochrome"2)、CRY-DASH(crypto chrome-DASH)都屬于隱花色素基因家族,而CIB1(cryptochrome-interacting"basic-helix-loop-"helix"1)、CIB5(cryptochrome-interacting"basic-"helix-loop-helix"5)是一類重要的轉(zhuǎn)錄因子,可以在藍(lán)光的作用下與CRY2互作,進(jìn)而促進(jìn)擬南芥開花[41]。本研究發(fā)現(xiàn)CIB1基因在甘蔗鞭黑粉菌侵染后顯著上調(diào)表達(dá),推測甘蔗鞭黑粉菌可能通過上調(diào)CIB1表達(dá),進(jìn)而促進(jìn)甘蔗早花。
關(guān)于甘蔗鞭黑粉菌誘導(dǎo)甘蔗早花現(xiàn)象的研究鮮見報道,本研究基于RNA-Seq技術(shù)初步篩選了甘蔗響應(yīng)鞭黑粉菌侵染的與開花途徑相關(guān)的差異表達(dá)基因,并對部分基因的表達(dá)模式進(jìn)行了驗證分析,為甘蔗開花調(diào)控和育種提供了理論基礎(chǔ)。這些基因是如何響應(yīng)甘蔗鞭黑粉菌侵染,具體互作因子以及誘導(dǎo)提前開花的分子機理,還有待進(jìn)一步深入研究。
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