High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae)

Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.

Origin and parental genome characterization of the allotetraploid Stylosanthes scabra Vogel (Papilionoideae, Leguminosae), an important legume pasture crop

BACKGROUNDS AND AIMS

The genus Stylosanthes includes nitrogen-fixing and drought-tolerant species of considerable economic importance for perennial pasture, green manure and land recovery. Stylosanthes scabra is adapted to variable soil conditions, being cultivated to improve pastures and soils worldwide. Previous studies have proposed S. scabra as an allotetraploid species (2n = 40) with a putative diploid A genome progenitor S. hamata or S. seabrana (2n = 20) and the B genome progenitor S. viscosa (2n = 20). We aimed to provide conclusive evidence for the origin of S. scabra.

METHODS

We performed fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) experiments and Illumina paired-end sequencing of S. scabra, S. hamata and S. viscosa genomic DNA, to assemble and compare complete ribosomal DNA (rDNA) units and chloroplast genomes. Plastome- and genome-wide single nucleotide variation detection was also performed.

KEY RESULTS

GISH and phylogenetic analyses of plastid DNA and rDNA sequences support that S. scabra is an allotetraploid formed from 0.63 to 0.52 million years ago (Mya), from progenitors with a similar genome structure to the maternal donor S. hamata and the paternal donor S. viscosa. FISH revealed a non-additive number of 35S rDNA sites in S. scabra compared with its progenitors, indicating the loss of one locus from A genome origin. In S. scabra, most 5S rDNA units were similar to S. viscosa, while one 5S rDNA site of reduced size most probably came from an A genome species as revealed by GISH and in silico analysis.

CONCLUSIONS

Our approach combined whole-plastome and rDNA assembly with additional cytogenetic analysis to shed light successfully on the allotetraploid origin of S. scabra. We propose a Middle Pleistocene origin for S. scabra involving species with maternal A and paternal B genomes. Our data also suggest that variation found in rDNA units in S. scabra and its progenitors reveals differences that can be explained by homogenization, deletion and amplification processes that have occurred since its origin.

Miltefosine-loaded lipid nanoparticles: Improving miltefosine stability and reducing its hemolytic potential toward erythtocytes and its cytotoxic effect on macrophages

The toxic effects of miltefosine on the epithelial cells of the gastrointestinal tract and its hemolytic action on erythrocytes have limited its use as an antileishmanial agent. As part of our search for new strategies to overcome the side effects of miltefosine during the treatment of leishmaniasis, we have developed stable miltefosine-loaded lipid nanoparticles in an attempt to reduce the toxic effects of the drug. We have evaluated lipid nanoparticles containing varying amounts of miltefosine and cholesterol, prepared by sonication, in terms of their physicochemical properties, preliminary stability, hemolytic potential toward erythrocytes, and cytotoxicity to macrophages and to promastigote and amastigote forms of Leishmania (L.) chagasi. Miltefosine loading into lipid nanoparticles was 100% for low drug concentrations (7.0 to 20.0mg/mL). Particle size decreased from 143nm (control) to between 43 and 69nm. From fluorescence studies, it was observed that the presence of miltefosine and cholesterol (below 103μM) promoted ordering effects in the phospholipid region of the nanoparticles. The formulation containing 15mg/mL miltefosine was stable for at least six months at 4°C and in simulated gastrointestinal fluids, and did not promote epithelial gastrointestinal irritability in Balb/C mice. When loaded into lipid nanoparticles, the hemolytic potential of miltefosine and its cytotoxicity to macrophages diminished, while its antiparasitic activity remained unaltered. The results suggested that miltefosine-loaded lipid nanoparticles may be promising for the treatment of leishmaniasis and might be suitable for oral and parenteral use.