Chloroplast genome evolution in Passiflora

Detalhes bibliográficos
Autor(a) principal: Santos, Luiz Augusto Cauz dos
Data de Publicação: 2020
Tipo de documento: Tese
Idioma: eng
Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
Texto Completo: http://www.teses.usp.br/teses/disponiveis/11/11137/tde-04062020-160041/
Resumo: Chloroplast genomes (cpDNAs or plastomes) are highly conserved in Angiosperms. Although rearrangements have been observed in some lineages, the mechanisms that lead to rearrangements are still poorly elucidated. Our research group initially reported the structural organization of the plastome of Passiflora edulis (Passifloraceae) and rearrangments were identified. It is particularly worth noting that Passiflora presents different patterns of chloroplast inheritance and cytonuclear incompatibility. In order to investigate cpDNA evolutionary history in Passiflora and its possible implications for infrageneric taxonomic classification, a total of 35 complete chloroplast genomes were obtained, sampling for species of subgenera Astrophea, Decaloba, Deidamioides and Passiflora. The organization of the cpDNAs was uncommon, with large variation in size (~60 kb between shortest and longest), and highly rearranged genome structures. In addition, although large inverted repeat (IR) expansions were identified, the exact opposite (loss of an IR) was detected for the first time in Passiflora. This is indeed a rare event in angiosperms. A repertory of rearrangements, such as inversions and losses of genes was also found, making Passiflora one of the few groups with complex chloroplast genome evolution. Interestingly, a high number of rearrangements was detected in subgenus Decaloba, in which biparental chloroplast inheritance occur. A comparative genomic analysis revealed different organizational plastome structures, in accordance with the taxonomic classification within the subgenus Deidamioides. In addition, the plastid phylogenomics resulted in a highly supported tree with polyphyletic placement of Deidamioides species. Based on the combined results, we suggest elevating the status of the section Tryphostematoides (Deidamioides) to subgenus Tryphostematoides. Finally, apart from the contribution of this work to elucidating evolutionary history of Passiflora, our results also show that Passiflora provides a good model for the study of chloroplast genome evolution.
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spelling Chloroplast genome evolution in PassifloraEvolução do genoma cloroplastidial em PassifloraPassifloraPassifloraChloroplast genomeFilogenômicaGenoma cloroplastidialGenome rearrangementsPhylogenomicsRearranjos genômicosChloroplast genomes (cpDNAs or plastomes) are highly conserved in Angiosperms. Although rearrangements have been observed in some lineages, the mechanisms that lead to rearrangements are still poorly elucidated. Our research group initially reported the structural organization of the plastome of Passiflora edulis (Passifloraceae) and rearrangments were identified. It is particularly worth noting that Passiflora presents different patterns of chloroplast inheritance and cytonuclear incompatibility. In order to investigate cpDNA evolutionary history in Passiflora and its possible implications for infrageneric taxonomic classification, a total of 35 complete chloroplast genomes were obtained, sampling for species of subgenera Astrophea, Decaloba, Deidamioides and Passiflora. The organization of the cpDNAs was uncommon, with large variation in size (~60 kb between shortest and longest), and highly rearranged genome structures. In addition, although large inverted repeat (IR) expansions were identified, the exact opposite (loss of an IR) was detected for the first time in Passiflora. This is indeed a rare event in angiosperms. A repertory of rearrangements, such as inversions and losses of genes was also found, making Passiflora one of the few groups with complex chloroplast genome evolution. Interestingly, a high number of rearrangements was detected in subgenus Decaloba, in which biparental chloroplast inheritance occur. A comparative genomic analysis revealed different organizational plastome structures, in accordance with the taxonomic classification within the subgenus Deidamioides. In addition, the plastid phylogenomics resulted in a highly supported tree with polyphyletic placement of Deidamioides species. Based on the combined results, we suggest elevating the status of the section Tryphostematoides (Deidamioides) to subgenus Tryphostematoides. Finally, apart from the contribution of this work to elucidating evolutionary history of Passiflora, our results also show that Passiflora provides a good model for the study of chloroplast genome evolution.Os genomas de cloroplasto (cpDNAs ou plastomas) são altamente conservados em Angiospermas. Embora rearranjos tenham sido observados em algumas espécies, os mecanismos que levam a estes rearranjos ainda são pouco elucidados. Inicialmente, nosso grupo de pesquisa descreveu a organização estrutural do plastoma de Passiflora edulis (Passifloraceae) e rearranjos foram identificados. Particularmente, convém ressaltar que o gênero Passiflora apresenta diferentes padrões de herança cloroplastidial e incompatibilidade citonuclear. Para investigar a história evolutiva dos cpDNAs em Passiflora e possíveis implicações na classificação taxonômica infragenérica, foi obtido um total de 35 genomas cloroplastidiais completos, amostrando espécies dos diferentes subgêneros: Astrophea, Decaloba, Deidamioides e Passiflora. A organização dos cpDNAs mostrou-se não usual, com uma grande variação em tamanho (~60 kb entre o menor e o maior) e estruturas altamente rearranjadas. Além disso, ao mesmo tempo em que grandes expansões das regiões repetidas invertidas (IR) foram identificadas, o extremo oposto, a perda de uma IR foi detectada pela primeira vez em Passiflora, um evento raro em angiospermas. Um repertório de rearranjos, como inversões e perdas de genes, também foi constatado, tornando Passiflora um dos poucos grupos com uma complexa evolução de genomas cloroplastidiais. Interessantemente, um alto número de rearranjos foi detectado no subgênero Decaloba, no qual ocorre herança biparental de cloroplastos. Uma análise de genômica comparativa revelou diferentes estruturas de plastomas de acordo com a classificação dentro do subgênero Deidamioides. Além disso, a análise filogenômica baseada em genes plastidiais resultou em uma árvore de alto suporte, com posicionamento polifilético das espécies de Deidamioides. Combinando os resultados, sugere-se elevar o status da seção Tryphostemmatoides (Deidamioides) para subgênero Tryphostemmatoides. Por fim, além da contribuição deste trabalho para elucidar a história evolutiva de Passiflora, nossos resultados recomendam Passiflora como um excelente modelo para o estudo da evolução dos genomas cloroplastidiais.Biblioteca Digitais de Teses e Dissertações da USPVieira, Maria Lucia CarneiroSantos, Luiz Augusto Cauz dos2020-04-06info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisapplication/pdfhttp://www.teses.usp.br/teses/disponiveis/11/11137/tde-04062020-160041/reponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USPLiberar o conteúdo para acesso público.info:eu-repo/semantics/openAccesseng2022-06-04T12:59:27Zoai:teses.usp.br:tde-04062020-160041Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212022-06-04T12:59:27Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false
dc.title.none.fl_str_mv Chloroplast genome evolution in Passiflora
Evolução do genoma cloroplastidial em Passiflora
title Chloroplast genome evolution in Passiflora
spellingShingle Chloroplast genome evolution in Passiflora
Santos, Luiz Augusto Cauz dos
Passiflora
Passiflora
Chloroplast genome
Filogenômica
Genoma cloroplastidial
Genome rearrangements
Phylogenomics
Rearranjos genômicos
title_short Chloroplast genome evolution in Passiflora
title_full Chloroplast genome evolution in Passiflora
title_fullStr Chloroplast genome evolution in Passiflora
title_full_unstemmed Chloroplast genome evolution in Passiflora
title_sort Chloroplast genome evolution in Passiflora
author Santos, Luiz Augusto Cauz dos
author_facet Santos, Luiz Augusto Cauz dos
author_role author
dc.contributor.none.fl_str_mv Vieira, Maria Lucia Carneiro
dc.contributor.author.fl_str_mv Santos, Luiz Augusto Cauz dos
dc.subject.por.fl_str_mv Passiflora
Passiflora
Chloroplast genome
Filogenômica
Genoma cloroplastidial
Genome rearrangements
Phylogenomics
Rearranjos genômicos
topic Passiflora
Passiflora
Chloroplast genome
Filogenômica
Genoma cloroplastidial
Genome rearrangements
Phylogenomics
Rearranjos genômicos
description Chloroplast genomes (cpDNAs or plastomes) are highly conserved in Angiosperms. Although rearrangements have been observed in some lineages, the mechanisms that lead to rearrangements are still poorly elucidated. Our research group initially reported the structural organization of the plastome of Passiflora edulis (Passifloraceae) and rearrangments were identified. It is particularly worth noting that Passiflora presents different patterns of chloroplast inheritance and cytonuclear incompatibility. In order to investigate cpDNA evolutionary history in Passiflora and its possible implications for infrageneric taxonomic classification, a total of 35 complete chloroplast genomes were obtained, sampling for species of subgenera Astrophea, Decaloba, Deidamioides and Passiflora. The organization of the cpDNAs was uncommon, with large variation in size (~60 kb between shortest and longest), and highly rearranged genome structures. In addition, although large inverted repeat (IR) expansions were identified, the exact opposite (loss of an IR) was detected for the first time in Passiflora. This is indeed a rare event in angiosperms. A repertory of rearrangements, such as inversions and losses of genes was also found, making Passiflora one of the few groups with complex chloroplast genome evolution. Interestingly, a high number of rearrangements was detected in subgenus Decaloba, in which biparental chloroplast inheritance occur. A comparative genomic analysis revealed different organizational plastome structures, in accordance with the taxonomic classification within the subgenus Deidamioides. In addition, the plastid phylogenomics resulted in a highly supported tree with polyphyletic placement of Deidamioides species. Based on the combined results, we suggest elevating the status of the section Tryphostematoides (Deidamioides) to subgenus Tryphostematoides. Finally, apart from the contribution of this work to elucidating evolutionary history of Passiflora, our results also show that Passiflora provides a good model for the study of chloroplast genome evolution.
publishDate 2020
dc.date.none.fl_str_mv 2020-04-06
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language eng
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