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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 species in Theobroma L. (Malvaceae s.l.) genus are T. cacao, and T. grandiflorum. Besides the economic value, both species also show considerable biotechnology potential due to their other derived products, thus, aggregating additional economic value for the agroindustry. Here, we assembled and compared the mtDNA of Theobroma cacao and T. grandiflorum to generate a new genomics resource and unravel evolutionary trends. Graph-based analyses revealed that both mtDNA exhibit multiple alternative arrangements, confirming the dynamism commonly observed in plant mtDNA. The disentangled assembly graph revealed potential predominant circular molecules. The master circle molecules span 543,794 bp for T. cacao and 501,598 bp for T. grandiflorum, showing 98.9% of average sequence identity. Both mtDNA contains the same set of 39 plant mitochondrial genes, commonly found in other rosid mitogenomes. The main features are a duplicated copy of atp4, the absence of rpl6, rps2, rps8, and rps11, and the presence of two chimeric open-reading frames. Moreover, we detected few ptDNA integrations mainly represented by tRNAs, and no viral sequences were detected. Phylogenomics analyses indicate Theobroma spp. are nested in Malvaceae family. The main mtDNA differences are related to distinct structural rearrangements and exclusive regions associated with relics of Transposable Elements, supporting the hypothesis of dynamic mitochondrial genome maintenance and divergent evolutionary paths and pressures after species differentiation.

Made available in DSpace on 2022-04-29T08:35:42Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) 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 are from Podostemaceae. Here we assembled and compared six plastomes from members of the clusioids: five from Calophyllaceae (newly sequenced) and one from Clusiaceae. Putative regions for evolutionary studies were identified and the newly assembled chloroplasts were analyzed with other available chloroplasts for the group, focusing on Calophyllaceae. Our results mostly agree with recent studies which found a general conserved structure, except for the two Podostemaceae species that have a large inversion (trnK-UUU–rbcL) and lack one intron from ycf3. Within Calophyllaceae we observed a longer LSC and reduced IRs in Mahurea exstipulata, resulting in some genic rearrangement, and a short inversion (psbJ–psbE) in Kielmeyera coriacea. Phylogenetic analyses recovered the clusioids and the five families as monophyletic and revealed that conflicts in relationships reported in the literature for the group agree with nodes concentrating uninformative or conflicting gene trees. Our study brings new insights about clusioid plastome architecture and its evolution. Department of Plant Biology Biology Institute University of Campinas (UNICAMP), CP 6109 Macroecology Lab @ J3-166 Institute of Biological Sciences – ICB Federal University of Minas Gerais (UFMG), Belo Horizonte Departamento de Ciências e Linguagens Instituto Federal de Minas Gerais – Campus Bambuí Department of Technology UNESP - São Paulo State University, Campus Jaboticabal Volker Bittrich is an independent scientist Department of Technology UNESP - São Paulo State University, Campus Jaboticabal Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas: 1124/13 CNPq: 142484/2014-8 FAPESP: 2012/51781-0 FAPESP: 2018/02285-6 CNPq: 562299/2010-6 CAPES: code 001

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 clinical and subclinical mastitis cases deposited in public databases. The most prevalent adhesin genes (ebpS, atl, pls, sasH and sasF) were found in both clinical and subclinical isolates. However, the ebpS gene was absent in subclinical isolates of Staphylococcus arlettae, S. succinus, S. sciuri, S. equorun, S. galinarum, and S. saprophyticus. In contrast, the coa, eap, emp, efb, and vWbp genes were present more frequently in clinical (vs. subclincal) mastitis isolates and were highly correlated with the presence of the biofim operon (icaABCD) and its transcriptional regulator, icaR. Co-phylogenetic analyses suggested that many of these adhesins, biofilm, and associated regulatory genes could have been horizontally disseminated between clinical and subclinical isolates. Our results further suggest that several adhesins, biofilm, and related regulatory genes, which have been overlooked in previous studies, may be of use for virulence profiling of mastitis-related Staphylococcus strains or as potential targets for vaccine development.

Made available in DSpace on 2019-10-06T16:35:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 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 Utricularia branch and have some unusual morphological characters in their traps and calyx. Thus, our aims were to (i) determine whether the nectar sugar concentrations and composition in U. multifida and U. tenella are similar to those of other Utricularia species from the subgenera Polypompholyx and Utricularia, (ii) compare the nectary structure of U. multifida and U. tenella with those of other Utricularia species, and (iii) determine whether U. multifida and U. tenella use some of their floral trichomes as an alternative food reward for pollinators. We used light microscopy, histochemistry, and scanning and transmission electron microscopy to address those aims. The concentration and composition of nectar sugars were analysed using high-performance liquid chromatography. In all of the examined species, the floral nectary consisted of a spur bearing glandular trichomes. The spur produced and stored the nectar. We detected hexose-dominated (fructose + glucose) nectar in U. multifida and U. tenella as well as in U. violacea. In both U. multifida and U. tenella, there were trichomes that blocked the entrance into the throat and spur. Because these trichomes were rich in chromoplasts and contained lipid droplets, they may form an additional visual attractant. Bearing in mind the phylogenetic hypothesis for the genus, we suggest that an early ancestor of Utricularia had a nectariferous spur flower with a lower lip that formed a wide landing platform for bee pollinators. Department of Plant Cytology and Embryology Institute of Botany Faculty of Biology Jagiellonian University in Kraków, 9 Gronostajowa St. Botanic Garden Faculty of Biology University of Warsaw, Al. Ujazdowskie 4 Department of Animal Histology and Embryology University of Silesia in Katowice, 9 Bankowa St. School of Biological Sciences University of Western Australia, (M084) 35 Stirling Highway School of Biological Sciences Faculty of Science The University of Adelaide Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Biologia Aplicada à Agropecuária Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Biologia Aplicada à Agropecuária Universidade Estadual Paulista (Unesp)

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, and to date, there is no agreement on whether these genotypes belong to the same species or to different species. Objective: The aim of this study was to quickly and accurately identify wild cane plants using the nuclear ribosomal internal transcribed spacer (ITS1+ITS2), three chloroplast regions (matK, rbcL, ycf1), and their combinations. Methods: Different tests were used for discrimination: (1) inter and intraspecific distances, (2) Best Match (BM), Best Close Match (BCM), and tree-based method (3) Neighbor Joining (NJ) and (4) maximum likelihood and bayesian inference in molecular data. Results: The results showed that BM and BCM approaches revealed the low rate of correct species identification for ITS+matK (33.3 %) and ITS (28.6 %) loci, showing similarity among sequences. These results were further supported by tree-based analyses, where all individual regions and the different gene combinations had a zero discrimination rate. Conclusions: all genotypes belong to the same species of wild cane, therefore existing morphological differences can be related to phenotypic plasticity. Introducción: La fibra de Gynerium sagittatum Aubl. P. Beauv, es materia prima esencial para la elaboración de varias artesanías, que son símbolos de la identidad cultural colombiana. En el proceso de fabricación, se utilizan diferentes genotipos de acuerdo con la calidad de la fibra y el tipo de artesanía, pero se cree que Gynerium es una especie compleja y hasta la fecha, no hay un consenso sobre si estos genotipos pertenecen a la misma especie o especies diferentes. Objetivo: Identificar de forma rápida y precisa plantas de caña silvestre utilizando el espaciador transcrito interno ribosomal nuclear (ITS1+ITS2), tres regiones de cloroplasto (matK, rbcL, ycf1) y sus combinaciones. Métodos: Se utilizaron diferentes pruebas para la discriminación: (1) distancias inter e intraespecíficas, (2) Prueba Best Match (BM), Best Close Match (BCM) y método basado en árboles (3) Neighbor Joining (NJ) y (4) Probabilidad de inferencia bayesiana mediante datos moleculares. Resultados: Los resultados mostraron que los enfoques BM y BCM revelaron una baja tasa de identificación correcta de especies para los loci ITS+matK (33.3 %) e ITS (28.6 %), mostrando similitud entre las secuencias. Estos resultados fueron respaldados por análisis basados en árboles, donde todas las regiones individuales y las diferentes combinaciones de genes tuvieron una tasa de discriminación de cero (0 %). Conclusiones: los genotipos evaluados pertenecen a la misma especie de caña flecha y las diferencias morfológicas existentes pueden estar relacionadas con plasticidad fenotípica.

Made available in DSpace on 2020-12-10T20:02:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-06-03 Brazilian National Science Fund (Conselho Nacional de Desenvolvimento Cientifico and Tecnologico) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) BackgroundMost 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 taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste.ResultsThe assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication.ConclusionsThe total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators. Univ Sao Paulo, Fac Med Ribeirao Preto, Dept Genet, Ribeirao Preto, SP, Brazil Univ Fed Alfenas, Inst Ciencias Biomed, Dept Biol Celular & Desenvolvimento, Alfenas, MG, Brazil Univ Fed Vales Jequitinhonha & Mucuri, Fac Ciencias Biol & Saude, Dept Ciencias Biol, Diamantina, MG, Brazil Univ Fed Sao Carlos, Ctr Ciencias Biol & Saude, Dept Genet & Evolucao, Sao Carlos, SP, Brazil Univ Tecnol Fed Parana, Cornelio Procopio, PR, Brazil Univ Sao Paulo, Fac Med Ribeirao Preto, Dept Biol Celular & Mol & Bioagentes Patogen, Av Bandeirantes 3900, BR-14049900 Ribeirao Preto, SP, Brazil Univ, Estadual Paulista Julio de Mesquita Filho, Fac Ciencias Agr & Vet, Dept Tecnol, Jaboticabal, SP, Brazil Univ Sao Paulo, Fac Filosofia Ciencias & Letras Ribeirao Preto, Dept Biol, Ribeirao Preto, SP, Brazil Univ, Estadual Paulista Julio de Mesquita Filho, Fac Ciencias Agr & Vet, Dept Tecnol, Jaboticabal, SP, Brazil Brazilian National Science Fund (Conselho Nacional de Desenvolvimento Cientifico and Tecnologico): 454103/2014-0 FAPESP: 2015/06657-0 CAPES: 001

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), affecting all citrus species. In this work, we performed an in silico analysis of genes and transcripts from MATE, ABC, and MFS families to infer the role of membrane transporters in Citrus-Xac interaction. Using as reference, the available Citrus sinensis genome and the citrus reference transcriptome from CitrusKB database, 67 MATE, 91 MFS, and 143 ABC genes and 82 MATE, 139 MFS, and 226 ABC transcripts were identified and classified into subfamilies. Duplications, alternative-splicing, and potentially non-transcribed transporters&rsquo, genes were revealed. Interestingly, MATE I and ABC G subfamilies appear differently regulated during Xac infection. Furthermore, Citrus spp. showing distinct levels of CC susceptibility exhibited different sets of transporters transcripts, supporting dissimilar molecular patterns of membrane transporters in Citrus-Xac interaction. According to our findings, 4 MATE, 10 ABC, and 3 MFS are potentially related to plant-defense mechanisms. Overall, this work provides an extensive analysis of MATE, ABC, and MFS transporters&rsquo, in Citrus-Xac interaction, bringing new insights on membrane transporters in plant-pathogen interactions.

Additional file 1 : Figure S1: Multiple alignment (A) and Maximum Parsimony phylogenetic tree (B) of miR-34.

Additional file 8 : Figure S8 Unrooted phylogenetic trees for core set of genes of the JAK/STAT and RNAi pathways. Amino acid sequences were aligned using MAFFT and the tree was generated in an ML approach (1000 replicates). In red are the orthologs of Frieseomelitta varia. Gene names are abbreviated. Species names are in three letters acronyms, Acer: Apis cerana, Ador: Apis dorsata, Aflo: Apis florea, Amel: Apis mellifera, Bter: Bombus terrestris, Bimp: Bombus impatiens, Dnov: Dufourea novaeangliae, Edil: Euglossa dilemma, Emex: Eufriesea mexicana, Fvar: Frieseomelitta varia, Hlab: Habropoda laboriosa, Lalb: Lasioglossum albipes, Mrot: Megachile rotundata, Mqua: Melipona quadrifasciata.

Additional file 9 : Table S1 Genome databases used in blastp searches for protein-coding genes included in the gene set for manual curation of their MAKER 2 gene model predictions.

Made available in DSpace on 2020-12-12T01:31:42Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-07-02 Ministerstwo Nauki i Szkolnictwa Wyższego Uniwersytet Śląski w Katowicach Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Kunming Institute of Botany, Chinese Academy of Sciences European Social Fund European Commission 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 compare the tuber structure of two taxonomically and phylogenetically divergent terrestrial carnivorous plants: Genlisea tuberosa and Utricularia menziesii. Additionally, we analyzed tubers of U. mannii. We constructed phylogenetic trees using chloroplast genes matK/trnK and rbcL and used studied characters for ancestral state reconstruction. All examined species contained mainly starch as histologically observable reserves. The ancestral state reconstruction showed that specialized organs such as turions evolved once and tubers at least 12 times from stolons in Lentibulariaceae. Different from other clades, tubers probably evolved from thick stolons for sect. Orchidioides and both structures are primarily water storage structures. In contrast to species from section Orchidioides, G. tuberosa, U. menziesii and U. mannii form starchy tubers. In G. tuberosa and U. menziesii, underground tubers provide a perennating bud bank that protects the species in their fire-prone and seasonally desiccating environments. Department of Plant Cytology and Embryology Institute of Botany Faculty of Biology Jagiellonian University in Kraków, Gronostajowa 9 St. Laboratory of Plant Systematics School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp Faculty of Natural Sciences Institute of Biology Biotechnology and Environmental Protection University of Silesia in Katowice, Jagiellońska 28 School of Molecular and Life Sciences Curtin University, Kent Street, Bentley Laboratory of Plant Systematics School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp CNPq: # 312908/2018-0 Kunming Institute of Botany, Chinese Academy of Sciences: N18/DBS/000002 European Social Fund: POWR.03.05.00-00Z309/17-00 European Commission: POWR.03.05.00-00Z309/17-00

Additional file 7 : Figure S7 Unrooted phylogenetic trees for core set of genes of the Toll (A) and IMD/JNK pathways. Amino acid sequences were aligned using MAFFT and the tree was generated in an ML approach (1000 replicates). In red are the orthologs of Frieseomelitta varia. Gene names are abbreviated. Species names are in three letters acronyms, Acer: Apis cerana, Ador: Apis dorsata, Aflo: Apis florea, Amel: Apis mellifera, Bter: Bombus terrestris, Bimp: Bombus impatiens, Dnov: Dufourea novaeangliae, Edil: Euglossa dilemma, Emex: Eufriesea mexicana, Fvar: Frieseomelitta varia, Hlab: Habropoda laboriosa, Lalb: Lasioglossum albipes, Mrot: Megachile rotundata, Mqua: Melipona quadrifasciata.

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&ndash, death&ndash, 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.

Made available in DSpace on 2018-12-11T17:15:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The carnivorous plant genus Utricularia L. (bladderwort) comprises about 240 species distributed worldwide and is traditionally classified into two subgenera (Polypompholyx and Utricularia) and 35 sections, based mainly on general and trap morphology. It is one out of the largest carnivorous genera, representing ca. 30% of all carnivorous plant species, and is also the most widely distributed. According to previous phylogenetic studies, most infrageneric sections are monophyletic, but there are several incongruences considering their relationships and also the dissenting position of some species as a result of a too few (mostly one or two) molecular markers analyzed. Thus, here we present a multilocus phylogeny for Utricularia species with a wide taxonomic sampling (78 species and 115 accessions) based on six plastid (rbcL, matK, rpl20-rps12, rps16, trnL-F) and nuclear DNA (ITS region) sequences. The aim is to reconstruct a well-resolved tree to propose evolutionary and biogeographic hypotheses for the radiation of lineages with inferences about the divergence times of clades using a molecular clock approach. Universidade Estadual Paulista (Unesp) Instituto de Biociências Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Biologia Aplicada à Agropecuária Office of Environment and Heritage Department of Premier and Cabinet Institute of Botany of the Czech Academy of Sciences Universidade Estadual Paulista (Unesp) Instituto de Biociências Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Biologia Aplicada à Agropecuária CNPq: 309040/2014–0

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.