Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids
Premise Multiple transitions from insect to wind pollination are associated with polyploidy and unisexual flowers in Thalictrum (Ranunculaceae), yet the underlying genetics remains unknown. We generated a draft genome of Thalictrum thalictroides, a representative of a clade with ancestral floral tra...
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doaj-1c4bcf23a9e3422fb332db1a7c37fe422021-02-04T17:00:31ZengWileyApplications in Plant Sciences2168-04502021-01-0191n/an/a10.1002/aps3.11407Genomic and transcriptomic resources for candidate gene discovery in the RanunculidsTatiana Arias0Diego Mauricio Riaño‐Pachón1Verónica S. Di Stilio2School of Biological Sciences The University of Hong Kong Pokfulam Hong KongLaboratory of Computational, Evolutionary and Systems Biology Center for Nuclear Energy in Agriculture University of São Paulo Piracicaba São Paulo13416‐000BrazilDepartment of Biology University of Washington, Seattle Washington98195‐1800USAPremise Multiple transitions from insect to wind pollination are associated with polyploidy and unisexual flowers in Thalictrum (Ranunculaceae), yet the underlying genetics remains unknown. We generated a draft genome of Thalictrum thalictroides, a representative of a clade with ancestral floral traits (diploid, hermaphrodite, and insect pollinated) and a model for functional studies. Floral transcriptomes of T. thalictroides and of wind‐pollinated, andromonoecious T. hernandezii are presented as a resource to facilitate candidate gene discovery in flowers with different sexual and pollination systems. Methods A draft genome of T. thalictroides and two floral transcriptomes of T. thalictroides and T. hernandezii were obtained from HiSeq 2000 Illumina sequencing and de novo assembly. Results The T. thalictroides de novo draft genome assembly consisted of 44,860 contigs (N50 = 12,761 bp, 243 Mbp total length) and contained 84.5% conserved embryophyte single‐copy genes. Floral transcriptomes contained representatives of most eukaryotic core genes, and most of their genes formed orthogroups. Discussion To validate the utility of these resources, potential candidate genes were identified for the different floral morphologies using stepwise data set comparisons. Single‐copy gene analysis and simple sequence repeat markers were also generated as a resource for population‐level and phylogenetic studies.https://doi.org/10.1002/aps3.11407draft genomefloral transcriptomepollination syndromeRanunculaceaesexual systemThalictrum hernandezii |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Tatiana Arias Diego Mauricio Riaño‐Pachón Verónica S. Di Stilio |
spellingShingle |
Tatiana Arias Diego Mauricio Riaño‐Pachón Verónica S. Di Stilio Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids Applications in Plant Sciences draft genome floral transcriptome pollination syndrome Ranunculaceae sexual system Thalictrum hernandezii |
author_facet |
Tatiana Arias Diego Mauricio Riaño‐Pachón Verónica S. Di Stilio |
author_sort |
Tatiana Arias |
title |
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids |
title_short |
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids |
title_full |
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids |
title_fullStr |
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids |
title_full_unstemmed |
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids |
title_sort |
genomic and transcriptomic resources for candidate gene discovery in the ranunculids |
publisher |
Wiley |
series |
Applications in Plant Sciences |
issn |
2168-0450 |
publishDate |
2021-01-01 |
description |
Premise Multiple transitions from insect to wind pollination are associated with polyploidy and unisexual flowers in Thalictrum (Ranunculaceae), yet the underlying genetics remains unknown. We generated a draft genome of Thalictrum thalictroides, a representative of a clade with ancestral floral traits (diploid, hermaphrodite, and insect pollinated) and a model for functional studies. Floral transcriptomes of T. thalictroides and of wind‐pollinated, andromonoecious T. hernandezii are presented as a resource to facilitate candidate gene discovery in flowers with different sexual and pollination systems. Methods A draft genome of T. thalictroides and two floral transcriptomes of T. thalictroides and T. hernandezii were obtained from HiSeq 2000 Illumina sequencing and de novo assembly. Results The T. thalictroides de novo draft genome assembly consisted of 44,860 contigs (N50 = 12,761 bp, 243 Mbp total length) and contained 84.5% conserved embryophyte single‐copy genes. Floral transcriptomes contained representatives of most eukaryotic core genes, and most of their genes formed orthogroups. Discussion To validate the utility of these resources, potential candidate genes were identified for the different floral morphologies using stepwise data set comparisons. Single‐copy gene analysis and simple sequence repeat markers were also generated as a resource for population‐level and phylogenetic studies. |
topic |
draft genome floral transcriptome pollination syndrome Ranunculaceae sexual system Thalictrum hernandezii |
url |
https://doi.org/10.1002/aps3.11407 |
work_keys_str_mv |
AT tatianaarias genomicandtranscriptomicresourcesforcandidategenediscoveryintheranunculids AT diegomauriciorianopachon genomicandtranscriptomicresourcesforcandidategenediscoveryintheranunculids AT veronicasdistilio genomicandtranscriptomicresourcesforcandidategenediscoveryintheranunculids |
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