Saura Rodrigues Silva

São Paulo State University | Unesp · Department of Biology

Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT)...

Staphylococcus aureus causes nosocomial and intramammary infections in humans and cattle, respectively. A large number of virulence factors are thought to play important roles in the pathogenesis of this bacterium. Currently, genome-wide and data-analysis studies are being used to better understand its epidemiology. In this study, we conducted a ge...

Psychotria viridis (Rubioideae: Rubiaceae), popularly known as chacrona, is commonly found as a shrub in the Amazon region and is well-known to produce psychoactive compounds, such as the N,N-dimethyltryptamine (DMT). Together with the liana Banisteropsis caapi, P. viridis is one of the main components of the Amerindian traditional, entheogenic bev...

Unlike the chloroplast genomes (ptDNA), the plant mitochondrial genomes (mtDNA) are much more plastic in structure and size but maintain a conserved and essential gene set related to oxidative phosphorylation. Moreover, the plant mitochondrial genes and mtDNA are good markers for phylogenetic, evolutive, and comparative analyses. The two most known...

The chapter presents concepts and foundations about phylogeography. It briefly addresses the main molecular techniques for phylogenetic approaches, evolutionary and ecological aspects, as well as biotechnological applications.

The shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiver-sity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxo-nomic impediment to biodiversity research and conservation planning. The taxonomic impedi...

Sequenced genomic data for carnivorous plants are scarce, especially regarding the mitogenomes (MTs) and further studies are crucial to obtain a better understanding of the topic. In this study, we sequenced and characterized the mitochondrial genome of the tuberous carnivorous plant Genlisea tuberosa, being the first of its genus to be sequenced....

The shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impedime...

Abstract Mimusops coriacea (A. DC.) Miq. (Sapotoideae, Sapotaceae, Ericales) is native to Madagascar and the Comoro Islands. This species is cultivated in many countries around the world and grows on sand in coastal vegetation. Here we sequenced, assembled, and annotated the first complete chloroplast genome of M. coriacea. The newly assembled chlo...

The shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiver-sity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxo-nomic impediment to biodiversity research and conservation planning. The taxonomic impedi...

The genus Utricularia includes around 250 species of carnivorous plants, commonly known as bladderworts. The generic name Utricularia was coined by Carolus Linnaeus in reference to the carnivorous organs (Utriculus in Latin) present in all species of the genus. Since the formal proposition by Linnaeus, many species of Utricularia were described, bu...

A complete chloroplast genome is not yet available for numerous species of plants. Among the groups that lack plastome information is the clusioid clade (Malpighiales), which includes five families: Bonnetiaceae, Calophyllaceae, Clusiaceae, Hypericaceae, and Podostemaceae. With around 2200 species, it has few published plastomes and most of them ar...

Mastitis is a common and costly disease on dairy farms, commonly caused by Staphylococcus spp. though the various species are associated with different clinical outcomes. In the current study, we performed genomic analyses to determine the prevalence of adhesion, biofilm, and related regulatory genes in 478 staphylococcal species isolated from clin...

Bovine mastitis is the costliest diseases on dairy farms and is caused by different Staphylococcus species. However, staphylococci associated with clinical mastitis infections are different from subclinical ones, indicating a complex mechanism related to bovine mastitis pathogenesis. Here, we performed genomic analyses to determine the prevalence o...

The urge to organise the world around us is an essential part of human nature. Naming and categorising enable us to store and access information ef ciently. The need to name and categorise extends to the natural world and, in particular, to living organisms. The science underpinning this area of knowledge is called Taxonomy, and is as old as humani...

Introduction: The fiber of the Gynerium sagittatum Aubl. P. Beauv is raw material for the elaboration of several handcrafts, which are symbols of Colombian cultural identity. In the manufacture process, different genotypes are used according to the fiber quality and the type of craftsmanship, but it is believed that Gynerium is a complex species, a...

Carnivorous plants from the Lentibulariaceae form a variety of standard and novel vegetative organs and survive unfavorable environmental conditions. Within Genlisea, only G. tuberosa, from the Brazilian Cerrado, formed tubers, while Utricularia menziesii is the only member of the genus to form seasonally dormant tubers. We aimed to examine and com...

The multi-antimicrobial extrusion (MATE), ATP-binding cassette (ABC), and major facilitator superfamily (MFS) are the main plant transporters families, playing an essential role in the membrane-trafficking network and plant-defense mechanism. The citrus canker type A (CC), is a devastating disease caused by Xanthomonas citri subsp. citri (Xac), aff...

Background: Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonom...

Background Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomic...

Genlisea hawkingii, which is a new species of Genlisea subgen. Tayloria (Lentibulariaceae) from cerrado in southwest Brazil, is described and illustrated. This species has been found in only one locality thus far, in the Serra da Canastra, which is located in the Delfinó polis municipality in Minas Gerais, Brazil. The new species is morphologically...

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 evo...

Utricularia amethystina Salzm. ex A.St.-Hil. & Girard (Lentibulariaceae) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three U. amethystina morphotypes: purple-, white-, and yellow-flowered, were sequenced, compared, and putative markers for syst...

Utricularia (Lentibulariaceae) is a genus comprising around 240 species of herbaceous, carnivorous plants. Utricularia is usually viewed as an insect-pollinated genus, with the exception of a few bird-pollinated species. The bladderworts Utricularia multifida and U. tenella are interesting species because they represent an early evolutionary Utricu...

The Global Strategy for Plant Conservation (GSPC) was established by the Conference of Parties in 2002 to decrease the loss of plant diversity, reduce poverty and contribute to sustainable development. To achieve this overarching goal, the GSPC has established a series of targets, one of which is to ensure that plant diversity is well understood, s...

The Global Strategy for Plant Conservation (GSPC) was established by the Conference of Parties in 2002 to decrease the loss of plant diversity, reduce poverty and contribute to sustainable development. To achieve this overarching goal, the GSPC has established a series of targets, one of which is to ensure that plant diversity is well understood, s...

In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structur...

Coverage and read identity plots for the reconstructed plastid genomes of Genlisea species. All quality-trimmed reads from sequencing data sets have been mapped back to the reconstructed plastid supercontig. The upper plot indicates the identity per site and the lower plot shows the coverage plot per species. (DOCX)

Matrix with codified characters of ndh genes for Lentibulariaceae. The characters were codified according the S2 Table. (G. = Genlisea; P. = Pinguicula; U. = Utricularia). (DOCX)

Phylogenomic trees based on different datasets for Genlisea species. Numbers above are parsimony bootstrap (left), maximum likelihood bootstrap (right) and posterior probability values are represented below. Lamiales species were used as outgroup. (DOCX)

Summary of sequencing data for Genlisea species. (DOCX)

ndh genes length variation among Genlisea and Utricularia gibba species. Numbers within table refer to sequence length (bp). Colors refer to the state of character: white–deleted gene; yellow–pseudogenized; pink–decayed gene; grey–complete gene; n/a–absent. (DOCX)

Phylogenetically informative characters (PIC) and p-distance of each gene for Genlisea species. Deleted ndh genes in all Genlisea species and boundaries between ndh pseudogenes are uncertain and were not included in this analysis (represented as n/a). (DOCX)

Agarose gel electrophoresis (0.8%) of PCR products of the cpDNA IR/LSC boundary of Genlisea violacea (3 bioreplicates = 3 specimens), G. aurea, G. filiformis, and G. tuberosa. Note the product of G. violacea cpDNA that presents the duplication of rps19 gene and rpl22 as pseudogene (amplicon with 1,194 bp), while the other species present an expecte...

Correlation between p-distance and phylogenetically informative characters (PICs). Statistics from Spearman correlation tests are given near the corresponding trend lines. (DOCX)

Phylogenetically informative characters (PIC) and p-distance in Genlisea cpDNA based on alignment data. PIC values are represented as bars and cpDNA region is marked by colors. Black dots represent p-distance. Only PIC of ndhs were not calculated to avoid p-distance alignment artefact (see S6 Table). (DOCX)

Characters and states codified of ndh genes for Lentibulariaceae. (DOCX)

Repeats (direct, palindromic and tandem) for each Genlisea species. F–Direct repeats; P–Palindromic repeats; T–Tandem repeats (inside parenthesis the repeated nucleotide). Common genes with repeats between the six species are highlighted with yellow background color in G. aurea table. (DOCX)

Codon usage and amino acid frequencies for Genlisea plastomes. (DOCX)

The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mech...

List of all identified open reading frames and detected signal peptide and transmembrane domains. (XLSX)

Assembly graph of Utricularia reniformis mtDNA based on the paired-read (2x300bp) assembly, generated by the Bandage software. The assembled contigs (nodes, represented as colored bars) with multiple inputs and outputs, and dead ends; and the connections between those contigs (edges, represented as black connectors) are shown. (TIF)

Mitochondrial genes (atp1, cox1, matR, nad5, rps3) from 32 different species from the Lamiales order used in the phylogenetic analysis. (XLSX)

RNAseq analysis of all identified genes of U. reniformis mtDNA. (XLSX)

The 147 RNA edit sites identified on the traditional mitochondrial coding-regions by RNAseq read mapping. (XLSX)

A paired-end (mate-pairs) mapping read-track displaying the reads and coverage generated by CLC Genomics Workbench v9.5.2 tool. Blue lines represent the paired reads located on the border of the repeat region; the yellow lines represent the paired reads located on each repeated region. Mismatches between the reads and reference are shown as narrow...

The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mech...

Background and Aims The ‘orchid-like’ bladderworts (Utricularia) comprise 15 species separated into two sections: Orchidioides and Iperua. These robust and mostly epiphytic species were originally grouped within the section Orchidioides by the first taxonomical systems. These species were later split into two sections when sect. Iperua was proposed...

Background and aims: The 'orchid-like' bladderworts ( Utricularia ) comprise 15 species separated into two sections: Orchidioides and Iperua . These robust and mostly epiphytic species were originally grouped within the section Orchidioides by the first taxonomical systems. These species were later split into two sections when sect. Iperua was pro...

Lentibulariaceae is the richest family of carnivorous plants spanning three genera including Pinguicula, Genlisea, and Utricularia. Utricularia is globally distributed, and, unlike Pingui-cula and Genlisea, has both aquatic and terrestrial forms. In this study we present the analysis of the chloroplast (cp) genome of the terrestrial Utricularia ren...

Utricularia foliosa L., commonly known as leafy bladderwort, is a widespread aquatic carnivorous plant from the Lentibulariaceae family. The species of the Utricularia and Genlisea genera are known to possess the smallest nuclear genomes across angiosperms. This study reveals that U. foliosa have a typical chloroplast genome of 150,851 bp in length...

Phylogenomic and phylogenetic analysis. (A) List of the chloroplast genomes used in the phylogenomics analysis with their respective GenBank accession number. (B) List of chloroplast genes used in the phylogenomics analysis. (C) The matK genes used in the phylogenetic analysis with their respective GenBank accession number. (D) The matK genes gener...

The remaining paired-end reads (2x300bp; 229,830; 18.3%) which were assembled into contigs containing fragments of incomplete or truncated cp genes. The distribution, number of these contigs, truncated gene content and alignment to the Utricularia reniformis cp genome is shown. (DOCX)

RNAseq experiment table, showing the expression profile of all chloroplast related genes of Utricularia reniformis. (DOCX)

An updated inventory of Brazilian seed plants is presented and offers important insights into the country’s biodiversity. This work started in 2010, with the publication of the Plants and Fungi Catalogue, and has been updated since by more than 430 specialists working online. Brazil is home to 32,086 native Angiosperms and 23 native Gymnosperms, sh...

Phylogenetic approaches and its main characteristics (Neighbor-joining, Maximum Parsimony, Maximum Likelihood, Bayesian and Molecular clock)

Background: Phenotypic variations have been observed in populations of west Cuban Pinguicula species. Such populations occur in patches under different ecological conditions associated with specialised habitats and separated by geographical and ecological barriers, which can lead to morphological differentiation. Aims: To analyse morphological dive...

Detailed explanation about how to avoid problems dealing with DNA extraction from fresh tissue, exsiccate, etc.