A roadmap of phylogenomic methods for studying polyploid plant genera

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dc.citation.volumeEarly View
dc.contributor.authorNing W
dc.contributor.authorMeudt HM
dc.contributor.authorTate JA
dc.date.accessioned2024-07-18T01:43:36Z
dc.date.available2024-07-18T01:43:36Z
dc.date.issued2024-04-22
dc.description.abstractPhylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.
dc.description.confidentialfalse
dc.edition.edition2024
dc.identifier.citationNing W, Meudt HM, Tate JA. (2024). A roadmap of phylogenomic methods for studying polyploid plant genera. Applications in Plant Sciences. Early View.
dc.identifier.doi10.1002/aps3.11580
dc.identifier.eissn2168-0450
dc.identifier.elements-typejournal-article
dc.identifier.issn2168-0450
dc.identifier.numbere11580
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70224
dc.languageEnglish
dc.publisherJohn Wiley and Sons, Inc., on behalf of Botanical Society of America
dc.publisher.urihttps://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11580
dc.relation.isPartOfApplications in Plant Sciences
dc.rights(c) 2024 The Author/s
dc.rightsCC BY-NC 4.0
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.subjectallopolyploid
dc.subjectphylogenomics
dc.subjectphylotranscriptomics
dc.subjectpolyploidy
dc.subjectreticulation
dc.subjectsequencing
dc.subjectsingle‐copy genes
dc.titleA roadmap of phylogenomic methods for studying polyploid plant genera
dc.typeJournal article
pubs.elements-id488574
pubs.organisational-groupOther
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