Unravelling the genetic differentiation among varieties of the Neotropical savanna tree Hancornia speciosa Gomes

Mitochondrial genome of Hancornia speciosa gomes: intergenic regions containing retrotransposons and predicted genes

BACKGROUND

Plant mitochondrial genomes are characterized by high homologous recombination, extensive intergenic spacers, conservation in DNA sequences, and gene content. The Hancornia genus belongs to the Apocynaceae family, with H. speciosa Gomes being the sole species in the genus. It is an siganificant commercial fruit crop; however, only a number of studies have been conducted. In this study, we present the mitochondrial genome of H. speciosa and compare it with other mitochondrial genomes within the Apocynaceae family.

METHODS AND RESULTS

A total of 2.8 Gb of Illumina paired-end reads were used to obtain the mitogenome, resulting in 22 contigs that were merged using 6.1 Gb of Illumina mate-pair reads to obtain a circular chromosome. The mitochondrial genome of H. speciosa is circular, containing 63 predicted functional genes, spanning a length of 741,811 bp, with a CG content of 44%. Within the mitogenome, 50 chloroplast DNA sequences, equivalent to 1.72% of the genome, were detected. However, intergenic spaces accounted for 703,139 bp (94.79% of the genome), and 287 genes were predicted, totaling 173,721 bp.

CONCLUSION

This suggests the incorporation of nuclear DNA into the mitogenome of H. speciosa and self duplication. Comparative analysis among the mitogenomes in the Apocynaceae family revealed a diversity in the structure mediated by recombination, with similar gene content and large intergenic spaces.

Forecasting effects of climate changes on the population genetic structure of Anacardium occidentale in the Cerrado biome, Brazil

There has been a continuous interest in understanding the patterns of genetic diversity in natural populations because of the role of intraspecific genetic diversity as the basis of all evolutionary change and thus, its potential effects on population persistence when facing environmental changes. Here, we provided the first description of genetic diversity distribution and population structure of Anacardium occidentale L. (cashew) from the Brazilian Cerrado, one of the most economically important tropical crops in the world. We applied Bayesian clustering approaches (STRUCTURE and POPS) that allow predicting the effects of future climatic changes on the population genetic structure of A. occidentale. We identified distinct genetic groups corresponding to the southwestern, central, and northern regions of the species' range. The characterized genetic clusters will disappear under future climate change scenarios, leading to a homogenization of genetic variability across the landscape. Our findings suggest a high likelihood for the loss of genetic diversity, which in turn will reduce the evolutionary potential of the species to cope with predicted future climatic changes. Results from this study may help develop management strategies to conserve the genetic diversity and structure of natural cashew populations.

Pharmaceutical, food potential, and molecular data of Hancornia speciosa Gomes: a systematic review

Hancornia speciosa Gomes is a fruit and medicinal tree species native to South America, which in Brazil is considered of potential economic value and priority for research and development. We present a map of the state-of-art, including articles, patents, and molecular data of the species to identify perspectives for future research. The annual scientific production, intellectual, social, and conceptual structure were evaluated, along with the number of patent deposits, components of the plant used, countries of deposit, international classification and assignees, and the accessibility of available molecular data. Brazil has the most significant publications (306) between 1992 and 2020. Technological products (29) have been developed from different tissues of the plant. Most of the articles and patents were developed by researchers from public universities from different regions of Brazil. The molecular data are sequences of nucleotides (164) and proteins (236) of the chloroplast genome and are described to identify the species as DNA barcodes and proteins involved in photosynthesis. The compilation and report of scientific, technological, and molecular information in the present review allowed the identification of new perspectives of research to be developed based on the gaps in knowledge regarding the species and perspectives for the definition of future research.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10722-021-01319-w.

Landscape and Climate Influence the Patterns of Genetic Diversity and Inbreeding in Cerrado Plant Species

The anthropization of the landscape of the Cerrado biome that has occurred over the past few decades has fragmented its natural environments, impacting the connectivity of the plant populations and altering their gene flow. Plant species may also reduce population size in response to sub-optimal climatic and environmental conditions, and observed distribution patterns may align with theoretical schemes, such as the center–periphery model, that is, it is possible that populations on the edge have lower genetic diversity than center populations, theoretically submitted to environmental conditions closer to the optimum. In this context, we evaluate whether the genetic diversity and inbreeding coefficients of Cerrado plant species are affected by landscape features and climate characteristics, and in particular, if the distribution of the genetic diversity of these plants is consistent with the center–periphery model. To do this, we conducted a literature search for genetic studies of Cerrado plant populations using Scopus, Web of Science, and Scielo databases and the species found were used as a proxy to explore patterns throughout the biome. The data were analyzed using generalized linear mixed models (GLMM) and multiple matrix regressions (MMRRs) to evaluate the effects of landscape features and climatic variables on the observed (HO) and expected heterozygosity (HE), allelic richness (AR) and inbreeding (Fis) patterns of the local populations. The landscape was evaluated in terms of the percentage land cover of agriculture (AG), forestry (FO), remnant vegetation (RV), urban areas (UA), pasture (PA), and water (WA) within buffers of 1 km, 3 km, and 5 km around the study populations. We analyzed 121 populations of 31 plant species. The GLMMs showed that HO was affected by FO regardless of buffer size, while HE was also affected by FO, but also by WA and UA. AR was affected by WA and UA in all three buffer zones while the Fis was affected by FO and AU. The MMRRs showed that WA may affect HO, HE, and Fis within the 1 km buffer, while FO affects HO and UA affects AR within the 5 km buffer. In the case of the 1 km and 3 km buffers, however, the geographic distance between populations was identified as a factor determining the genetic diversity and inbreeding indices, indicating that isolation by distance may be an important factor defining the breeding patterns of the Cerrado plant populations. The GLMMs and MMRRs also showed that the mean annual temperature (MAT) and, to a lesser extent, isothermality (ISO) can explain the variation in genetic diversity observed in the Cerrado plant populations. We also found that the center–periphery model fits the distribution pattern observed in most of the species evaluated, including Annona crassiflora,Annona coriacea, Copaifera langsdorffii, and Eugenia dysenterica. Our results indicate that changes in the climate and the landscape of Brazilian Cerrado must be considered carefully to guarantee minimizing the impacts of these processes on the genetic diversity of Cerrado plant species and ensuring the long-term conservation of these species in this biome.