RNA-Seq在果树学研究中的应用RNA-Seq technology and its application in fruit research
冯超;朱长青;徐昌杰;陈昆松;
摘要(Abstract):
RNA-Seq为植物功能基因组学研究的重要手段,近年来在果树上也有不少成功应用。应用这一技术,可获得高通量的转录本序列信息及表达量数据。本文首先简要介绍RNA-Seq研究背景及其在果实发育与品质形成、芽发育及其调控、果树胁迫响应等方面的应用概况,然后着重分物种追踪了柑橘、葡萄、香蕉、草莓、苹果、梨、桃、樱桃、杨梅、蓝莓这10个常见果树的30余个RNA-Seq实例,介绍了具体应用进展。最后就存在的测序成本和数据处理技术等问题以及测序平台和文库制备等方面的发展趋势进行了讨论。
关键词(KeyWords): 果树;第2代测序技术;RNA-Seq;转录组学;果实发育;果实成熟;胁迫
基金项目(Foundation): 863项目(2013AA102606);; 国家自然科学基金(31030052,31071781);; 国家公益性行业(农业)科研专项(200903044,201203089)
作者(Author): 冯超;朱长青;徐昌杰;陈昆松;
Email:
DOI: 10.13925/j.cnki.gsxb.2014.01.019
参考文献(References):
- [1]XU Chang-jie,ZHU Chang-qing,GAO Zhong-shan,CHEN Kunsong.Application of fruit crop EST in studies on fruit development and ripening[J].Journal of Fruit Science,2009,26(3):353-360.徐昌杰,朱长青,高中山,陈昆松.果树EST在果实发育和成熟研究中的应用[J].果树学报,2009,26(3):353-360.
- [2]QI Yun-xia,LIU Yong-bin,RONG Wei-heng.RNA-Seq and its application:a new technology for transcriptomics[J].Hereditas,2011,33(11):1191-1202.祈云霞,刘永斌,荣威恒.转录组研究新技术:RNA-Seq及其应用[J].遗传,2011,33(11):1191-1202.
- [3]WANG Xi,WANG Xiao-wo,WANG Li-kun,FENG Zhi-xing,WANG Xue-gong.A review on the processing and analysis of next generation RNA-seq data[J].Process in Biochemistry and Biophysics,2010,37(8):834-846.王曦,汪小我,王立坤,冯智星,张学工.新一代高通量RNA测序数据的处理与分析[J].生物化学与生物物理进展,2010,37(8):834-846.
- [4]GRABHERR M G,HAAS B J,YASSOUR M,LEVIN J Z,THOMPSON D A,AMIT I,ADICONIS X,FAN L,RAYCHOWDHURY R,ZENG Q D,CHEN Z H,MAUCELI E,HACOHEN N,GNIRKE A,RHIND N,DI PALMA F,BIRREN B W,NUSBAUM C,LINDBLAD-TOH K,FRIEDMAN N,REGEV A.Full-length transcriptome assembly from RNA-Seq data without a reference genome[J].Nature Biotechnology,2011,29(7):644-652.
- [5]LANGMEAD B,SALZBERG S L.Fast gapped-read alignment with Bowtie 2[J].Nature Methods,2012,9(4):357-359.
- [6]QUAIL M A,SMITH M,COUPLAND P,OTTO T D,HARRIS S R,CONNOR T R,BERTONI A,SWERDLOW H P,GU Y.A tale of three next generation sequencing platforms:comparison of Ion Torrent,Pacific Biosciences and Illumina MiSeq sequencers[J].BMC Genomics,2012,13:341.
- [7]MELLMANN A,HARMSEN D,CUMMINGS C A,ZENTZ E B,LEOPOLD S R,RICO A,PRIOR K,SZCZEPANOWSKI R,JI Y M,ZHANG W L,MCLAUGHLIN S F,HENKHAUS J K,LEOPOLD B,BIELASZEWSKA M,PRAGER R,BRZOSKA P M,MOORE R L,GUENTHER S,ROTHBERG J M,KARCH H.Prospective genomic of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology[J].PLoS One,2011,6(7):e22751.
- [8]LI R Q,ZHU H M,RUAN J,QIAN W B,FANG X D,SHI Z B,LI Y R,LI S T,SHAN G,KRISTIANSEN K,LI S G,YANG H M,WANG J.De novo assembly of human genomes with massively parallel short read sequencing[J].Genome Research,2010,20(2):265-272.
- [9]FRENCH-ITALIAN PUBLIC.The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla[J].Nature,2007,449(7161):463-467.
- [10]MING R,HOU S B,FENG Y,YU Q Y,DIONNE-LAPORTE A,SAW J H,SENIN P,WANG W,LY B V,LEWIS K L T,SALZBERG S L,FENG L,JONES M R,SKELTON R L,MURRAY J E,CHEN C X,QIAN W B,SHEN J G,DU P,EUSTICE M,TONG E,TANG H B,LYONS E,PAULL R E,MICHAEL T P,WALL K,RICE D W,ALBERT H,WANG M L,ZHU Y J,SCHATZ M,NAGARAJAN N,ACOB R A,GUAN P Z,BLAS A,WAI C M,ACKERMAN C M,REN Y,LIU C,WANG J M,WANG J P,NA J K,SHAKIROV E V,HAAS B,THIMMAPURAM J,NELSON D,WANG X Y,BOWERS J E,GSCHWEND A R,DELCHER A L,SINGH R,SUZAUKI J Y,TRIPATHI S,NEUPANE K,WEI H R,IRIKURA B,PAIDI M,JIANG N,ZHANG W L,PRESTING G,WINDSOR A,NAVAJAS-PEREZ R,TORRES M J,FELTUS F A,PORTER B,LI Y J,BURROUGHS A M,LUO M C,LIU L,CHRISTOPHER D A,MOUNT S M,MOORE P H,SUGIMURA T,JIANG J M,SCHULER M A,FRIEDMAN V,MITCHELL-OLDS T,SHIPPEN D E,DEPAMPHILIS C W,PALMER J D,FREELING M,PATERSON A H,GONSALVES D,WANG L,ALAM M.The draft genome of the transgenic tropical fruit tree papaya(Carica papaya Linnaeus)[J].Nature,2008,452(7190):991-996.
- [11]VELASCO R,ZHARKIKH A,AFFOURTIT J,DHINGRA A,CESTARO A,KALYANARAMAN A,FONTANA P,BHATNAGAR S,K,TROGGIO M,PRUSS D,SALVI S,PINDO M,BALDI P,CASTELLETTI S,CAVAIUOLO M,COPPOLA G,COSTA F,COVA V,DAL RI A,GOREMYKIN V,KOMJANC M,LONGHI S,MAGNAGO P,MALACARNE G,MALNOY M,MICHELETTI D,MORETTO M,PERAZZOLLI M,SI-AMMOUR A,VEZZULLI S,ZINI E,ELDREDGE G,FITZGERALD L M,GUTIN N,LANCHBURY J,MACALMA T,MITCHELL J T,REID J,WARDELL B,KODIRA C,CHEN Z,DESANY B,NIAZI F,PALMER M,KOEPKE T,JIWAN D,SCHAEFFER S,KRISHNAN V,WU C,CHU V T,KING S T,VICK J,TAO Q,MRAZ A,STORMO A,STORMO K,BOGDEN R,EDERLE D,STELLA A,VECCHIETTI A,KATER M M,MASIERO S,LASSERRE P,LESPINASSE Y,ALLAN A C,BUS V,CHAGNE D,CROWHURST R N,GLEAVE A P,LAVEZZO E,FAWCETT J A,PROOST S,ROUZE P,STERCK L,TOPPO S,LAZZARI B,HELLENS R P,DUREL C E,GUTIN A,BUMGARNER R E,GARDINER S E,SKOLNICK M,EGHOLM M,VAN DE PEER Y,SALAMINI F,VIOLA R.The genome of the domesticated apple(Malus×domestica Borkh.)[J].Nature Genetics,2010,42(10):833-839.
- [12]SHULAEV V,SARGENT D J,CROWHURST R N,MOCKLER T C,FOLKERTS O,DELCHER A L,JAISWAL P,MOCKAITIS K,LISTON A,MANE S P,BURNS P,DAVIS T M,SLOVIN J P,BASSIL N,HELLENS R P,EVANS C,HARKINS T,KODIRA C,DESANY B,CRASTA O R,JENSEN R V,ALLAN A C,MICHAEL T P,SETUBAL J C,CELTON J M,REES D J G,WILLIAMS K P,HOLT S H,ROJAS J J R,CHATTERJEE M,LIU B,SILVA H,MEISEL L,ADATO A,FILICHKIN S A,TROGGIO M,VIOLA R,ASHMAN T L,WANG H,DHARMAWARDHANA P,ELSER J,RAJA R,PRIEST H D,BRYANT D W,FOX S E,GIVAN S A,WILHELM L J,NAITHANI S,CHRISTOFFELS A,SALAMA D Y,CARTER J,GIRONA E L,ZDEPSKI A,WANG W Q,KERSTETTER R A,SCHWAB W,KORBAN S S,DAVIK J,MONFORT A,DENOYES-ROTHAN B,ARUS P,MITTLER R,FLINN B,AHARONI A,BENNETZEN J L,SALZBERG S L,DICKERMAN A W,VELASCO R,BORODOVSKY M,VEILLEUX R E,FOLTA K M.The genome of woodland strawberry(Fragaria vesca)[J].Nature Genetics,2011,43(2):109-116.
- [13]D'HONT A,DENOEUD F,AURY J M,BAURENS F C,CARREEL F,GARSMEUR O,NOEL B,BOCS S,DROC G,ROUARD M,DA SILVA C,JABBARI K,CARDI C,POULAIN J,SOUQUET M,LABADIE K,JOURDA C,LENGELLE J,RODIERGOUD M,ALBERTI A,BERNARD M,CORREA M,AYYAMPALAYAM S,MCKAIN M R,LEEBENS-MACK J,BURGESS D,FREELING M,MBEGUIE-A-MBEGUIE D,CHABANNES M,WICKER T,PANAUD O,BARBOSA J,HRIBOVA E,HESLOPHARRISON P,HABAS R,RIVALLAN R,FRANCOIS P,POIRON C,KILIAN A,BURTHIA D,JENNY C,BAKRY F,BROWN S,GUIGNON V,KEMA G,DITA M,WAALWIJK C,JOSEPH S,DIEVART A,JAILLON O,LECLERCQ J,ARGOUT X,LYONS E,ALMEIDA A,JERIDI M,DOLEZEL J,ROUX N,RISTERUCCI A M,WEISSENBACH J,RUIZ M,GLASZMANN J C,QUETIER F,YAHIAOUI N,WINCKER P.The banana(Musa acuminata)genome and the evolution of monocotyledonous plants[J].Nature,2012,488(7410):213-217.
- [14]WU J,WANG Z W,SHI Z B,ZHANG S,MING R,ZHU S L,KHAN M A,TAO S T,KORBAN S S,WANG H,CHEN N J,NISHIO T,XU X,CONG L,QI K J,HUANG X S,WANG Y T,ZHAO X,WU J Y,DENG C,GOU C Y,ZHOU W L,YIN H,QIN G H,SHA Y H,TAO Y,CHEN H,YANG Y A,SONG Y,ZHAN D L,WANG J,LI L T,DAI M S,GU C,WANG Y Z,SHI D H,WANG X W,ZHANG H P,ZENG L,ZHENG D M,WANG C L,CHEN M S,WANG G B,XIE L,SOVERO V,SHA S F,HUANG W J,ZHANG S J,ZHANG M Y,SUN J M,XU L L,LI Y,LIU X,LI Q S,SHEN J H,WANG J Y,PAULL R E,BENNETZEN J L,ZHANG S L.The genome of pear(Pyrus bretschneideri Rehd.)[J].Genome Research,2012,23:396-408.
- [15]XU Q,CHEN L L,RUAN X A,CHEN D J,ZHU A D,CHEN C L,BERTRAND D,JIAO W B,HAO B H,LYON M P,CHEN J J,GAO S,XING F,LAN H,CHANG J W,GE X H,LEI Y,HU Q,MIAO Y,WANG L,XIAO S X,BISWAS M K,ZENG W F,GUO F,CAO H B,YANG X M,XU X W,CHENG Y J,XU J,LIU J H,LUO O J,TANG Z H,GUO W W,KUANG H H,ZHANG H Y,ROOSE M L,NAGARAJAN N,DENG X X,RUAN Y J.The draft genome of sweet orange(Citrus sinensis)[J].Nature Genetics,2012,45:59-66.
- [16]International Peach Genome Initiative.The high-quality draft genome of peach(Prunus persica)identifies unique patterns of genetic diversity,domestication and genome evolution[J].Nature Genetics,2013,45:487-494.
- [17]XU Q,YU K Q,ZHU A D,YE J L,LIU Q,ZHANG J,C,DENG X X.Comparative transcripts profiling reveals new insight into molecular processes regulating lycopene accumulation in a sweet orange(Citrus sinensis)red-flesh mutant[J].BMC Genomics,2009,10:540.
- [18]YU K Q,XU Q,DA X L,GUO F,DING Y D,DENG X X.Transcriptome changes during fruit development and ripening of sweet orange(Citrus sinensis)[J].BMC Genomics,2012,13:10.
- [19]MARCET-HOUBEN M,BALLESTER A R,DE LA FUENTE B,HARRIES E,MARCOS J F,GONZALEZ-CANDELAS L,GABALDON T.Genome sequence of the necrotrophic fungus Penicillium digitatum,the main postharvest pathogen of citrus[J].BMC Genomics,2012,13:691.
- [20]MARTINELLI F,URATSU S L,ALBRECHT U,REAGAN R L,PHU M L,BRITTON M,BUFFALO V,FASS J,LEICHT E,ZHAO W X,LIN D W,D'SOUZA R,DAVIS C E,BOWMAN K D,DANDEKAR A M.Transcriptome profiling of citrus fruit response to Huanglongbing disease[J].PLoS One,2012,7(5):e38039.
- [21]FACCHINI P J,BOHLMANN J,COVELLO P S,DE LUCA V,MAHADEVAN R,PAGE J E,RO D K,SENSEN C W,STORMS R,MARTIN V J J.Synthetic biosystems for the production of highvalue plant metabolites[J].Trends In Biotechnology,2012,30(3):127-131.
- [22]ZHENG B B,WU X M,GE X X,DENG X X,GROSSER J W,GUO W W.Comparative transcript profiling of a male sterile cybrid pummelo and its fertile type revealed altered gene expression related to flower development[J].PLoS One,2012,7(8):e43758.
- [23]ZHANG J Z,AI X Y,SUN L M,ZHANG D L,GUO W W,DENG X X,HU C G.Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wildtype Poncirus trifoliata(L.)Raf.by massively parallel signature sequencing[J].BMC Genomics,2011,12:63.
- [24]AI X Y,LIN G,SUN L M,HU C G,GUO W W,DENG X X,ZHANG J Z.A global view of gene activity at the flowering transition phase in precocious trifoliate orange and its wild-type[Poncirus trifoliata(L.)Raf.]by transcriptome and proteome analysis[J].Gene,2012,510(1):47-58.
- [25]BELLIN D,FERRARINI A,CHIMENTO A,KAISER O,LEVENKOVA N,BOUFFARD P,DELLEDONNE M.Combining nextgeneration pyrosequencing with microarray for large scale expression analysis in non-model species[J].BMC Genomics,2009,10:555.
- [26]VENTURINI L,FERRARINI A,ZENONI S,TORNIELLI G B,FASOLI M,DAL SANTO S,MINIO A,BUSON G,TONONI P,ZAGO E D,ZAMPERIN G,BELLIN D,PEZZOTTI M,DELLEDONNE M.De novo transcriptome characterization of Vitis vinifera cv.Corvina unveils varietal diversity[J].BMC Genomics,2013,14:41.
- [27]ZENONI S,FERRARINI A,GIACOMELLI E,XUMERLE L,FASOLI M,MALERBA G,BELLIN D,PEZZOTTI M,DELLEDONNE M.Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq[J].Plant Physiology,2010,152(4):1787-1795.
- [28]SWEETMAN C,WONG D C J,FORD C M,DREW D P.Transcriptome analysis at four developmental stages of grape berry(Vitis vinifera cv.Shiraz)provides insights into regulated and coordinated gene expression[J].BMC Genomics,2012,13:691.
- [29]VANNOZZI A,DRY I B,FASOLI M,ZENONI S,LUCCHIN M.Genome-wide analysis of the grapevine stilbene synthase multigenic family:genomic organization and expression profiles upon biotic and abiotic stresses[J].BMC Plant Biology,2012,12:130.
- [30]PERAZZOLLI M,MORETTO M,FONTANA P,FERRARINI A,VELASCO R,MOSER C,DELLEDONNE M,PERTOT I.Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes[J].BMC Genomics,2012,13:660.
- [31]YANG Q S,WU J H,LI C Y,WEI Y R,SHENG O,HU C H,KUANG R B,HUANG Y H,PENG X X,MCCARDLE J A,CHEN W,YANG Y,ROSE J K C,ZHANG S,YI G J.Quantitative proteomic analysis reveals that antioxidation mechanisms contribute to cold tolerance in plantain(Musa paradisiaca L.;ABB Group)seedlings[J].Molecular&Cellular Proteomics,2012,11:1853-1869.
- [32]LI C Y,DENG G M,YANG J,VILJOEN A,JIN Y,KUANG R B,ZUO C W,LV Z C,YANG Q S,SHENG O,WEI Y R,HU C H,DONG T,YI G J.Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f.sp.Cubense tropical race 4[J].BMC Genomics,2012,13:374.
- [33]WANG Z,ZHANG J B,JIA C H,LIU J H,LI Y Q,YIN X M,XU B Y,JIN Z Q.De Novo characterization of the banana root transcriptome and analysis of gene expression under Fusarium oxysporum f.sp.Cubense tropical race 4 infection[J].BMC Genomics,2012,13:650.
- [34]PASSOS M A,DE CRUZ V O,EMEDIATO F,DE TEIXEIRA C C,AZEVEDO V C R,BRASILEIRO A C,AMORIM E,FERREIRA C,MARTINS N,TOGAWA R,PAPPAS G,DA SILVA O B,MILLER R N.Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola:gene assembly,annotation and marker development[J].BMC Genomics,2013,14:78.
- [35]FOLTA K M,CLANCY M A,CHAMALA S,BRUNINGS A M,DHINGRA A,GOMIDE L,KULATHINAL R J,PERES N,DAVIS T M,BARBAZUK W B.A transcript accounting from diverse tissues of a cultivated strawberry[J].Plant Genome,2010,3:90-105.
- [36]ZHANG Y,ZHU J,DAI H.Characterization of transcriptional differences between columnar and standard apple trees using RNA-Seq[J].Plant Molecular Biology Reporter,2012,30(4):957-965.
- [37]LIU G Q,LI W S,ZHENG P H,XU T,CHEN L J,LIU D F,HUSSAIN S,TENG Y W.Transcriptomic analysis of‘Suli’pear(Pyrus pyrifolia white pear group)buds during the dormancy by RNA-Seq[J].BMC Genomics,2012,13:700.
- [38]SOCQUET-JUGLARD D,KAMBER T,POTHIER J F,CHRISTEN D,GESSLER C,DUFFY B,PATOCCHI A.Comparative RNA-Seq analysis of early-infected peach leaves by the invasive phytopathogen xanthomonas arboricola pv.pruni[J].PLoS One,2013,8(1):54196.
- [39]KOEPKE T,SCHAEFFER S,KRISHNAN V,JIWAN D,HARPER A,WHITING M,ORAGUZIE N,DHINGRA A.Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'-UTR sequencing[J].BMC Genomics,2012,13:18.
- [40]ALKIO M,JONAS U,SPRINK T,VAN NOCKER S,KNOCHE M.Identification of putative candidate genes involved in cuticle formation in Prunus avium(sweet cherry)fruit[J].Annals of Botany,2012,110(1):101-112.
- [41]FENG C,CHEN M,XU C J,BAI L,YIN X R,LI X,ALLAN A C,FERGUSON I B,CHEN K S.Transcriptomic analysis of Chinese bayberry(Myrica rubra)fruit development and ripening using RNA-Seq[J].BMC Genomics,2012,13:19.
- [42]ZHANG S Y,LI X,FENG C,ZHU C Q,GRIERSON D,XU C J,CHEN K S.Development and characterization of 109 polymorphic EST-SSRs derived from Chinese bayberry(Myrica rubra)transcriptome[J].Journal of American Botany,2012,99(12):e501-507.
- [43]ROWLAND L J,ALKHAROUF N,DARWISH O,OGDEN E L,POLASHOCK J J,BASSIL N V,MAIN D.Generation and analysis of blueberry transcriptome sequences from leaves,developing fruit,and flower buds from cold acclimation through deacclimation[J].BMC Plant Biology,2012,12:46.
- [44]LIU Q,ZHU A,CHAI L,ZHOU W,YU K,DING J,XU J,DENG X.Transcriptome analysis of a spontaneous mutant in sweet orange Citrus sinensis(L.)Osbeck during fruit development[J].Journal of Experimental Botany,2009,60(3):801-813.
- [45]HANSEN K D,WU Z,IRIZARRY R A,LEEK J T.Sequencing technology does not eliminate biological variability[J].Nature Biotechnology,2011,29(7):572-573.
- [46]LEVIN J Z,YASSOUR M,ADICONIS X,NUSBAUM C,THOMPSON D A,FRIEDMAN N,GNIRKE A,REGEV A.Comprehensive comparative analysis of strand-specific RNA sequencing methods[J].Nature Methods,2010,7(9):709-715.
- [47]ZHONG S,JOUNG J G,ZHENG Y,CHEN Y R,LIU B,SHAO Y,XIANG J Z,FEI Z,GIOVANNONI J J.High-throughput illumina strand-specific RNA sequencing library preparation[J].Cold Spring Harbor Protocols,2011,8:940-949.