•We sequenced the first complete chloroplast genome ofEugenia klotzschiana Berg.•The chloroplast genomes of the Myrteae tribe show a high level of conservation (sequence similarity and gene content), ...probably due to the recent diversification of the group.•For the first time, Eugenia klotzschianais included in a molecular phylogeny. Also, the combination of the two commonly used barcode loci, matK and rbcL, recovered some differences in the Myrtales tree topology when compared to the use of 61 plastid protein-coding genes combined.•Two plastid genes (rps12 and psaI) are under neutral evolution and the major number of mutational hotspots in chloroplast genomes from the Myrteae tribe occur in intergenic regions, except by the ycf1 gene.
Myrteae is the most diversified tribe in the Myrtaceae family and has great ecological and economic importance. Here, we performed the assembly and annotation of the chloroplast genome of Eugenia klotzschiana O. Berg and used this in a comparative analysis with other 13 species from the Myrteae tribe. The E. klotzschiana plastome exhibited a length of 158,977 bp and a very conserved structure and gene composition when compared with other Myrteae genomes. We identified 34 large repetitive sequences and 94 SSR repeats in E. klotzschiana plastome. The trnT-trnL, rpl32-trnL, ndhF-rpl32, psbE-petL, and ycf1 regions were identified as mutational hotspots. A negative selection signal was detected in 74 protein-coding genes while neutral evolution was detected in two genes (rps12 and psaI). Furthermore, 222 RNA editing sites were identified in the E. klotzschiana plastome. We also obtained a plastome-based Myrtales phylogenetic tree, including E. klotzschiana for the first time in a molecular phylogeny, recovering its sister relationship for all other Eugenia species. Our results illuminate how evolution shaped the chloroplast genome structure and composition in the Myrteae tribe, especially in the E. klotzschiana plastome.
Serjania erecta
Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species ...remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of
S. erecta
and used it in a comparative analysis within the Sapindaceae family.
S. erecta
has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis,
S. erecta
has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of
rpl22
,
rps19
, and
rps3
genes; (2) Pseudogenization of the
rps2
gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of
trnH-GUG
in
X. sorbifolium
and the absence of
trnT-CGU
in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (
tRNA-Lys — rps16, ndhC – tRNA-Val, petA – psbJ, ndhF, rpl32 – ccsA
, and
ycf1
) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of
Serjania
. We identified that the
psaI
gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the
ndhF
,
rpoC2
,
ycf1
, and
ycf2
genes. The genes
ndhF
and
ycf1
also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family’s evolutionary history.
The neotropical fruit plant Eugenia klotzschiana Berg. is endemic from South America and occurs in the Brazilian savannah areas, a biome threatened by intensive agriculture. This species is a plant ...listed on the Brazilian list of Plants for the Future. The E. klotzschiana fruits have great nutritional value and antioxidant activity and are consumed in natura or processed into juice or jelly. However, their harvest is predominantly in native areas and needs further studies for large-scale commercialization. Nuclear genomic data and population genetic tools are still quite scarce for the species. Here, we provide data on the first partially assembled genome of E. klotzschiana (211 Mbp, ∼75.16% genome coverage, N50 = 3,407, and 46.8% BUSCO completeness), the raw Illumina sequencing reads, and two sets of primers for microsatellite (SSRs) high-throughput genotyping-by-sequencing (SSR-Seq) identified in the nuclear genome. These genomic resources are fundamental for this species conservation strategies and the development of a future breeding program.
Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. ...guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.
Background: The species Pterodon emarginatus and P. pubescens , popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and ...reforestation. They are sister species with evolutionary proximity.
Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.
Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases.
Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens . The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx , both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed.
Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.
Biodiversity is organized in three fundamental hierarchical levels in nature: diversity of genes within species, diversity of species in communities, and diversity of ecosystems. The analyses of the ...Species-Genetic Diversity Correlation (SGDC) are important for understanding the ecological and evolutionary mechanisms underlying the patterns of biodiversity in time and space and, at the same time, have contributed to the planning of the simultaneous conservation of these levels. Thus, SGDC can be important to establish a framework to evaluate diversity patterns and develop conservation programs in widely explored areas such as the Brazilian Cerrado, generating knowledge for species of great ecological and economic importance. An example is
Stryphnodendron adstringens
, a tree that occurs in the Brazilian Cerrado and has medicinal properties. In this study, SGDC analyses were applied to verify if there is a correlation between the genetic diversity of
S. adstringens
and the diversity of species of
Stryphnodendron
and other phylogenetically related genera. Ecological niche modeling procedures were used to estimate the occurrence area and species diversity of
Stryphnodendron
and related genera in the Brazilian Cerrado, which enabled the construction of maps of environmental suitability. The
α
-SGDC and
β
-SGDC correlations were calculated in two different situations, one using microsatellite genetic data and the other using chloroplastidal DNA (cpDNA) genetic data. The analyses revealed a significant negative relationship between the haplotypic diversity of
S. adstringens
and the diversity of species of
Stryphnodendron
and other genera. The negative
α
-SGDC detected is an indication that to develop a conservation plan for the set of species analyzed, it is necessary to combine conservation strategies that cover more than one level of biological diversity.
Species Cichla piquiti and Cichla kelberi are found in the Serra da Mesa reservoir, Goiás and are sedentary with diurnal habits. This study aimed to evaluate the magnitude and distribution of genetic ...variability in subpopulations of C. piquiti with specific microsatellite loci and to test transferability in other microsatellite markers for C. kelberi. We analyzed 99 individuals of C. piquiti from seven points to evaluate genetic diversity and structure with 10 microsatellite loci. Transferability of 75 loci was tested in C. kelberi to increase microsatellite markers available. Genetic structure was assessed with Bayesian clustering. Global FST for C. piquiti was weak (0.056), but FIS (0.598) and FIT (0.621) were significantly high, indicating that the mating system has a strong influence on the organization of genetic variability with most mating among related. Two genetic groups were evidenced with most individuals allocated to a single group. Transferability of microsatellite loci for C. kelberi had low polymorphism. The level of genetic diversity was low, increasing inbreeding and suggesting that few individuals of C. piquiti colonized the reservoir during its installation due founder effect. Other factors as reproductive behavior and overfishing can act to decrease genetic diversity. Therefore, we reinforce the need for genetic monitoring to avoid loss of genetic diversity that can be intensified both construction of hydropower plants and ecological and reproductive aspects in some fish species.
ABSTRACT Hymenaea stigonocarpa (Mart. Ex Hayne), popularly known as jatobá-do-cerrado, is a fruit tree widely distributed in the Brazilian Savanna, has multiple uses and is a promising genetic ...resource. This study aimed to physically characterize fruits and seeds of H. stigonocarpa, as well as to estimate the phenotypic variability at three hierarchical levels: populations, mother trees within populations, and fruits/seeds within mother trees. Fruits from six mother trees were sampled from each of the 25 natural populations found in the Brazilian Savanna. The morphometric characterization of 742 fruits was carried out by evaluating 10 quantitative traits in fruits and seeds. In addition, comparative analyses were performed between the average values of H. stigonocarpa and the botanical variety H. stigonocarpa var. brevipetiolata. Significant phenotypic variations were noticed at all hierarchical levels. A high phenotypic differentiation among the populations was observed for quantitative traits (fruit mass and size, pulp mass and seed mass), being higher when H. stigonocarpa var. brevipetiolata was included in the analysis.
RESUMO Hymenaea stigonocarpa (Mart. Ex Hayne), popularmente conhecida como jatobá-do-cerrado, é uma árvore frutífera amplamente distribuída no Cerrado, a qual possui múltiplos usos e é um recurso genético promissor. Objetivou-se caracterizar fisicamente frutos e sementes de H. stigonocarpa, bem como estimar a variabilidade fenotípica em três níveis hierárquicos: populações, matrizes dentro de populações e frutos/sementes dentro de matrizes. Frutos de seis matrizes foram amostrados de cada uma das 25 populações naturais encontradas no Cerrado. A caracterização morfométrica de 742 frutos foi realizada avaliando-se 10 caracteres quantitativos em frutos e sementes. Além disso, foram realizadas análises comparativas entre os valores médios de H. stigonocarpa e a variedade botânica H. stigonocarpa var. brevipetiolata. Variações fenotípicas significativas ocorreram em todos os níveis hierárquicos. Observou-se alta diferenciação fenotípica entre as populações para caracteres quantitativos (massa e tamanho do fruto, massa da polpa e da semente), a qual foi ainda maior quando H. stigonocarpa var. brevipetiolata foi incluída na análise
Conceptions of Science influence educational practices and interpretations about the construction of scientific knowledge. Therefore, this study aimed to use scientific practice to test the ...efficiency of non-formal educational environments in training candidates for teacher certification in Biological Sciences. Training of candidates was performed in four meetings held on the State University of Goiás in Anápolis, which features an interpretative trail for environmental education. To test the hypothesis that the training was effective, a paired t-test was performed on the grades obtained in the questionnaires before and at the end of the activities (pretest and post-test). The test showed that the course was effective and led to an increase in students’ knowledge of the content covered (t test: t = 2.95, df = 16, p = 0.01), showing that on average, the scores of students increased in the post-test. This denotes a cognitive gain at the end of the course.KEYWORDS: Science education. Interpretative trails. Pre- and post-tests.
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