Biology subjects

Vaio, M.

Publications and source records attributed to Vaio, M..

8 recordsLinked to original sources

bioRxiv2026

Unveiling the intraspecific genomic diversity of South American lowland maize landraces

Abstract Background and Aims South American Lowland maize landraces constitute an important reservoir of the species diversity, although research regarding the territories of Uruguay and Brazil remains comparatively unexplored. This study aimed to evaluate the intragenomic variability of maize landraces from Uruguay and Brazil. Methods We estimated the genome size, number of heterochromatic knobs, and presence of B chromosomes in 15 maize landraces representing 13 races, and finally, we conducted an analysis of repetitive sequences in landraces from both countries. Key Results Regarding DNA content, a north-to-south gradient of decreasing genome size was found, significantly associated with latitude. At the knob level, a model incorporating the Country x Race interaction detected significant effects, revealing a reversal of the pattern of knob number per race among countries. B chromosomes were found only in Uruguayan races, whereas regarding repetitive sequences, a trend of increasing retrotransposons and decreasing knobs was observed as DNA content decreased. Conclusions Taken together, these results suggest that genome size may be influenced by selective pressures associated with local adaptation, although further investigation is needed to test this hypothesis. Furthermore, the knob profiles of specific races across countries, as well as the presence of B chromosomes in Uruguay, may reflect distinct histories of dispersal, local selection, and even introgression, highlighting the complexity of the processes shaping maize genomic architecture across geographic gradients.

genetics↗

bioRxiv2025

Exploring the Repetitive DNA Diversity in Solanum betaceum (Solanaceae)

The Solanaceae family, known for its diverse and economically important crops, includes the genus Solanum, which comprises 1,245 species. Solanum betaceum (tree tomato), native to the Andes and cultivated globally, is a promising species due to its nutritional value and market potential. The Cyphomandra clade, which includes the tree tomato, is characterized by huge genomes and chromosomes, with repetitive DNA elements (e.g., retrotransposons and satellite DNA) playing crucial roles in genomic and evolutionary studies. Despite its importance, genetic research on S. betaceum remains limited. This study addresses this knowledge gap by characterizing the repetitive DNA fraction to better understand intraspecific variation and develop molecular markers. Samples from five populations in northwestern Argentina were cultivated, and genome size was assessed via flow cytometry. Illumina HiSeq sequencing combined with RepeatExplorer analysis was used to identify repetitive DNA elements. Cytogenetic techniques, including CMA/DAPI staining and fluorescence in situ hybridization (FISH), were employed to detect satellite DNA patterns. Genome size analysis revealed slight variation among populations. Repetitive DNA accounted for 63.5% of the genome, with Ty3-gypsy retrotransposons being the most abundant (51.44%). Satellite DNA and rDNA were less prevalent, comprising 0.93% and 0.30% of the genome, respectively. Population comparisons showed consistent proportions of repetitive DNA overall, with notable differences in Ty3-gypsy-Tekay and satellite DNA fractions. This study provides a detailed profile of the repetitive DNA landscape in S. betaceum, uncovering intraspecific differences and delivering valuable genomic insights for future breeding and conservation efforts.

genomics↗

bioRxiv2025

Apomixis frequency in polyploid wild populations of Psidium cattleyanum f. lucidum (Myrteae, Myrtaceae)

Background and AimsApomictic reproduction and polyploidy are closely related in plants, and their causes and consequences have given rise to numerous hypotheses that continue to evolve as more representative taxa are studied. Psidium cattleyanum is a valuable model for investigating this relationship, as it is a polyploid species with multiple ploidy levels and exhibits pseudogamous gametophytic apomixis. In addition, it is a fruit tree of commercial, agricultural, and medicinal interest in its native range, but it is also an aggressive invasive species in regions where it has been introduced. In this study, we aim to determine the predominant reproductive mode in natural populations of the polyploid Psidium cattleyanum f. lucidum and to investigate whether this mode is associated with specific ploidy levels. Furthermore, we investigate whether these reproductive traits are linked to patterns of genetic diversity and population genetic structure. MethodsWe assessed the reproductive mode in wild populations representing the four ploidy levels (2C = 5x, 6x, 7x, 8x) present in Uruguay. Reproductive pathways were inferred by combining flow cytometric seed screen (FCSS) analysis with microsatellite (SSR) genotyping of progeny arrays. Population-level differences were evaluated across both data sets. Key ResultsPseudogamous apomixis is the predominant reproductive mode in Uruguayan P. cattleyanum f. lucidum populations. The proportions of apomictic versus sexual reproduction, and the types of progenies produced, differed significantly among populations and ploidy levels. Genotyping revealed predominantly clonal progeny, yet with high genetic variability, and populations exhibit strong genetic structure. The ploidy level of the gametes and their combinations were characteristic of each population, leading to different reproductive strategies. ConclusionsFacultative pseudogamous apomixis is the primary reproductive mode in natural populations of Psidium cattleyanum f. lucidum. Ploidy level influences reproductive strategy, as reflected in the apomixis/sexuality ratios and the type of progeny produced. Population genetic structure is shaped by the reproductive strategy adopted by each population.

plant biology↗

bioRxiv2025

Shedding light on the embryo:endosperm balance diversity that pseudogamy can achieve in the polyploid apomictic Psidium cattleyanum (Myrtaceae, Myrteae)

Apomixis is defined as the asexual mode of reproduction through seeds. Nearly all gametophytic apomictic species are polyploid. Psidium cattleyanum, a polyploid species with various described ploidy levels, exhibits apomixis and requires effective pollination for fruiting (pseudogamy). The aim of this study was to determine the frequency of apomixis and sexuality in P. cattleyanum among heptaploid and octoploid accessions, and to analyze the maternal and paternal contribution to endosperm formation. Flow cytometry was employed on mature seeds obtained from hand-pollinated crosses between two octoploid and two heptaploid accessions to determine the ploidy levels of embryo and endosperm. Within the 492 analyzed seeds the ploidy balance of embryo:endosperm ranged from the expected 2:5 (64.2%, pseudogamous apomixis) and 2:3 (4.7%, sexuality involving reduced gametophytes), to unexpected values, including 1:3 (0.4%),), 2:6 (2.4%), 2:7 (0.2%), 3:5 (8.8%), 2:3:5 (18.5%) and 2:4:6 (0.8%), associated with polyhaploid parthenogenesis, pseudogamous apomixis involving reduced and unreduced gametophytes, and female gametophytes with two or three polar nuclei in the central cell. The interpretations and implications of these results for apomictic polyploid species and their consequences for wild populations are discussed.

genetics↗

bioRxiv2025

Cenchrus purpureus and Cenchrus americanus repeatome provide chromosomal markers to distinguish subgenomes

Cenchrus L. is an important genus within the Poaceae family, comprising several species of high agronomic significance, such as Cenchrus purpureus and Cenchrus americanus, for production of forage and grains, respectively. Cenchrus americanus is a diploid species (2n = 2x = 14, AA genome), while Cenchrus purpureus is an allotetraploid (2n = 4x = 28, AABB genome). The A subgenome is believed to be homeologous to and possibly derived from the A subgenome, while the origin of the B subgenome remains undefined. Despite their distinct subgenomic compositions, both species exhibit a high level of genome homology. The objective of the present work was the in silico characterization and comparative analysis of the repetitive fraction of the genomes of Cenchrus purpureus and Cenchrus americanus using genome skimming and a graph-based clustering approach, as well as the in situ hybridization of specific satellite DNA clusters into the chromosomes of both species. The repetitive fraction of the genome of C. purpureus and C. americanus corresponds to 52.23% and 76.82%, respectively. The most abundant repetitive elements in both species are the LTR retrotransposons. Satellite DNA sequences correspond to 2.55% and 4.17% of the genome of each species, respectively. Four new satellite sequences were identified as subgenome-specific sequences for both species, along with new centromeric variants. The ancestral relationship and the polyploidization-diploidization cycles played a fundamental role in the composition of their repetitive fraction. These cycles led Cenchrus americanus, a possible paleopolyploid, to a greater abundance of transposable elements compared to Cenchrus purpureus, a recent allopolyploid.

genomics↗

bioRxiv2022

Development of nuclear microsatellite markers in Yerba mate (Ilex paraguariensis St. Hil., Aquifoliaceae Bartl.) from whole-genome sequence data

Ilex paragariensis St. Hil. (yerba mate) (Aquifoliaceae Bartl.) is a plant species with great economic and cultural importance because its leaves are processed and ground to make infusions like mate or terere. The species is distributed in a continuous area that includes southern Brazil, and part of Paraguay and Argentina. Uruguay represents the southern distribution limit of the species, where small populations can be found as part of riparian forests. Although there are previous reports of molecular markers for this and other species in the genus, the available markers were not informative enough to represent the intra and interpopulation genetic diversity in these marginal populations. In this study, we developed highly informative nuclear polymorphic microsatellite markers to optimize genetic studies in I. paraguariensis. Markers were identified in contigs from the genome sequence of two individuals and then tested for amplification and polymorphism in a diverse panel and at population level. Markers which passed these tests detected levels of heterozygosity similar to those reported for Brazilian populations and great diversity within populations from Uruguay. This set of markers were successfully multiplexed, substantially reducing the costs of the analysis. In combination with previously reported nuclear and plastid markers, they can be used to evaluate the genetic diversity of rear edge populations, identify genotypes for paternity studies and provide relevant information for the conservation and management of germplasm.

plant biology↗

bioRxiv2020

Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs. MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome.

evolutionary biology↗

bioRxiv2019

Nondisjunction and unequal spindle organization accompany the drive of Aegilops speltoides B chromosomes

Supernumerary B chromosomes (Bs), which are often preferentially inherited, deviating from usual Mendelian segregation. This chromosome drive is one of the most important features of Bs. Here we analyzed the drive mechanism of Aegilops speltoides Bs and provide direct insight into its cellular mechanism. Comparative genomics resulted in the identification of the tandem repeat AesTR-183 of Ae. speltoides Bs, which also can be found on the Bs of Ae. mutica and rye, was used to track Bs during microgametogenesis. Nondisjunction of CENH3-positive, tubulin interacting B sister chromatids and an asymmetric spindle during first pollen grain mitosis are likely components of the accumulation process. A quantitative flow cytometric approach revealed, that independent on the number of Bs present in the mother plant Bs accumulate in the generative nuclei with more than 93%. Nine of eleven tested (peri)centromeric repeats were shared by A and B chromosomes. A common origin of the drive process in Poaceae is likely.

genetics↗