辣椒全基因组测序

admin管理员组

文章数量:1530893

2024年4月23日发(作者：)

Whole-genomesequencingofcultivatedandwild

peppersprovidesinsightsintoCapsicumdomestication

andspecialization

ChengQin

a,b,c,1

,ChangshuiYu

b,1

,YaouShen

a,1

,XiaodongFang

d,e,1

,LangChen

b,1

,JiumengMin

d,1

,JiaowenCheng

c

,

ShancenZhao

d

,MengXu

d

,YongLuo

b

,YulanYang

d

,ZhimingWu

f

,LikaiMao

d

,HaiyangWu

d

,ChangyingLing-Hu

b

,

HuangkaiZhou

d

,HaijianLin

a

,SandraGonzález-Morales

g

,-Saavedra

h

,HaoTian

b

,XinTang

c

,MaojunZhao

i

,

ZhiyongHuang

d

,AnweiZhou

b

,XiaomingYao

d

,JunjieCui

c

,WenqiLi

d

,ZheChen

a

,YongqiangFeng

b

,YongchaoNiu

d

,

ShiminBi

b

,XiuweiYang

b

,WeipengLi

c

,HuiminCai

d

,XirongLuo

b

,SalvadorMontes-Hernández

j

,

-González

g

,ZhiqiangXiong

d

,XiujingHe

a

,LijunBai

d

,ShuTan

c

,XiangqunTang

b

,DanLiu

d

,JinwenLiu

d

,

ShangxingZhang

b

,MaoshanChen

d

,LuZhang

d,k

,LiZhang

c

,YinchaoZhang

a

,WeiqinLiao

b

,YanZhang

d

,MinWang

b

,

XiaodanLv

d

,BoWen

d

,HongjunLiu

a

,HemiLuan

d

,YonggangZhang

b

,ShuangYang

d

,XiaodianWang

b

,JiaohuiXu

d

,

XueqinLi

b

,ShuaichengLi

k

,JunyiWang

d

,AlainPalloix

l

,d

m

,YingruiLi

d

,AndersKrogh

e

,

-Bustamante

h

,LuisHerrera-Estrella

g,2

,YeYin

d,2

,JipingYu

b,2

,KailinHu

c,2

,andZhimingZhang

a,2

a

KeyLaboratoryofBiologyandGeneticImprovementofMaizeinSouthwestRegion,MinistryofAgriculture,MaizeResearchInstituteofSichuanAgricultural

University,Wenjiang611130,China;

b

PepperInstitute,

d

ZunyiAcademyofAgriculturalSciences,Zunyi563102,China;

c

CollegeofHorticulture,SouthChina

AgriculturalUniversity,Guangzhou510642,China;BeijingGenomicsInstitute-Shenzhen,Shenzhen518083,China;

e

DepartmentofBiology,Universityof

Copenhagen,DK-2200Copenhagen,Denmark;

f

CollegeofHorticultureandLandscapeArchitecture,ZhongkaiUniversityofAgricultureandEngineering,

Guangzhou510225,China;

g

LaboratorioNacionaldeGenómicaparalaBiodiversidad(Langebio)delCentrodeInvestigaciónydeEstudiosAvanzados

(Cinvestav),Irapuato,36821,Mexico;

h

DepartamentodeIngenieríaGenética,CentrodeInvestigaciónydeEstudiosAvanzadosdelIPN(Cinvestav)-Unidad

Irapuato,Irapuato,36821,México;

i

CollegeofBiologyandScience,SichuanAgriculturalUniversity,Ya’an625014,China;

j

InstitutoNacionaldeInvestigaciones

Forestales,AgrícolasyPecuarias,CampoExperimentalBajío,Celaya,38010,México;

k

DepartmentofComputerScience,CityUniversityofHongKong,Hong

Kong999077,China;

l

INRAProvence-Alpes-Côted’Azur,UR1052,UnitédeGénétiqueetAméliorationdesFruitsetLégumes,CS60094,F-84140Montfavet

Cedex,France;and

m

ChilePepperInstitute,NewMexicoStateUniversity,LasCruces,NM88003

ContributedbyLuisHerrera-Estrella,January19,2014(sentforreviewDecember12,2013)

Asaneconomiccrop,peppersatisfiespeople’sspicytasteandhas

ofpepper,themolecularmechanismsthatmodulatefruitsize,

abetterunderstandingofCap-

shape,andyieldaremostlyunknown.

sicumevolution,domestication,andspecialization,wepresenthere

Sincethe1990s,geneticdiversityandallelicshiftsamong

thegenomesequenceofthecultivatedpepperZunla-1(L.)

cultivars,domesticatedlandraces,andwildaccessionshavebeen

anditswildprogenitorChiltepin(usculum).

partiallyexploredusingrestrictedsetsofanonymousorneutral

Weestimatethatthepeppergenomeexpanded∼0.3Mya(with

respecttothegenomeofotherSolanaceae)byarapidamplification

Significance

ofretrotransposonselements,resultinginagenomecomprisedof

∼81%imately79%of3.48-Gbscaffolds

containing34,476protein-codinggeneswereanchoredtochromo-

Thetwopeppergenomestogetherwith20resequencingac-

isonofcultivatedand

cessions,including3accessionsthatareclassifiedassemiwild/

wildpeppergenomeswith20resequencingaccessionsrevealed

wild,provideabetterunderstandingoftheevolution,domes-

molecularfootprintsofartificialselection,providinguswithalistof

tication,anddivergenceofvariouspepperspeciesandultimately,

foundthatdosagecompen-

willenhancefuturegeneticimprovementofthisimportant

sationeffectoftandemduplicationgenesprobablycontributedtothe

worldwidecrop.

sicumreferencegenome

Authorcontributions:C.Q.,R.F.R.-B.,L.H.-E.,,J.Y.,K.H.,edresearch;

providescrucialinformationforthestudyofnotonlytheevolutionof

C.Q.,C.Y.,Y.S.,X.F.,L.C.,,,,Z.W.,C.L.-H.,,S.G.-M.,D.L.T.-S.,

thepeppergenomebutalso,theSolanaceaefamily,anditwillfacil-

H.T.,XinTang,M.Z.,A.Z.,,Z.C.,Y.F.,Y.N.,S.B.,,WeipengLi,H.C.,,

itatetheestablishmentofmoreeffectivepepperbreedingprograms.

S.M.-H.,M.A.L.-G.,Z.X.,S.T.,XiangqunTang,J.L.,,M.C.,LiZhang,,Yan

Zhang,M.W.,B.W.,,,YonggangZhang,X.W.,,S.L.,A.P.,P.W.B.,A.K.,

|

R.F.R.-B.,L.H.-E.,J.Y.,K.H.,medresearch;WenqiLi,L.B.,,S.Y.,J.X.,

denovogenomesequencegenomeexpansion

|

Solanaceaeevolution

J.W.,ributednewreagents/analytictools;C.Q.,J.M.,,M.X.,,

Z.W.,L.M.,H.W.,H.Z.,Z.H.,A.Z.,,,S.B.,,S.M.-H.,M.A.L.-G.,X.H.,

P

epper(Capsicum)isaneconomicallyimportantgenusofthe

XiangqunTang,D.L.,LuZhang,andYinchaoZhanganalyzeddata;andC.Q.,X.F.,,

andL.H.-hepaper.

Solanaceaefamily,

Theauthorsdeclarenoconflictofinterest.

genusincludesatleast32speciesnativetotropicalAmerica(1),of

FreelyavailableonlinethroughthePNASopenaccessoption.

L.,umL.,seJacq.,-

Datadeposition:usculumwhole-

tescensL.,ens(Ruiz&Pavon)weredomesticated

genomeshotgunsequencesreportedinthispaperhavebeendepositedintheGenBank

veAmericans(2).Peppershave

database(00000000andASJV00000000,respectively).TheRNA-sequence

awidediversityoffruitshape,size,tpeppersare

readsandsmallRNA-sequencereadsdatareportedinthispaperhavebeendepositedinthe

GeneExpressionOmnibus(GEO)database,/geo(accessionnos.

usedasspices,he

GSE45037,GSE45040,andGSE45154).AdditionalinformationisaccessiblethroughthePep-

returnofColumbusfromAmericain1492andsubsequentvoyages

perGenomeDatabasewebsite().

ofexploration,peppersspreadaroundtheworldbecauseofadap-

SeeCommentaryonpage5069.

tationtodifferentagroclimaticregionsandrapidadoptionofpep-

1

C.Q.,C.Y.,Y.S.,X.F.,L.C.,butedequallytothiswork.

perindifferentculturesasfood,medicine,andornamentals(3,4).

2

Towhomcorrespondencemaybeaddressed.E-mail:lherrera@tav.

Pepperglobalproductionin2011reached34.6milliontonsfresh

mx,yinye@,yujiping62@,hukailin@,orzzmmaize@

fruitand3.5milliontonsdriedpodsharvestedin3.9millionhec-

.

tares().Despitethegrowingcommercialimportance

/lookup/suppl/doi:10.

1073/pnas.1400975111/-/DCSupplemental.

/cgi/doi/10.1073/pnas.1400975111PNAS

|

April8,2014

|

vol.111

|

no.14

|

5135–5140

Y

R

A

T

N

E

M

M

O

C

E

E

S

L

A

R

U

S

E

T

C

L

U

N

C

E

I

I

R

C

G

S

A

molecularmarkers(5–9)andannotatedDNAsequences(10).

Thesestudiesreportedthatthegeneticvariabilityamongsweet

cultivarswasveryrestrictedandsug-

gestedthatchangesintheallelicfrequenciesandasubsequentloss

ofdiversityduringthetransitionfromwildtocultivatedpopu-

a-

tivelylowlevelsofgeneticdiversityintheprimarygenepoolhave

rprimaryreason

forlimitedappliedandbasicresearchinpepperhasbeenlackof

areferencegenomesequenceof∼3.3Gb(11).Recentwork

comparingtwomembersoftheSolanaceaefamily(pepperand

tomato)hasbeguntoshedlightontheprocessesthatinfluence

thedynamicsofgenomesizeinangiosperms(12,13).

Tocontributetotheunderstandingofpepperbiologyand

evolutionandaccelerateagriculturalapplications,wegenerated

andanalyzedtworeferencegenomesequencesofcultivated

Zunla-1andwildChiltepin(2n=2x=24).Thetwopeppergenomes

togetherwith20resequencingaccessions,including3accessions

thatareclassifiedassemiwild/wild,provideabetterunderstand-

ingoftheevolution,domestication,anddivergenceofvarious

pepperspeciesandultimately,willenhancefuturegeneticim-

provementofthisimportantworldwidecrop.

ResultsandDiscussion

LargeGenomeAssemblyandChromosomeAnchoring.

Becauseof

theircommercialandgeneticadvantages,weselectedthewidely

accessionZunla-1anditwildprogenitor

Chiltepinforgenomesequencing(SIAppendix,SIText).Using

thewhole-genomeshotgunapproach,wegeneratedatotalof

325-and205-Gbhigh-qualityreadsfromvariousIlluminase-

quencinglibrariesforZunla-1andChiltepin,respectively(SI

Appendix,TablesS1andS2).Asexpected,thegenomesizeof

Zunla-1wasestimatedtobe3.26Gb,whichisslightlylargerthan

the3.07-GbsizeofChiltepinbyK-meranalysis(SIAppendix,Fig.

S1andTableS3);estimationsareconsistentwithaprevious

report(11).Shortsequencingreads,correspondingto99-and

67-foldgenomicdepths(SIAppendix,Fig.S2),werehierarchi-

callyanditerativelyassembledintocontigswithN50lengths

(50%ofthegenomeisinfragmentsofthislengthorlonger)of

55and52kbforZunla-1andChiltepin,respectively(Table1).

Pair-endinformationwasusedsequentiallyinassemblerSOAP-

denovo(14)togeneratescaffoldscomprising3.48-and3.35-Gb

scaffoldswithN50lengthsof1.23Mband445kb,respectively

(Table1andSIAppendix,TableS4).ThesmallerN50scaffold

lengthforChiltepinwasprimarilycausedbyalowersequencing

nalysis,wereferto

genome.

Weassessedthequalityandcoverageofthetwogenomesusing

1.7-Mb

sequencesfrom15BACs,∼97%couldbecoveredbythescaffolds

withidentityof0.95andEvalueof1e-20,indicatingreliablelocal

assembly(SIAppendix,TableS5).Morethan98%of83,029ESTs

couldbealignedtothegenomesbythecriteriaoflength>200bp

andhit>97%,whichshowedextensivegenomiccoverage(SIAp-

pendix,TableS6).Inaddition,23and18largenuclearregions

matchingthechloroplastgenome(>2kband>98%sequence

identity)wereidentifiedinthereferenceandChiltepingenomes,

respectively(DatasetS1).Thisphenomenonissimilartothat

observedintomato(15)andtobacco(16),suggestingactive

genetransferfromthecholoroplastintothenucleargenomeof

theSolanaceae.

Thescaffoldswerethenanchoredto12linkagegroupsby7,657

SNPmarkersinournewlydevelopedhigh-densitygeneticmap

(SIAppendix,SIText)(17),andtheycouldbeassignedaschro-

mosomes1–12(Chr01–Chr12)accordingtothecytological

analysis(1,18)(Fig.1,trackA).Thepseudochromosomes

consistof4,956scaffoldswith31,201geneslocated,corre-

spondingto79%ofthereference(Table1andSIAppendix,

Fig.S3andTableS7).Ithasbeenreportedthat,duringdo-

mestication,chromosometranslocationeventsdifferentiate

cultivarsfromwildprogenitors(19),whichhelpedustoprecisely

anchor29,081scaffolds(2.42Gb;30,123genes)ofChiltepinto

chromosomes(Table1andSIAppendix,TableS7).Wealsoob-

servedSshapewhenthegeneticandphysicaldistanceswerean-

alyzed(SIAppendix,Fig.S3),reflectingextensiverecombination

suppressionaroundthecentromeres(Fig.1,tracksAandB).

Interestingly,Chr08showedashortterminalarm(Fig.1,track

AandSIAppendix,Fig.S3),supportingtheconclusionthat

thechromosomeisacrocentric(19).

ofhomology-basedsearchesandabinitiomodeling,wefound

thatmorethan81%(∼2.7Gb)ofthepeppergenomeswere

composedofdifferenttransposableelements(TEs),whichis

significantlyhigherthanTEs(∼61%)inpotatoandtomato

(Table1andDatasetS2).MostoftheplantTEcategorieswere

identifiedinpepper,including70.3%LTRretrotransposonsand

4.5%DNAtransposons(Table1).Clearly,LTRretrotrans-

posonscontributedmoretothegenomeexpansionthanthose

inpotato(47.2%),tomato(50.3%),andgrape(46.2%),which

parallelsthegenomictopologyofthemaizegenome(75%)(20).

RepetitiveElementsandGenomeExpansion.

Usingacombination

isonoffeaturesofpepper,tomato,andpotatogenomes

Genomefeatures

Assembledgenomesize(Mb)

‡

Numberofscaffolds

§

ContigN50(bp)

{

ScaffoldN50(bp)

{

GCcontent(%)

Repeatrate(%)

LTRrate(%)

Predictedprotein-codinggenes

Averagegenelength(bp)

AverageCDSlength(bp)

Averageexonnumberpergene

Sequenceanchoredonchromosome(%)

Genesanchoredonchromosome(%)

Cultivatedpepper

3,349

967,017

55,436

1,226,833

34.9

80.9

70.3

35,336

3,363

1,020

4.27

78.95

88.29

Wildpepper

3,480

1,973,483

52,229

445,585

35.0

81.4

70.1

34,476

3,235

1,006

4.04

69.68

87.37

Tomato*

760

NA

NA

NA

34.0

61.3

50.3

33,726

3,006

1,063

4.6

NA

NA

Potato

†

727

NA

NA

NA

34.8

61.6

47.2

38,492

2,476

928

3.49

NA

NA

NA,notavailable;GC,guanine-cytosine;CDS,codingDNAsequence.

*Modifiedfromref.15.

†

Modifiedfromref.27.

‡

Thefragmentsoftheungappedgenomeassembly.

§

Thelengthshorterthan100bpwasnotincludedinthestatistics.

{

N50valuesofthegenomeassemblywerecalculatedusingthefragmentslongerthan100bp.

5136

|

/cgi/doi/10.1073/pnas.1400975111Qinetal.

本文标签： 辣椒测序基因组