Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)

Whereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genu...

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Autores: Karbstein, Kevin, Choudhary, Nancy, Xie, Ting, Tomasello, Salvatore, Wagner, Natascha D., Barke, Birthe H., Paetzold, Claudia, Bradican, John P., Preick, Michaela, Himmelbach, Axel, Stein, Nils, Papantonis, Argyris, Irisarri, Iker, de Vries, Jan, Pucker, Boas, Hörandl, Elvira
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:dnet:digitalcsic_::87d372270d530cfb1861ef317888b4c8
Acceso en línea:http://hdl.handle.net/10261/428111
Access Level:acceso abierto
Palabra clave:De novo assembly strategies
Gene evolution
Illumina vs. Nanopore vs. PacBio sequencing
Large non-model plant genomes
Mitogenome
Nuclear genome
Plastome
Ranunculaceae
Ranunculus auricomus species complex
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dc.title.none.fl_str_mv Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
title Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
spellingShingle Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
Karbstein, Kevin
De novo assembly strategies
Gene evolution
Illumina vs. Nanopore vs. PacBio sequencing
Large non-model plant genomes
Mitogenome
Nuclear genome
Plastome
Ranunculaceae
Ranunculus auricomus species complex
title_short Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
title_full Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
title_fullStr Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
title_full_unstemmed Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
title_sort Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
dc.creator.none.fl_str_mv Karbstein, Kevin
Choudhary, Nancy
Xie, Ting
Tomasello, Salvatore
Wagner, Natascha D.
Barke, Birthe H.
Paetzold, Claudia
Bradican, John P.
Preick, Michaela
Himmelbach, Axel
Stein, Nils
Papantonis, Argyris
Irisarri, Iker
de Vries, Jan
Pucker, Boas
Hörandl, Elvira
author Karbstein, Kevin
author_facet Karbstein, Kevin
Choudhary, Nancy
Xie, Ting
Tomasello, Salvatore
Wagner, Natascha D.
Barke, Birthe H.
Paetzold, Claudia
Bradican, John P.
Preick, Michaela
Himmelbach, Axel
Stein, Nils
Papantonis, Argyris
Irisarri, Iker
de Vries, Jan
Pucker, Boas
Hörandl, Elvira
author_role author
author2 Choudhary, Nancy
Xie, Ting
Tomasello, Salvatore
Wagner, Natascha D.
Barke, Birthe H.
Paetzold, Claudia
Bradican, John P.
Preick, Michaela
Himmelbach, Axel
Stein, Nils
Papantonis, Argyris
Irisarri, Iker
de Vries, Jan
Pucker, Boas
Hörandl, Elvira
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Commission
German Research Foundation
Agencia Estatal de Investigación (España)
Federal Ministry of Education and Research (Germany)
University of Göttingen
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv De novo assembly strategies
Gene evolution
Illumina vs. Nanopore vs. PacBio sequencing
Large non-model plant genomes
Mitogenome
Nuclear genome
Plastome
Ranunculaceae
Ranunculus auricomus species complex
topic De novo assembly strategies
Gene evolution
Illumina vs. Nanopore vs. PacBio sequencing
Large non-model plant genomes
Mitogenome
Nuclear genome
Plastome
Ranunculaceae
Ranunculus auricomus species complex
description Whereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genus Ranunculus (Ranunculaceae) is an important angiosperm group for the study of polyploidy, apomixis, and reticulate evolution. However, neither mitochondrial nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) and PacBio (HiFi) long-read, and hybrid-read assembly strategies. We sequenced the diploid progenitor species R. cassubicifolius (R. auricomus species complex) and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome sequence, we favored a PacBio-based assembly polished three times with filtered short reads and subsequently scaffolded into eight pseudochromosomes by chromatin conformation data (Hi-C). We obtained a haploid genome sequence of 2.69 Gbp, with 94.1% complete BUSCO genes found and 35 482 annotated genes, and inferred ancient gene duplications compared to existing Ranunculales genomes. The genomic information presented here will enable advanced evolutionary-functional analyses for the species complex, but also for the genus and beyond Ranunculaceae.
publishDate 2025
dc.date.none.fl_str_mv 2025
2026
2026
2026
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dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/428111
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dc.publisher.none.fl_str_mv John Wiley & Sons
publisher.none.fl_str_mv John Wiley & Sons
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instname:Consejo Superior de Investigaciones Científicas (CSIC)
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spelling Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)Karbstein, KevinChoudhary, NancyXie, TingTomasello, SalvatoreWagner, Natascha D.Barke, Birthe H.Paetzold, ClaudiaBradican, John P.Preick, MichaelaHimmelbach, AxelStein, NilsPapantonis, ArgyrisIrisarri, Ikerde Vries, JanPucker, BoasHörandl, ElviraDe novo assembly strategiesGene evolutionIllumina vs. Nanopore vs. PacBio sequencingLarge non-model plant genomesMitogenomeNuclear genomePlastomeRanunculaceaeRanunculus auricomus species complexWhereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genus Ranunculus (Ranunculaceae) is an important angiosperm group for the study of polyploidy, apomixis, and reticulate evolution. However, neither mitochondrial nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) and PacBio (HiFi) long-read, and hybrid-read assembly strategies. We sequenced the diploid progenitor species R. cassubicifolius (R. auricomus species complex) and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome sequence, we favored a PacBio-based assembly polished three times with filtered short reads and subsequently scaffolded into eight pseudochromosomes by chromatin conformation data (Hi-C). We obtained a haploid genome sequence of 2.69 Gbp, with 94.1% complete BUSCO genes found and 35 482 annotated genes, and inferred ancient gene duplications compared to existing Ranunculales genomes. The genomic information presented here will enable advanced evolutionary-functional analyses for the species complex, but also for the genus and beyond Ranunculaceae.Lindemann-foundation (University of Göttingen); German Research Foundation; European Research Council; European Commission; Spanish Ministry of Science and Innovation; European Social Fund Plus; German Federal Ministry of Education and Research; German Network for Bioinformatics InfrastructurePeer reviewedJohn Wiley & SonsEuropean CommissionGerman Research FoundationAgencia Estatal de Investigación (España)Federal Ministry of Education and Research (Germany)University of GöttingenConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2026202620252026info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/428111reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/852725info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/RYC2022-038245-Iinfo:eu-repo/grantAgreement/DFG/SPP 1991/Ho4395info:eu-repo/grantAgreement/DFG/SPP 2237/422691801info:eu-repo/grantAgreement/DFG/SPP 2237/528076711info:eu-repo/grantAgreement/DFG/GRK 2984/1info:eu-repo/grantAgreement/BMBF/de.NBI/031A532Binfo:eu-repo/grantAgreement/BMBF/de.NBI/031A533Ainfo:eu-repo/grantAgreement/BMBF/de.NBI/031A533Binfo:eu-repo/grantAgreement/BMBF/de.NBI/031A534Ainfo:eu-repo/grantAgreement/BMBF/de.NBI/031A535Ainfo:eu-repo/grantAgreement/BMBF/de.NBI/031A537Ainfo:eu-repo/grantAgreement/BMBF/de.NBI/031A537Binfo:eu-repo/grantAgreement/BMBF/de.NBI/031A537Cinfo:eu-repo/grantAgreement/BMBF/de.NBI/031A537Dinfo:eu-repo/grantAgreement/BMBF/de.NBI/031A538Ainfo:eu-repo/grantAgreement/University of Göttingen//Lindemann-foundationhttp://dx.doi.org/10.1111/tpj.70390Síinfo:eu-repo/semantics/openAccessoai:dnet:digitalcsic_::87d372270d530cfb1861ef317888b4c82026-05-22T06:33:51Z
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