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Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers...

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Autores principales: Pelosi, Jessie A., Kim, Emily H., Barbazuk, W. Brad, Sessa, Emily B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9330400/
https://www.ncbi.nlm.nih.gov/pubmed/35909764
http://dx.doi.org/10.3389/fpls.2022.882441
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author Pelosi, Jessie A.
Kim, Emily H.
Barbazuk, W. Brad
Sessa, Emily B.
author_facet Pelosi, Jessie A.
Kim, Emily H.
Barbazuk, W. Brad
Sessa, Emily B.
author_sort Pelosi, Jessie A.
collection PubMed
description Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree–species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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spelling pubmed-93304002022-07-29 Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns Pelosi, Jessie A. Kim, Emily H. Barbazuk, W. Brad Sessa, Emily B. Front Plant Sci Plant Science Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree–species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored. Frontiers Media S.A. 2022-07-14 /pmc/articles/PMC9330400/ /pubmed/35909764 http://dx.doi.org/10.3389/fpls.2022.882441 Text en Copyright © 2022 Pelosi, Kim, Barbazuk and Sessa. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Pelosi, Jessie A.
Kim, Emily H.
Barbazuk, W. Brad
Sessa, Emily B.
Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns
title Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns
title_full Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns
title_fullStr Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns
title_full_unstemmed Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns
title_short Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns
title_sort phylotranscriptomics illuminates the placement of whole genome duplications and gene retention in ferns
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9330400/
https://www.ncbi.nlm.nih.gov/pubmed/35909764
http://dx.doi.org/10.3389/fpls.2022.882441
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