Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants
GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds of members per plant species. To facilitate functional transfer between them, we conducted a genome-wide classification of GELP in 46 plant species. First, we applied an iterative phylogenetic method using a selected set of representative angiosperm genomes (three monocots and five dicots) and identified 10 main clusters, subdivided into 44 orthogroups (OGs). An expert curation for gene structures, orthogroup composition, and functional annotation was made based on a literature review. Then, using the HMM profiles as seeds, we expanded the classification to 46 plant species. Our results revealed the variable evolutionary dynamics between OGs in which some expanded, mostly through tandem duplications, while others were maintained as single copies. Among these, dicot-specific clusters and specific amplifications in monocots and wheat were characterized. This approach, by combining manual curation and automatic identification, was effective in characterizing a large gene family, allowing the establishment of a classification framework for gene function transfer and a better understanding of the evolutionary history of GELP.
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2022-10-11
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Subjects: | genomes, bioinformatics, genetic databases, genomas, bioinformática, base de datos de recursos genéticos, spectroscopy, molecular biology, catalysis, |
Online Access: | https://hdl.handle.net/10568/124991 https://doi.org/10.3390/ijms232012114 |
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dig-cgspace-10568-1249912023-12-08T19:36:04Z Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants Cenci, Alberto Concepción-Hernández, Mairenys Guignon, Valentin Angenon, Geert Rouard, Mathieu genomes bioinformatics genetic databases genomas bioinformática base de datos de recursos genéticos spectroscopy molecular biology catalysis GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds of members per plant species. To facilitate functional transfer between them, we conducted a genome-wide classification of GELP in 46 plant species. First, we applied an iterative phylogenetic method using a selected set of representative angiosperm genomes (three monocots and five dicots) and identified 10 main clusters, subdivided into 44 orthogroups (OGs). An expert curation for gene structures, orthogroup composition, and functional annotation was made based on a literature review. Then, using the HMM profiles as seeds, we expanded the classification to 46 plant species. Our results revealed the variable evolutionary dynamics between OGs in which some expanded, mostly through tandem duplications, while others were maintained as single copies. Among these, dicot-specific clusters and specific amplifications in monocots and wheat were characterized. This approach, by combining manual curation and automatic identification, was effective in characterizing a large gene family, allowing the establishment of a classification framework for gene function transfer and a better understanding of the evolutionary history of GELP. 2022-10-11 2022-10-12T14:39:54Z 2022-10-12T14:39:54Z Journal Article Cenci, A.; Concepción-Hernández, M.; Guignon, V.; Angenon, G.; Rouard, M. (2022) Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants. International Journal Molecular Sciences 23(20): 12114 20 p. ISSN: 1661-6596 1661-6596 https://hdl.handle.net/10568/124991 https://doi.org/10.3390/ijms232012114 en CC-BY-4.0 Open Access 20 p. application/pdf MDPI International Journal Molecular Sciences |
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genomes bioinformatics genetic databases genomas bioinformática base de datos de recursos genéticos spectroscopy molecular biology catalysis genomes bioinformatics genetic databases genomas bioinformática base de datos de recursos genéticos spectroscopy molecular biology catalysis Cenci, Alberto Concepción-Hernández, Mairenys Guignon, Valentin Angenon, Geert Rouard, Mathieu Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants |
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GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds of members per plant species. To facilitate functional transfer between them, we conducted a genome-wide classification of GELP in 46 plant species. First, we applied an iterative phylogenetic method using a selected set of representative angiosperm genomes (three monocots and five dicots) and identified 10 main clusters, subdivided into 44 orthogroups (OGs). An expert curation for gene structures, orthogroup composition, and functional annotation was made based on a literature review. Then, using the HMM profiles as seeds, we expanded the classification to 46 plant species. Our results revealed the variable evolutionary dynamics between OGs in which some expanded, mostly through tandem duplications, while others were maintained as single copies. Among these, dicot-specific clusters and specific amplifications in monocots and wheat were characterized. This approach, by combining manual curation and automatic identification, was effective in characterizing a large gene family, allowing the establishment of a classification framework for gene function transfer and a better understanding of the evolutionary history of GELP. |
format |
Journal Article |
topic_facet |
genomes bioinformatics genetic databases genomas bioinformática base de datos de recursos genéticos spectroscopy molecular biology catalysis |
author |
Cenci, Alberto Concepción-Hernández, Mairenys Guignon, Valentin Angenon, Geert Rouard, Mathieu |
author_facet |
Cenci, Alberto Concepción-Hernández, Mairenys Guignon, Valentin Angenon, Geert Rouard, Mathieu |
author_sort |
Cenci, Alberto |
title |
Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants |
title_short |
Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants |
title_full |
Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants |
title_fullStr |
Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants |
title_full_unstemmed |
Genome-Wide classification and phylogenetic analyses of the GDSL-Type Esterase/Lipase (GELP) family in flowering plants |
title_sort |
genome-wide classification and phylogenetic analyses of the gdsl-type esterase/lipase (gelp) family in flowering plants |
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MDPI |
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2022-10-11 |
url |
https://hdl.handle.net/10568/124991 https://doi.org/10.3390/ijms232012114 |
work_keys_str_mv |
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