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Comparative genomics and molecular evolution of carnivorous plants of the genus Utricularia (Lentibulariaceae)

Grant number: 18/02285-6
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Effective date (Start): June 01, 2018
Effective date (End): October 31, 2021
Field of knowledge:Biological Sciences - Genetics - Plant Genetics
Principal Investigator:Alessandro de Mello Varani
Grantee:Saura Rodrigues da Silva
Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil

Abstract

The carnivorous plants of the family Lentibulariaceae, which include the genera Pinguicula, Genlisea and Utricularia, have drawn the attention of the scientific community in recent years since they are good candidates for model plants. It isn't only their atypical morphological and physiological adaptations for obtaining nutrients that make then an ideal model, it is also the ease of cultivation in the laboratory, as well as their minimal genome sizes. It is known that species of the genus Utricularia has genome sizes ranging from 79 to 706 megabases (Mb) and, with some species of Genlisea, they possess the smallest genomes known for angiosperms. Concerning genome dynamics, independent events of Transposable Elements (TEs) hopping and genomic duplications contributed to genomic expansion. In contrast, genome size reduction is due to TEs loss and reduction of duplications, possibly due to high nucleotide substitution rates related to carnivory, or even positive selection of genes. In addition, the Utricularia organellar genomes have peculiar characteristics, such as pseudogenization and deletion in the cpDNA of NAD (P) H-dehydrogenase (ndh) complexes in the terrestrial species. The mtDNA has ndh and several other genes from cpDNA origin, TEs fragments, repeats and duplications. From a phylogenetic point of view, the correct placement and taxonomy position of some species and sections are controversial, with some paraphyletic and polyphyletic taxa. Therefore, the present proposal intends to study 24 sequenced additional Utricularia species, which will be analyzed using comparative and phylogenetic genomics: a) to estimate size, to assemble, to annotate and to compare the nuclear and organellar genomes; b) to infer the diversity and role of TEs and duplications with the process of genomic contraction and expansion; c) to study the processes that guide the evolution of ndh genes and lateral transfer between organelles; and d) to propose a new robust and solid phylogenetic hypotheses among Utricularia species, based on organellar (cpDNA and mtDNA) and nuclear genes. (AU)

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Scientific publications (10)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
RAFAELA JORGE TRAD; SAURA RODRIGUES DA SILVA; MARIA DO CARMO ESTANISLAU DO AMARAL. The first complete plastome of Mimusops coriacea (A. DC.) Miq. (Sapotaceae). GENETICS AND MOLECULAR BIOLOGY, v. 45, n. 1, . (18/02285-6, 12/51781-0)
MIRANDA, VITOR F. O.; SILVA, SAURA R.; REUT, MARKUS S.; DOLSAN, HUGO; STOLARCZYK, PIOTR; RUTISHAUSER, ROLF; PLACHNO, BARTOSZ J.. A Historical Perspective of Bladderworts (Utricularia): Traps, Carnivory and Body Architecture. PLANTS-BASEL, v. 10, n. 12, . (20/11053-1, 13/05144-0, 18/02285-6)
SILVA, SAURA RODRIGUES; PLACHNO, BARTOSZ JAN; MEDEIROS CARVALHO, SAMANTA GABRIELA; OLIVEIRA MIRANDA, VITOR FERNANDES. Genlisea hawkingii (Lentibulariaceae), a new species from Serra da Canastra, Minas Gerais, Brazil. PLoS One, v. 15, n. 1, . (18/02285-6)
SILVA, SAURA R.; MORAES, ANA PAULA; PENHA, HELEN A.; JULIAO, MARIA H. M.; DOMINGUES, DOUGLAS S.; MICHAEL, TODD P.; MIRANDA, VITOR F. O.; VARANI, ALESSANDRO M.. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 21, n. 1, . (13/25164-6, 18/02285-6, 13/05144-0, 11/22215-3)
TRAD, RAFAELA JORGE; CABRAL, FERNANDA NUNES; BITTRICH, VOLKER; DA SILVA, SAURA RODRIGUES; ESTANISLAU DO AMARAL, MARIA DO CARMO. Calophyllaceae plastomes, their structure and insights in relationships within the clusioids. SCIENTIFIC REPORTS, v. 11, n. 1, . (12/51781-0, 18/02285-6)
MATOS, RAMON GUEDES; SILVA, SAURA RODRIGUES; PLACHNO, BARTOSZ J.; ADAMEC, LUBOMIR; MICHAEL, TODD P.; VARANI, ALESSANDRO MELLO; MIRANDA, VITOR F. O.. The complete mitochondrial genome of carnivorous Genlisea tuberosa (Lentibulariaceae): Structure and evolutionary aspects. Gene, v. 824, p. 8-pg., . (20/11053-1, 18/02285-6)
SILVA, SAURA R.; MIRANDA, VITOR F. O.; MICHAEL, TODD P.; PLACHNO, BARTOSZ J.; MATOS, RAMON G.; ADAMEC, LUBOMIR; POND, SERGEI L. K.; LUCACI, ALEXANDER G.; PINHEIRO, DANIEL G.; VARANI, ALESSANDRO M.. The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae). Molecular Phylogenetics and Evolution, v. 181, p. 18-pg., . (20/11053-1, 18/02285-6, 13/05144-0)
JULIAO, MARIA H. M.; SILVA, SAURA R.; FERRO, JESUS A.; VARANI, ALESSANDRO M.. A Genomic and Transcriptomic Overview of MATE, ABC, and MFS Transporters in Citrus sinensis Interaction with Xanthomonas citri subsp. citri. PLANTS-BASEL, v. 9, n. 6, . (13/25164-6, 18/02285-6)
SILVA, SAURA R.; PINHEIRO, DANIEL G.; PENHA, HELEN A.; PLACHNO, BARTOSZ J.; MICHAEL, TODD P.; MEER, ELLIOTT J.; MIRANDA, VITOR F. O.; VARANI, ALESSANDRO M.. Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 20, n. 24, . (13/25164-6, 18/02285-6, 13/05144-0)
TRAD, RAFAELA JORGE; DA SILVA, SAURA RODRIGUES; ESTANISLAU DO AMARAL, MARIA DO CARMO. he first complete plastome of Mimusops coriacea (A. DC.) Miq. (Sapotaceae. GENETICS AND MOLECULAR BIOLOGY, v. 45, n. 1, . (18/02285-6, 12/51781-0)

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