The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity

Silva, Saura R.; Moraes, Ana Paula; Penha, Helen A.; Julião, Maria H. M.; Domingues, Douglas S.; Michael, Todd P.; Miranda, Vitor F. O.; Varani, Alessandro M.

doi:10.3390/ijms21010003

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The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity

¹,

¹,

³,

⁴

^5,*

and

Alessandro M. Varani

^1,*

Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil

Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo 09606-070, Brazil

Departamento de Botânica, Instituto de Biociências, UNESP—Universidade Estadual Paulista, Rio Claro 13506-900, Brazil

⁴

J. Craig Venter Institute, La Jolla, CA 92037, USA

⁵

Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil

Authors to whom correspondence should be addressed.

Int. J. Mol. Sci. 2020, 21(1), 3; https://doi.org/10.3390/ijms21010003

Received: 23 October 2019 / Revised: 13 December 2019 / Accepted: 15 December 2019 / Published: 18 December 2019

(This article belongs to the Special Issue Plant Genomics 2019)

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Abstract

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, GO enrichment 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. View Full-Text

Keywords: evolution; genome fractionation; ABC transporters; transcription factors; transposable elements; whole-genome duplication

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Doi: 10.5281/zenodo.3268745
Link: http://doi.org/10.5281/zenodo.3268745
Description: The terrestrial carnivorous plant Utricularia reniformis sheds light on environmental and life-form genome plasticity: Annotation, Gene Ontology, and Raw Data

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Silva, S.R.; Moraes, A.P.; Penha, H.A.; Julião, M.H.M.; Domingues, D.S.; Michael, T.P.; Miranda, V.F.O.; Varani, A.M. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. Int. J. Mol. Sci. 2020, 21, 3. https://doi.org/10.3390/ijms21010003

AMA Style

Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. International Journal of Molecular Sciences. 2020; 21(1):3. https://doi.org/10.3390/ijms21010003

Chicago/Turabian Style

Silva, Saura R., Ana P. Moraes, Helen A. Penha, Maria H.M. Julião, Douglas S. Domingues, Todd P. Michael, Vitor F.O. Miranda, and Alessandro M. Varani. 2020. "The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity" International Journal of Molecular Sciences 21, no. 1: 3. https://doi.org/10.3390/ijms21010003

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The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity

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