Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.
In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.
Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2026-04-21 01:33:10.599212","timezone_type":1,"timezone":"+02:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":"Biodiversity; Genome scan; Genotyping by sequencing; In silico digestion; RADseq; Southern Ocean","OtherDescriptors":null,"Notes":null,"AnaPub":2021,"MonPub":null,"DateUpdate":"2022-08-04","DateCreate":"2022-07-01","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":"WOS:000687149000001","VABBcode":null,"OpenAcc":1,"DOI":"10.1186/s12864-021-07917-3"},"refs":null,"anarec":{"AnaID":353289,"PubliDate":2021,"Pagination":"625","XtraPublOfAnaID":null,"ISBN":null,"Volume":"22","Issue":"1","BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":198247,"SerRR":"BMC Genomics. BioMed Central: London. e-ISSN 1471-2164","StandardTitleSer":"BMC Genomics","ISSN":null,"AbbrevSer":"BMC Genom.","StandardTitleMon":null,"StartPage":20,"Pages":null,"ToPubliDate":null,"BRefBibLvlCode":"S","SerNotes":null},"monrec":null,"serrec":null,"relations":null,"relationsRev":null,"addrec":null,"othpubs":null,"ownerships":null,"authors":[{"AutName":"Christiansen","Firstname":"Henrik","Initials":"H.","Affiliation":"Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":317347,"OrderNr":1,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"LBEG","InsFSN":"KU Leuven; Departement Biologie; Ecology, Evolution and Biodiversity Conservation Section; Laboratorium voor Biodiversiteit en Evolutionaire Genomica","ORCID":"0000-0001-7114-5854","PersID":31955,"InsID":12175},{"AutName":"Heindler","Firstname":"Franz Maximilian","Initials":"F.M.","Affiliation":"Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":317345,"OrderNr":2,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"LBEG","InsFSN":"KU Leuven; Departement Biologie; Ecology, Evolution and Biodiversity Conservation Section; Laboratorium voor Biodiversiteit en Evolutionaire Genomica","ORCID":"0000-0003-4305-7296","PersID":34274,"InsID":12175},{"AutName":"Hellemans","Firstname":"Bart","Initials":"B.","Affiliation":"Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":157752,"OrderNr":3,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"LBEG","InsFSN":"KU Leuven; Departement Biologie; Ecology, Evolution and Biodiversity Conservation Section; Laboratorium voor Biodiversiteit en Evolutionaire Genomica","ORCID":"0000-0001-5963-8074","PersID":2665,"InsID":12175},{"AutName":"Jossart","Firstname":"Quentin","Initials":"Q.","Affiliation":"Marine Biology Group, Vrije Universiteit Brussel (VUB)","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":493270,"OrderNr":4,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":"Vrije Universiteit Brussel; Faculteit Wetenschappen & Bio-ingenieurswetenschappen; Vakgroep Biologie; Ecology and Biodiversity; Onderzoeksgroep Mariene Biologie","ORCID":"0000-0002-2280-243X","PersID":30150,"InsID":11956},{"AutName":"Pasotti","Firstname":"Francesca","Initials":"F.","Affiliation":"Marine Biology Research Group, Ghent University","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":214711,"OrderNr":5,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"MARBIOL","InsFSN":"Universiteit Gent; Faculteit Wetenschappen; Vakgroep Biologie; Onderzoeksgroep Mariene Biologie","ORCID":"0000-0002-8971-8195","PersID":19361,"InsID":13},{"AutName":"Robert","Firstname":"Henri","Initials":"H.","Affiliation":"OD Nature, Royal Belgian Institute of Natural Sciences","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":493272,"OrderNr":6,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"OD Natuur","InsFSN":"Koninklijk Belgisch Instituut voor Natuurwetenschappen; Operationele Directie Natuurlijk Milieu","ORCID":"0000-0002-3593-4802","PersID":13080,"InsID":13002},{"AutName":"Verheye","Firstname":"Marie","Initials":"M.","Affiliation":"OD Nature, Royal Belgian Institute of Natural Sciences","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":493273,"OrderNr":7,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"OD Natuur","InsFSN":"Koninklijk Belgisch Instituut voor Natuurwetenschappen; Operationele Directie Natuurlijk Milieu","ORCID":"0000-0001-8702-9292","PersID":34511,"InsID":13002},{"AutName":"Danis","Firstname":"Bruno","Initials":"B.","Affiliation":"Marine Biology Laboratory, Université Libre de Bruxelles (ULB)","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":273910,"OrderNr":8,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"BIOMAR","InsFSN":"Université Libre de Bruxelles; Faculté des Sciences; Département de Biologie des Organismes; Centre Interuniversitaire de Biologie Marine (ULB - UMH); Unité de Biologie Marine","ORCID":"0000-0002-9037-7623","PersID":3861,"InsID":158},{"AutName":"Kochzius","Firstname":"Marc","Initials":"M.","Affiliation":"Marine Biology Group, Vrije Universiteit Brussel (VUB)","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":493275,"OrderNr":9,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":"Vrije Universiteit Brussel; Faculteit Wetenschappen & Bio-ingenieurswetenschappen; Vakgroep Biologie; Ecology and Biodiversity; Onderzoeksgroep Mariene Biologie","ORCID":"0000-0001-8953-4719","PersID":23711,"InsID":11956},{"AutName":"Leliaert","Firstname":"Frederik","Initials":"F.","Affiliation":"Marine Biology research group, Ghent University","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":255054,"OrderNr":10,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"MARBIOL","InsFSN":"Universiteit Gent; Faculteit Wetenschappen; Vakgroep Biologie; Onderzoeksgroep Mariene Biologie","ORCID":"0000-0002-4627-7318","PersID":227,"InsID":13},{"AutName":"Moreau","Firstname":"Camille","Initials":"C.","Affiliation":"Marine Biology Laboratory, Université Libre de Bruxelles (ULB)","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":273912,"OrderNr":11,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"BIOMAR","InsFSN":"Université Libre de Bruxelles; Faculté des Sciences; Département de Biologie des Organismes; Centre Interuniversitaire de Biologie Marine (ULB - UMH); Unité de Biologie Marine","ORCID":"0000-0002-0981-7442","PersID":31084,"InsID":158},{"AutName":"Patel","Firstname":"Tasnim","Initials":"T.","Affiliation":"OD Nature, Royal Belgian Institute of Natural Sciences","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":493280,"OrderNr":12,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"OD Natuur","InsFSN":"Koninklijk Belgisch Instituut voor Natuurwetenschappen; Operationele Directie Natuurlijk Milieu","ORCID":null,"PersID":36709,"InsID":13002},{"AutName":"Van de Putte","Firstname":"Anton","Initials":"A.P.","Affiliation":"Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":492633,"OrderNr":13,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"LBEG","InsFSN":"KU Leuven; Departement Biologie; Ecology, Evolution and Biodiversity Conservation Section; Laboratorium voor Biodiversiteit en Evolutionaire Genomica","ORCID":"0000-0003-1336-5554","PersID":5287,"InsID":12175},{"AutName":"Vanreusel","Firstname":"Ann","Initials":"A.","Affiliation":"Marine Biology Research Group, Ghent University","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":214282,"OrderNr":14,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"MARBIOL","InsFSN":"Universiteit Gent; Faculteit Wetenschappen; Vakgroep Biologie; Onderzoeksgroep Mariene Biologie","ORCID":"0000-0003-2983-9523","PersID":32,"InsID":13},{"AutName":"Volckaert","Firstname":"Filip","Initials":"F.A.M.","Affiliation":"Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":157751,"OrderNr":15,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"LBEG","InsFSN":"KU Leuven; Departement Biologie; Ecology, Evolution and Biodiversity Conservation Section; Laboratorium voor Biodiversiteit en Evolutionaire Genomica","ORCID":"0000-0003-4342-4295","PersID":13,"InsID":12175},{"AutName":"Schön","Firstname":"Isa","Initials":"I.","Affiliation":"OD Nature, Royal Belgian Institute of Natural Sciences","Discriminator":null,"CorporateFlag":0,"BEntID":350998,"AutID":493286,"OrderNr":16,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"OD Natuur","InsFSN":"Koninklijk Belgisch Instituut voor Natuurwetenschappen; Operationele Directie Natuurlijk Milieu","ORCID":"0000-0001-9269-6487","PersID":34614,"InsID":13002}],"mapdetails":null,"datasets":null,"monographs":null,"monparts":null,"serparts":null,"BEntOpen":null,"BEntPrivate":null,"availability":[{"BInstID":378639,"LibID":36,"BRefID":353289,"EmbargoDate":null,"FullEmbargoDate":null,"PhysMedID":16,"hasOCRd":1,"ShelfLocCode":"378639","RFID":null,"PaidValue":null,"Medium":"Server","Description":"VLIZ Open Access","Acronym":"VLIZ","Library":"Vlaams Instituut voor de Zee","DutchTerm":"Open access","URL":null,"ClassifID":53,"Classification":"Open access","ReqLink":null,"ClassifTypID":1,"URLLocation":"https://www.vliz.be/imisdocs/publications/","SubDir":null,"InternalReq":0,"LoggedInReq":0,"Disclaimer":null,"DutchDisclaimer":null,"FileFormat":".pdf","FileDescr":"pdf","InsPub":1,"InsID":36,"FileFormID":6,"LendableFlag":1,"PublicFlag":1,"orderLib":"A","Notes":null,"AccConID":null,"AccessConstraint":null,"LicURL":null}],"litstyles":null,"thespers":null,"arch2discl":null,"SERpubls":[{"PublName":"BioMed Central","City":"London"}],"MONpubls":null,"pictures":[],"thestermsPath":null,"thestermsASFA":null,"taxtermsASFA":null,"geotermsASFA":null,"collections":[{"Collection":"OMA - Open Marien Archief","ShortName":"OMA"}],"conf":null,"proj":null,"Physdatasets":null,"spcols":{"222":{"SpName":"BMB - Belgische Mariene Bibliografie","SpColID":222,"ParSpColID":null,"TopParID":null,"ShortName":"BMB","URLLocation":null,"LibID":36,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":null,"SpColPath":"BMB"},"991":{"SpName":"EMBRC acknowledged","SpColID":991,"ParSpColID":null,"TopParID":null,"ShortName":"EMBRC ackn","URLLocation":null,"LibID":36,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":null,"SpColPath":"EMBRC ackn"},"1019":{"SpName":"EMBRC Acknowledged A1","SpColID":1019,"ParSpColID":991,"TopParID":991,"ShortName":"EMBRC Ackn A1","URLLocation":null,"LibID":36,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":991,"SpColPath":"EMBRC ackn/EMBRC Ackn A1"},"221":{"SpName":"OMA - Open Marien Archief","SpColID":221,"ParSpColID":null,"TopParID":null,"ShortName":"OMA","URLLocation":null,"LibID":36,"OpenRepoFlag":1,"SpTypID":null,"TopParIDNotWebsite":null,"SpColPath":"OMA"},"422":{"SpName":"Section Marine Biology","SpColID":422,"ParSpColID":null,"TopParID":null,"ShortName":"MarBiol","URLLocation":null,"LibID":null,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":null,"SpColPath":"MarBiol"}},"doi":null,"publs":null,"serparttypes":null,"monauthors":null,"MParts":null,"SParts":null,"hLibs":null,"langs":[{"BEntID":350998,"AbstractFlag":0,"LangID":15,"LangCode":"en","Lang":"English","DutchTerm":"Engels","LangCodeExtended":"eng"},{"BEntID":350998,"AbstractFlag":1,"LangID":15,"LangCode":"en","Lang":"English","DutchTerm":"Engels","LangCodeExtended":"eng"}],"urls":[{"URL":"https://dx.doi.org/10.1186/s12864-021-07917-3","externalID":"10.1186/s12864-021-07917-3","URLTypeCode":"DOI","URLID":104006,"URLTypID":13,"URLType":"DOI","URLPrefix":"http://dx.doi.org/"}],"thesterms":null,"taxterms":null,"geoterms":null,"othterms":null,"asfacodes":null,"asfa2codes":null,"thestermsFRIS":null,"taxtermsFRIS":null,"geotermsFRIS":null,"othtermsFRIS":null,"resmessage":"","complete":1,"sessions":{"newSesName":"Bouchti, Zohra, Z.","newSesDate":{"date":"2022-07-01 14:21:55.743000","timezone_type":3,"timezone":"Europe/Brussels"},"updSesName":"Chisala, Chilekwa, C.","updSesDate":{"date":"2022-08-04 09:20:24.317000","timezone_type":3,"timezone":"Europe/Brussels"}}}