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Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns

While roots and leaves have evolved independently in lycophytes, ferns and seed plants, there is still confusion regarding the morphological evolution of ferns, especially in whisk ferns, which lack true leaves and roots and instead only exhibit leaf-like appendages and absorptive rhizoids. In this...

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Autores principales: Xia, Zengqiang, Liu, Li, Wei, Zuoying, Wang, Faguo, Shen, Hui, Yan, Yuehong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9103481/
https://www.ncbi.nlm.nih.gov/pubmed/35567199
http://dx.doi.org/10.3390/plants11091198
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author Xia, Zengqiang
Liu, Li
Wei, Zuoying
Wang, Faguo
Shen, Hui
Yan, Yuehong
author_facet Xia, Zengqiang
Liu, Li
Wei, Zuoying
Wang, Faguo
Shen, Hui
Yan, Yuehong
author_sort Xia, Zengqiang
collection PubMed
description While roots and leaves have evolved independently in lycophytes, ferns and seed plants, there is still confusion regarding the morphological evolution of ferns, especially in whisk ferns, which lack true leaves and roots and instead only exhibit leaf-like appendages and absorptive rhizoids. In this study, analyses of comparative transcriptomics on positively selected genes were performed to provide insights into the adaptive evolution of whisk fern morphologies. Significantly clustered gene families specific to whisk ferns were mainly enriched in Gene Ontology (GO) terms “binding proteins” and “transmembrane transporter activity”, and positive selection was detected in genes involved in transmembrane transporter activities and stress response (e.g., sodium/hydrogen exchanger and heat shock proteins), which could be related to the adaptive evolution of tolerance to epiphytic environments. The analysis of TF/TR gene family sizes indicated that some rapidly evolving gene families (e.g., the GRF and the MADS-MIKC families) related to the development of morphological organs were commonly reduced in whisk ferns and ophioglossoid ferns. Furthermore, the WUS homeobox-containing (WOX) gene family and the knotted1-like homeobox (KNOX) gene family, both associated with root and leaf development, were phylogenetically conserved in whisk ferns and ophioglossoid ferns. In general, our results suggested that adaptive evolution to epiphytic environments might have occurred in whisk ferns. We propose that the simplified and reduced leaf and root system in whisk ferns is the result of reduction from the common ancestor of whisk ferns and ophioglossoid ferns, rather than an independent origin.
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spelling pubmed-91034812022-05-14 Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns Xia, Zengqiang Liu, Li Wei, Zuoying Wang, Faguo Shen, Hui Yan, Yuehong Plants (Basel) Article While roots and leaves have evolved independently in lycophytes, ferns and seed plants, there is still confusion regarding the morphological evolution of ferns, especially in whisk ferns, which lack true leaves and roots and instead only exhibit leaf-like appendages and absorptive rhizoids. In this study, analyses of comparative transcriptomics on positively selected genes were performed to provide insights into the adaptive evolution of whisk fern morphologies. Significantly clustered gene families specific to whisk ferns were mainly enriched in Gene Ontology (GO) terms “binding proteins” and “transmembrane transporter activity”, and positive selection was detected in genes involved in transmembrane transporter activities and stress response (e.g., sodium/hydrogen exchanger and heat shock proteins), which could be related to the adaptive evolution of tolerance to epiphytic environments. The analysis of TF/TR gene family sizes indicated that some rapidly evolving gene families (e.g., the GRF and the MADS-MIKC families) related to the development of morphological organs were commonly reduced in whisk ferns and ophioglossoid ferns. Furthermore, the WUS homeobox-containing (WOX) gene family and the knotted1-like homeobox (KNOX) gene family, both associated with root and leaf development, were phylogenetically conserved in whisk ferns and ophioglossoid ferns. In general, our results suggested that adaptive evolution to epiphytic environments might have occurred in whisk ferns. We propose that the simplified and reduced leaf and root system in whisk ferns is the result of reduction from the common ancestor of whisk ferns and ophioglossoid ferns, rather than an independent origin. MDPI 2022-04-28 /pmc/articles/PMC9103481/ /pubmed/35567199 http://dx.doi.org/10.3390/plants11091198 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Xia, Zengqiang
Liu, Li
Wei, Zuoying
Wang, Faguo
Shen, Hui
Yan, Yuehong
Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns
title Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns
title_full Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns
title_fullStr Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns
title_full_unstemmed Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns
title_short Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns
title_sort analysis of comparative transcriptome and positively selected genes reveal adaptive evolution in leaf-less and root-less whisk ferns
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9103481/
https://www.ncbi.nlm.nih.gov/pubmed/35567199
http://dx.doi.org/10.3390/plants11091198
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