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Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages

BACKGROUND: In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its...

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Autores principales: Chen, Huilong, Zhang, Yingchao, Feng, Shuyan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10228137/
https://www.ncbi.nlm.nih.gov/pubmed/37254040
http://dx.doi.org/10.1186/s12864-023-09389-z
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author Chen, Huilong
Zhang, Yingchao
Feng, Shuyan
author_facet Chen, Huilong
Zhang, Yingchao
Feng, Shuyan
author_sort Chen, Huilong
collection PubMed
description BACKGROUND: In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages. RESULTS: Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations. CONCLUSIONS: This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09389-z.
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spelling pubmed-102281372023-05-31 Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages Chen, Huilong Zhang, Yingchao Feng, Shuyan BMC Genomics Research BACKGROUND: In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages. RESULTS: Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations. CONCLUSIONS: This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09389-z. BioMed Central 2023-05-30 /pmc/articles/PMC10228137/ /pubmed/37254040 http://dx.doi.org/10.1186/s12864-023-09389-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Chen, Huilong
Zhang, Yingchao
Feng, Shuyan
Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages
title Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages
title_full Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages
title_fullStr Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages
title_full_unstemmed Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages
title_short Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages
title_sort whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of tlp genes in seven representative poaceae lineages
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10228137/
https://www.ncbi.nlm.nih.gov/pubmed/37254040
http://dx.doi.org/10.1186/s12864-023-09389-z
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