The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3390/ijms21010003 http://hdl.handle.net/11449/199855 |
Resumo: | Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover,GOenrichment analyses suggest an ongoing gene birth–death–innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes. |
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The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticityABC transportersEvolutionGenome fractionationTranscription factorsTransposable elementsWhole-genome duplicationUtricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover,GOenrichment analyses suggest an ongoing gene birth–death–innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes.Departamento de Tecnologia Faculdade de Ciências Agrárias e Veterinárias UNESP—Universidade Estadual PaulistaCentro de Ciências Naturais e Humanas Universidade Federal do ABCDepartamento de Botânica Instituto de Biociências UNESP—Universidade Estadual PaulistaJ. Craig Venter Institute, La JollaDepartamento de Biologia Aplicada � Agropecuária Faculdade de Ciências Agrárias e Veterinárias UNESP—Universidade Estadual PaulistaDepartamento de Tecnologia Faculdade de Ciências Agrárias e Veterinárias UNESP—Universidade Estadual PaulistaDepartamento de Botânica Instituto de Biociências UNESP—Universidade Estadual PaulistaDepartamento de Biologia Aplicada � Agropecuária Faculdade de Ciências Agrárias e Veterinárias UNESP—Universidade Estadual PaulistaUniversidade Estadual Paulista (Unesp)Universidade Federal do ABC (UFABC)J. Craig Venter InstituteSilva, Saura R. [UNESP]Moraes, Ana PaulaPenha, Helen A. [UNESP]Julião, Maria H. M. [UNESP]Domingues, Douglas S. [UNESP]Michael, Todd P.Miranda, Vitor F. O. [UNESP]Varani, Alessandro M. [UNESP]2020-12-12T01:51:11Z2020-12-12T01:51:11Z2020-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3390/ijms21010003International Journal of Molecular Sciences, v. 21, n. 1, 2020.1422-00671661-6596http://hdl.handle.net/11449/19985510.3390/ijms210100032-s2.0-85076970412Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengInternational Journal of Molecular Sciencesinfo:eu-repo/semantics/openAccess2024-06-07T15:32:11Zoai:repositorio.unesp.br:11449/199855Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T20:10:32.012227Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity |
title |
The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity |
spellingShingle |
The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity Silva, Saura R. [UNESP] ABC transporters Evolution Genome fractionation Transcription factors Transposable elements Whole-genome duplication |
title_short |
The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity |
title_full |
The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity |
title_fullStr |
The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity |
title_full_unstemmed |
The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity |
title_sort |
The terrestrial carnivorous plant utricularia reniformis sheds light on environmental and life-form genome plasticity |
author |
Silva, Saura R. [UNESP] |
author_facet |
Silva, Saura R. [UNESP] Moraes, Ana Paula Penha, Helen A. [UNESP] Julião, Maria H. M. [UNESP] Domingues, Douglas S. [UNESP] Michael, Todd P. Miranda, Vitor F. O. [UNESP] Varani, Alessandro M. [UNESP] |
author_role |
author |
author2 |
Moraes, Ana Paula Penha, Helen A. [UNESP] Julião, Maria H. M. [UNESP] Domingues, Douglas S. [UNESP] Michael, Todd P. Miranda, Vitor F. O. [UNESP] Varani, Alessandro M. [UNESP] |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidade Federal do ABC (UFABC) J. Craig Venter Institute |
dc.contributor.author.fl_str_mv |
Silva, Saura R. [UNESP] Moraes, Ana Paula Penha, Helen A. [UNESP] Julião, Maria H. M. [UNESP] Domingues, Douglas S. [UNESP] Michael, Todd P. Miranda, Vitor F. O. [UNESP] Varani, Alessandro M. [UNESP] |
dc.subject.por.fl_str_mv |
ABC transporters Evolution Genome fractionation Transcription factors Transposable elements Whole-genome duplication |
topic |
ABC transporters Evolution Genome fractionation Transcription factors Transposable elements Whole-genome duplication |
description |
Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover,GOenrichment analyses suggest an ongoing gene birth–death–innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-12-12T01:51:11Z 2020-12-12T01:51:11Z 2020-01-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3390/ijms21010003 International Journal of Molecular Sciences, v. 21, n. 1, 2020. 1422-0067 1661-6596 http://hdl.handle.net/11449/199855 10.3390/ijms21010003 2-s2.0-85076970412 |
url |
http://dx.doi.org/10.3390/ijms21010003 http://hdl.handle.net/11449/199855 |
identifier_str_mv |
International Journal of Molecular Sciences, v. 21, n. 1, 2020. 1422-0067 1661-6596 10.3390/ijms21010003 2-s2.0-85076970412 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
International Journal of Molecular Sciences |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1808129168465985536 |