Evandro Novaes

Structure of the phenotypic variability of fruit and seed traits in natural populations of Eugenia dysenterica dc. (Myrtaceae)

1Suporte Financeiro: CAPES, CNPq (GENPAC 10 Proc. 563727/2010-1) e FAPEG. 2Bióloga Doutora, Pós doutoranda bolsista PNPD/CAPES do Programa de Pós-Graduação em Genética e Melhoramento de Plantas da Universidade Federal de Goiás. E-mail: cboaventura@gmail.com 3Biólogo Mestre, Doutorando do Programa de Pós-Graduação em Genética e Melhoramento de Plantas da Universidade Federal de Goiás. E-mail: elias_emanuel@hotmail.com 4Engenheiro Florestal Doutor, Professor Adjunto da Escola de Agronomia da Universidade Federal de Goiás. E-mail: evnovaes@gmail.com 5Bióloga Doutora, Professora do Departamento de Genética da Universidade Federal de Goiás e da Escola de Ciências Agrárias e Biológicas da Pontifícia Universidade Católica de Goiás. E-mail: tellesmpc@gmail.com 6Engenheiro Agrônomo Doutor, Professor Titular da Escola de Agronomia da Universidade Federal de Goiás. E-mail: lchaves@ufg.br Abstract Eugenia dysenterica DC. (cagaita tree) is a fruit tree native to the Brazilian Cerrado. It is a promising species for cultivation, but little basic information exists on the phenotypic diversity and quantitative variation of its fruits and seeds at a population scale. Thus, the present study proposes to estimate the phenotypic parameters of the species’ fruits and seeds based on the variability among mother plants and among subpopulations, thereby aiming to increase knowledge for breeding and conservation of the species. For this, 25 natural subpopulations (local populations) were sampled in five Brazilian states. Within each subpopulation, 20 fruits were collected from each of six sampled mother plants. Data for biomass, transverse and longitudinal lengths of the fruits and seeds were subjected to estimates of descriptive parameters, correlation and hierarchical analysis of variance (ANOVA). Significant variation, including high levels of phenotypic variation, was observed among mother plants within the subpopulations and between the subpopulations. The high variation and the formation of phenotypically divergent groups are important elements for the breeding of cagaita tree, whose mother plants can now be selected for the traits studied. Phenotypic divergence between populations (PST) can be used as an indicator of the structuring of the phenotypic variation of the species in its natural area of occurrence.

Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree.

Abstract Background Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica. Regarded as the “new mahogany,” it is the second most expensive timber, the most logged species in Brazil, and currently under significant illegal trading pressure. The plant produces large amounts of quinoids, specialized metabolites with documented antitumorous and antibiotic effects. The development of genomic resources is needed to better understand and conserve the diversity of the species, to empower forensic identification of the origin of timber, and to identify genes for important metabolic compounds. Findings The genome assembly covers 503.7 Mb (N50 = 81 316 bp), 90.4% of the 557-Mbp genome, with 13 206 scaffolds. A repeat database with 1508 sequences was developed, allowing masking of ∼31% of the assembly. Depth of coverage indicated that consensus determination adequately removed haplotypes assembled separately due to the extensive heterozygosity of the species. Automatic gene prediction provided 31 688 structures and 35 479 messenger RNA transcripts, while external evidence supported a well-curated set of 28 603 high-confidence models (90% of total). Finally, we used the genomic sequence and the comprehensive gene content annotation to identify genes related to the production of specialized metabolites. Conclusions This genome assembly is the first well-curated resource for a Neotropical forest tree and the first one for a member of the Bignoniaceae family, opening exceptional opportunities to empower molecular, phytochemical, and breeding studies. This work should inspire the development of similar genomic resources for the largely neglected forest trees of the mega-diverse tropical biomes.

A proteomic dataset of secreted proteins by three Staphylococcus saprophyticus strains

This article presents a proteomic dataset generated from a comparative analysis of the exoproteome of Staphylococcus saprophyticus, ATCC 15305, 7108 and 9325 strains. The extract of secreted proteins were obtained after incubation of stationary phase cells in BHI medium. All samples were submitted to nano-ESI-UPLC-MSE, and the spectrum obtained was processed and analyzed by ProteinLynx Global Server (PLGS), Uniprot and Pedant databases, for identification, annotation and functional classification of proteins. Fold changes and protein relative abundances were properly reported. This report is related to the research article entitled “The exoproteome profiles of three Staphylococcus saprophyticus strains reveal diversity in protein secretion contents” (Oliveira et al., 2018). The proteomic data generated have been deposited to the ProteomeXchange Consortium, via the PRIDE partner repository, with a project number PXD008643, https://www.ebi.ac.uk/pride/archive/projects/PXD008643.

Complete Chloroplast Genome Sequence and Annotation of the Saccharum Hybrid Cultivar RB867515

ABSTRACT Here, we present the chloroplast genome sequence of the Saccharum hybrid cultivar RB867515, the most planted sugarcane cultivar in Brazil.

Percepção dos agricultores familiares brasileiros sobre suas condições de vida

Resumo: O trabalho traz a percepcao dos agricultores familiares brasileiros sobre suas condicoes de vida a partir de entrevistas realizadas em 10.362 domicilios rurais em todas as regioes do pais. Os agricultores percebem de forma positiva as condicoes de producao dentro da propriedade (incluindo area utilizada e mao de obra existente) e de forma negativa os resultados alcancados da porteira para fora (acesso a politicas publicas, insercao em mercados e relacoes sociais). Palavras-chave: Desenvolvimento local. Politicas publicas. Agricultura familiar.

The transcriptome of a Populus pseudo-backcross identifies genes and pathways co-expressed with monolignol biosynthesis

Background Lignin is the main impediment for efficient cellulose extraction and ethanol production from woody tissues. Even though, the biosynthesis of the lignin constituents the monolignols is well characterized, little is known about the genetic control of the natural variation in lignin content and composition. The few association studies performed to date in forest species only uncover 520% of the heritable variation of quantitative traits such as wood composition. The “missing heritability” can be explained in part by the low resolution of these pioneering association studies in forest species. However, as observed in genome-wide association studies with humans, a large proportion of the “missing heritability” is likely to occur due to other factors, such as the abundance of rare alleles observed in forest species and complex epistatic interaction between genetic elements. Causal rare alleles and genetic interactions remain undetectable with current statistical methods. In order to shed light on possible interactions between lignin biosynthesis genes and other pathways, we analyzed the transcriptome of 181 genotypes of a pseudo-backcross family of Populus. The analyses allowed identification of genes and pathways that were highly co-expressed with genes involved in the biosynthesis of monolignols. Correlations at the transcript level offer initial evidence of possible interactions between genetic elements for the production of monolignols. Methods A previously published microarray data [1] was utilized. Briefly, this microarray contains a gene expression probe for every gene annotated in the genome of Populus trichocarpa (v1.1.). Microarray chips were hybridized with cDNA synthesized from xylem tissue of 181 genotypes from a pseudo-backcross pedigree of Populus trichocarpa x P. deltoides. This family was also analyzed for lignin content on xylem tissue [2]. Genetic differences in gene expression allowed us to correlate the transcript abundance of 23 previously identified xylem-specific monolignol biosynthetic-genes [3] against the cDNA levels of all annotated genes of Populus. Correlation was estimated based on Spearman’s rank method in R. The top correlated genes (r > 0.75, p-value <0.001) were clustered with the 23 monolignol biosynthetic-genes based on a “Modulated Modularity Clustering” method [4]. The genes clustered with the 23 monolignol biosynthetic-genes were GO annotated based on the BlastP best hit against the Arabidopsis gene models. A Fisher’s exact test was applied to identify GO terms enriched within these clusters.

Genetic drift and uniform selection shape evolution of most traits in Eugenia dysenterica DC. (Myrtaceae)

Knowing how microevolutionary processes, such as genetic drift and natural selection, shape variation in adaptive traits is strategic for conservation measures. One way to estimate local adaptation is to compare divergences in quantitative traits (QST) and neutral loci (FST). Therefore, we have assessed the pattern of phenotypic and molecular genetic divergence among natural subpopulations of the fruit tree Eugenia dysenterica DC. A provenance and progeny test was performed to assess the quantitative traits of the subpopulations collected in a wide distribution area of the species in the Brazilian Cerrado. The sampled environments are in a biodiversity hotspot with heterogeneous soil and climate conditions. By associating quantitative trait variation in initial seedling development with neutral microsatellite marker variation, we tested the local adaptation of the traits by the QST–FST contrast. Genetic drift was prevalent in the phenotypic differentiation among the subpopulations, although the traits seedling emergence time and root green mass, which are relevant for adaptation to the Cerrado climate, showed signs of uniform selection. Our results suggest that E. dysenterica has a spatial genetic structure divided into two large groups, separated by a line that divides the Cerrado biome in a southwestern to northeastern direction. This structure must be taken into account for managing E. dysenterica genetic resources both for conservation and breeding purposes.

The exoproteome profiles of three Staphylococcus saprophyticus strains reveal diversity in protein secretion contents

Staphylococcus saprophyticus is a gram-positive microorganism responsible for urinary tract infections (UTIs). Although some virulence factors are characterized, such as urease, autolysins, adhesins and hemagglutinins, large-scale proteomic studies have not been performed within this species. We performed the characterization of the exoproteome from three S. saprophyticus strains: the reference strain ATCC 15,305, a non-capsular strain 7108 and the 9325 strain containing a thick capsule which were cultured in BHI medium and culture supernatants were analysed by using mass spectrometry approach. We observed a core of 72 secreted proteins. In addition, it was possible to detect diversity in the protein profiles of the exoproteomes. Interestingly, strain 7108 presented no secretion of three antigenic proteins, including the classical SsaA antigen. In addition, the level of antigenic proteins secreted by strain 9325 was higher than in ATCC 15,305. This result was confirmed by Western blot analysis using anti-SsaA polyclonal antibodies, and no production/ secretion of SsaA was detected in strain 7108. Transcriptional data shows that 7108 strain produces transcripts encoding SsaA, suggesting post-transcriptional regulation occurs in this strain. Moreover, when compared with the other strains that were analyzed, it was possible to detect higher levels of proteases secreted by strain 7108 and higher levels of antigenic proteins and transglycosylases secreted by 9325 strain. The results reveal diversity in protein secretion among strains. This research is an important first step towards understanding the variability in S. saprophyticus exoproteome profile and could be significant in explaining differences among strains.

Percepción de los campesinos brasileños acerca de sus condiciones de vida

Resumo: O trabalho traz a percepcao dos agricultores familiares brasileiros sobre suas condicoes de vida a partir de entrevistas realizadas em 10.362 domicilios rurais em todas as regioes do pais. Os agricultores percebem de forma positiva as condicoes de producao dentro da propriedade (incluindo area utilizada e mao de obra existente) e de forma negativa os resultados alcancados da porteira para fora (acesso a politicas publicas, insercao em mercados e relacoes sociais). Palavras-chave: Desenvolvimento local. Politicas publicas. Agricultura familiar.

Brazilian family farmers’ perception on their livelihoods

Resumo: O trabalho traz a percepcao dos agricultores familiares brasileiros sobre suas condicoes de vida a partir de entrevistas realizadas em 10.362 domicilios rurais em todas as regioes do pais. Os agricultores percebem de forma positiva as condicoes de producao dentro da propriedade (incluindo area utilizada e mao de obra existente) e de forma negativa os resultados alcancados da porteira para fora (acesso a politicas publicas, insercao em mercados e relacoes sociais). Palavras-chave: Desenvolvimento local. Politicas publicas. Agricultura familiar.