agbiodata pan-genome discussion · topics: 1. what is a "pan-genome” 2. examples of...

AgBioDatapan-genomediscussion

Wednesday,May6th,2020

We’vebeentalkingaboutpan-genomesforyearsnow,butwhatexactlyisapan-genome,whatisitgoodfor,andhowcandatabepresentedtohelpresearchers?

?

?

? ?

?

?

?

Topics:1.  Whatisa"pan-genome”

2.  Examplesofpan-genomes,tools,analyses.

3.  Discussion:howcanapan-genomebeuseful,whoisitusefulfor,howtomakedataaccessible,whatistheroleofdataportals?

Lighteningtalks:EloiDurant-PanacheFakepan-genomeviewerAlanCleary–GenomeContextViewerMarcelaTello-Ruiz-pangenomebrowsersforrice,maize,andgrape

Whatisapan-genome?

•  Genomeorgenefocused.•  Couldbereference-basedorall-by-all.•  CapturelargeorsmallstructuralvariaUon.•  Withinaspeciesorclade.•  Isitagraph,alignment,orsetofsyntenUcrelaUonships.

•  Whenisitapan-genome,whenisitvariaUondata?Isdiversitydataaformofpan-genome?

Somepan-genomeportalexamples

hXps://phytozome-next.jgi.doe.gov/cowpeapan

hXps://phytozome-next.jgi.doe.gov/brachypan

hXp://www.10wheatgenomes.com

hXp://animal.nwsuaf.edu.cn/code/index.php/panPig

hXp://animal.nwsuaf.edu.cn/code/index.php/panGoatTalks:

Somepan-genomevisualizaUons

•  Pan-tetris–standaloneJavaappforbacteriapan-genomes(download)–  hXps://www.ncbi.nlm.nih.gov/pmc/arUcles/PMC4547177/

•  Ricepan-genomeviewer:hXp://www.rmbreeding.cn/pan3k–  hXps://www.ncbi.nlm.nih.gov/pubmed/27940610

•  PPanGGOLiN:hXps://github.com/labgem/PPanGGOLiN–  hXp://dx.doi.org/10.1371/journal.pcbi.1007732

Somepan-genomecodefests

•  hXps://github.com/NCBI-Hackathons/TheHumanPangenome-workshoptodiscusstoolsinrelaUontopangenomeanalysis.Strategiesandtoolswerepresented.(Possiblefollow-upatBaylorCollegeofMedicineOctober11-13.)– hXps://f1000research.com/arUcles/8-1751

•  hXps://graph-genome.github.io/PantoGraphforSARS-CoV-2

Howcanapan-genomebeuseful,whoisitusefulfor,howtomakedataaccessible,whatistheroleofdata

portals?

PresentaUonsofpan-genomes,tools,analyses.

EloiDurant-PanacheFakepan-genomeviewer

hXps://meerketeer.ird.fr/PanacheFake

AlanCleary–GenomeContextViewer

hXps://legumeinfo.org/lis_context_viewer/

MarcelaTello-Ruiz–pan-genomebrowsersforrice,maize,andgrape

Rice:hXp://oge.gramene.org/(maize,grapevine,andsorghumareunderdevelopment)

How to think Pangenome

Visualization? Introducing Panache, a

pangenome explorer prototype

Éloi DURANT AgBioData Conference call – Pan-genomes

Introduction

[email protected] PhD student

MONTPELLIER

“Development of a tool for the visualization of plant

pangenomes”

Thinking visualization

Does it to scale to big genomes?

What representations can be done?

Seeing everything at once is a fantasy.

Thinking visualization Seeing everything at once is a

fantasy.

Overly complicated data are unreadable as such, cf. the ‘Hairball effect’

Detail is reached on focusing on specific perts

Information = visualization x data processing

Panache

Panache: PANgenome Analyzer with CHromosomal

Exploration

Summarization of information + exploration

Summarization: access to inner properties Exploration: manipulation of multiple representations

Panache

https://meerketeer.ird.fr/PanacheFake

https://meerketeer.ird.fr/PanacheNapus

Panache

What is missing?

Exploration through different zoom scales

More representations

“Pangenomes, why not, but I don’t want to loose all my previous analyses.”

Data

Contact

SingingMeerkat/Panache

[email protected]

@MeerkatSinging

GenomeContextViewer

Alan Cleary

Micro-Synteny

query gene

neighbors neighbors

genomic interval

chromosome

Query Track

Functional Annotations

Biology●  Intra-track homology

○  Copy number

physical distance

Micro-SyntenyTrack Search

alig

ned

sim

ilar

trac

ks

Dot PlotsBiology●  Inter-track homology

○  Copy number variation○  Gene presence/absence

variation○  Inversions

genomic interval

Macro-SyntenyBlock Search

similar blocks

query track

SpeciesBiology●  Preservation of large structures

AllTogether

Pangenomics-Arabidopsisthaliana

Pangenomics-Vignaunguiculata

Pangenomics-Vignaunguiculatapangenesets

Traditional gene families

Pan gene sets

Resources

Cleary, Alan, and Andrew Farmer. "Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny." Bioinformatics 34.9 (2017): 1562-1564. hXps://legumeinfo.org/lis_context_viewerhXps://github.com/legumeinfo/lis_context_viewerGlycineexampleArabidopsisexample

PlantPanGenomeBrowsers-UUlizingtheGramene&Ensembl

Infrastructure

MarcelaKareyTello-Ruiz,PhDMay6,2020

TypesofPanGenomesHomolog-basedstrategy(all-by-all)-Thegenomesofindividualsareindependentlyassembled,andthepresence/absenceinagenefamilyisdeterminedbyclusteringproteinsequencesintohomologs.

1.   “Map-to-pan”strategy(reference-based)-Pangenomesequencesareconstructedbycombiningawell-annotatedreferencegenomewithnewlyidenUfiednon-referencerepresentaUvesequences,fromwhichthepresence/absenceofageneisthendeterminedbasedonreadcoveragealerindividualreadsaremappedtothepangenome.Highlyrecommendedforeukaryo9cpangenomeanalysis.

Huetal(2020)

PhylogeneUcGeneTrees●  Clusterhomologousgenefamilies●  Consensusof5tree-buildingmethods

○  NJ-dN,NJ-dS,NJ-mm,Phyml-aa,Phyml-nt●  Infersorthologsandparalogs●  TaxonomicdaUng●  InteracUvetree-browserforCross-species

hXp://useast.ensembl.org/info/docs/compara/homology_method.htmlVilellaetal(2008);Schwartzetal(2003);Kentetal(2003)

UsingComparative PhylogenomicstoSupportaPan-GeneSpaceBrowser

Pan-Genome (gene space) Browsers

Oryza Genome Evolution (oge.gramene.org) Maize NAM Founders (maize-pangenome.gramene.org) ● PacBio/Bionano assembly of diverse maize

inbreds ● Kelly Dawe (U Georgia), Matt Hufford (Iowa

State U), Candice Hirsch, MaizeGDB: Carson Andorf, Maggie Woodhouse, Corteva: Kevin Fengler

Wild & cultivated Grapevine (vitis.gramene.org) ● Multiple PacBio & 10X genomes ● USDA-ARS VitisGen2 Project: Lance Cadle-Davidson (USDA-ARS, Geneva,

NY), Dario Cantu (UC Davis), Rachel Naegele (USDA-ARS, Parlier, CA) USDA-ARS portal for Sorghum genomics/breeding resources (sorghumbase.org) ● Multiple PacBio &10X genomes ● Chad Hayes (USDA-ARS, Lubbock TX), Corteva, community data sets JGI,

Terra Ref

SubsitesholdcollecUonsofcloselyrelatedreferencegenomes●  Withinspecies,genus,orcropgroup●  Outgroupspecies●  Sourcedbycollaboratorsandfundedprojects●  4subsitesinprogressforrice,maize,sorghum,&grapevine

UniformgeneannotaUonprotocol(inprogress)●  Species-customizedrepeatlibrary&evidencesets●  RNA-seqassemblies,PacBioIso-seq,EST,priorannotaUon●  Evidence-basedredicUon

Gramene/Ensembldatabases,Search,Views&PipelinesComparaGeneTrees&wholegenomealignment

●  Genefamilyassignment●  PhylogeneUctreebuild●  Ortholog&paralogcalling●  TaxonomicdaUng●  PairwiseWGA(BLASTZ-CHAIN-NET)●  GeneUcvariaUons(SVs&SNPs)

Gene-centeredpairwisesyntenymaps●  Mapscollinear&near-collinearorthologs●  Neighborhoodview

Pangenomeindex●  ClustersyntelogsbytransiUveclosure●  PresenceabsencevariaUon(PAV)●  CopynumbervariaUon(CNV)●  Core&dispensablegenome

Pan-Genome (gene space) Browsers

Gramene Search & Enhanced Tree Views

Pangenomicsearchsummary

Alternategene-treeviews●  Gene-neighborhood●  MulUplesequencealignment●  Protein-domainhighlighUng

MaizePan-Genome:Genetreealignmentview

Prototypesite:hXp://maize-pangenome-ensembl.gramene.org

MaizePan-Genome:MulUple-sequencealignmentview


MaizePan-Genome:GeneneighborhoodconservaUonview


Pan- Genome (gene space) Browsers


UniformgeneannotaUonprotocol(inprogress)●  Species-customizedrepeatlibrary&evidencesets●  RNA-seqassemblies,PacBioIso-seq,EST,priorannotaUon●  Evidence-based+abiniUopredicUon





Usecase:OriginofDomes@ca@ongenesforPAVs

Genetreeandwhole-genomealignmentconfirmspresenceofSh1inO.barthiiprogenitor,butabsenceinAfricanrice,aspreviouslyobserved(Wangetal.2014).


Futuretargets:●  Wholegenomealignmentscomplimentthe

proteingenetreesandcharacterizaUonofnon-codingtranscriberegions.

●  Regulatorynontranscribedregions








Futuretargets:●  SupportforanalysesworkflowtoextractPAV

&CNVs;Core&dispensablegenomes●  Novelviewstoimproveaccessand

interpretaUon●  ImprovedSearch







Thanks!WegratefullyacknowledgesupportfromgrantsNSF#1744001,NSF#1127112,andUSDA-ARS#58-8062-7-008.●  SharonWei-Analyses,web&Ensemblsolware●  AndrewOlson-APIdevelopment,search,views●  MarcelaK.Tello-Ruiz-Species-specificcollaboraUons&outreach●  WareLabmembers

Collaborators

●  Ensembl-Infrastructure●  OGEproject●  NAMproject●  VG2project

SomeIntroductoryPapersBayeretal.,2017.Assemblyandcomparisonoftwo

closelyrelatedBrassicanapusgenomes.Gaoetal.,2019.Thetomatopan-genomeuncovers

newgenesandararealleleregulaUngfruitflavorGoliczetal.,2020.Pangenomicscomesofage:

FrombacteriatoplantandanimalapplicaUons.Montenegroetal.,2017.Thepangenomeof

modernhexaploidbreadwheat.ShermanandSalzberg,2020.Pan-genomicsinthe

humangenomeera.

BayerPE,HurgobinB,GoliczA,ChanK,YuanY,LeeHT,RentonM,MengJ,LiR,LongY,ZouJ,BancrolI,ChalhoubB,KingG,BatleyJ,EdwardsD.(2017)AssemblyandcomparisonoftwocloselyrelatedBrassicanapusgenomes.PlantBiotechnologyJournal.15(12):1602-1610

DanileviczMF,TayFernandezCG,MarshJI,BayerPE,EdwardsD.(2020)PlantPangenomics:Approaches,ApplicaUonsandAdvancements.CurrentOpinioninPlantBiology.54:15-25

DolatabadianA,BayerP,TirnazS,HurgobinB,EdwardsD,BatleyJ.(2020)CharacterisaUonofdiseaseresistancegenesintheBrassicanapuspangenomerevealssignificantstructuralvariaUon.PlantBiotechnologyJournal.18(4):969-982

DolatabadianA,PatelDA,EdwardsDandBatleyJ.(2017)CopynumbervariaUonanddiseaseresistanceinplants.TheoreUcalandAppliedGeneUcs.130(12),2479-2490

GoliczA,BayerPE,BhallaPL,BatleyJ,EdwardsD.(2020)Pangenomicscomesofage:FrombacteriatoplantandanimalapplicaUons.TrendsinGeneUcs63(2):132-145

GoliczAA,BayerPE,BarkerG,EdgerPP,KimHR,MarUnezPA,ChanCKK,Severn-EllisA,McCombieR,ParkinIAP,PatersonAH,PiresJC,SharpeAG,TangH,R.TeakleGR,TownCD,BatleyJ,EdwardsD.(2016)ThepangenomeofanagronomicallyimportantcropBrassicaoleracea.NatureCommunicaUons7:13390

HirschCN,FoersterJM,JohnsonJM,SekhonRS,MuXoniG,VaillancourtB,PeñagaricanoF,LindquistE,PedrazaMA,BarryK,deLeonN,KaepplerSM,BuellCR.Insightsintothemaizepan-genomeandpan-transcriptome.PlantCell.2014Jan;26(1):121-35.doi:10.1105/tpc.113.119982.

Morereferences

Hübneretal..Sunflowerpan-genomeanalysisshowsthathybridizaUonalteredgenecontentanddiseaseresistance.NatPlants.2019Jan;5(1):54-62.doi:10.1038/s41477-018-0329-0.hepangenomeofanagronomicallyimportantcropBrassicaoleracea.NatureCommunicaUons7:13390.

HurgobinB,GoliczA,BayerP,ChanK,TirnazS,DolatabadianA,SchiesslS,SamansB,MontenegroJ,ParkinI,PiresC,ChalhoubB,KingG,SnowdonR,BatleyJandEdwardsD.Homoeologousexchangeisamajorcauseofgenepresence/absencevariaUonintheamphidiploidBrassicanapus.(2018)PlantBiotechnologyJournal.16(7),1265-1274

HurgobinHandEdwardsD.(2017)SNPdiscoveryusingapangenome:hasthesinglereferenceapproachbecomeobsolete?Biology6(1):E21

MontenegroJDM,GoliczAA,BayerPE,HurgobinB,LeeHT,ChanCKK,VisendiP,LaiK,DoleželJ,BatleyJ,EdwardsD.(2017)Thepangenomeofmodernhexaploidbreadwheat.PlantJournal.90(5):1007-1013

Ouetal.,2018.Pan-genomeofculUvatedpepper(Capsicum)anditsuseingenepresence–absencevariaUonanalyses.NewPhytologistVol220(2):360-363

Pinosioetal.,2016.CharacterizaUonofthePoplarPan-GenomebyGenome-WideIdenUficaUonofStructuralVariaUon.MolecularBiologyandEvoluUon,Volume33,Issue10,October2016,Pages2706–2719.

Readetal.,2013.PangenomeofthephytoplanktonEmilianiaunderpinsitsglobaldistribuUon.Naturevolume499,pages209–213.

SunC1,2,HuZ1,2,ZhengT3,LuK1,ZhaoY1,WangW3,ShiJ4,WangC3,LuJ1,ZhangD4,5,LiZ6,WeiC7,2.RPAN:ricepan-genomebrowserfor∼3000ricegenomes.NucleicAcidsRes.2017Jan25;45(2):597-605.doi:10.1093/nar/gkw958.

Morereferences-conUnued

Valliyodanetal..2019ConstrucUonandcomparisonofthreenewreference-qualitygenomeassembliesforsoybean.ThePlantJournal.100(5):1066-1082

Varshneyetal.,2019Resequencingof429chickpeaaccessionsfrom45countriesprovidesinsightsintogenomediversity,domesUcaUonandagronomictraits.NatureGeneUcs51,857-864.

Wangetal.,2018.GenomicvariaUonin3,010diverseaccessionsofAsianculUvatedrice.Naturevolume557,pg43–49.

YuJ,GoliczA,LuK,DossaK,ZhangY,ChenJ,WangL,YouJ,FanD,EdwardsD,ZhangX.(2019)InsightintotheevoluUonandfuncUonalcharacterisUcsofthepan-genomeassemblyfromsesamelandracesandmodernculUvars.PlantBiotechnologyJournal.17(5):881-892BayerPE;GoliczA,TirnazS,ChanKCC,EdwardsD,BatleyJ.(2019)VariaUoninabundanceofpredictedresistancegenesintheBrassicaoleraceapangenome.PlantBiotechnologyJournal.17(4):789-800

ZhaoJ,BayerPE,RuperaoP,SaxenaRK,KhanAW,GoliczAA,NguyenHT,BatleyJ,EdwardsD,VarshneyRK.2020TraitassociaUonsinthepangenomeofpigeonpea(Cajanuscajan)PlantBiotechnologyJournal.

Morereferences-conUnued

agbiodata pan-genome discussion · topics: 1. what is a "pan-genome” 2. examples of...

Documents