Biology subjects

Sader, M. A.

Publications and source records attributed to Sader, M. A..

6 recordsLinked to original sources

bioRxiv2026

Holocentromere diversity in Cyperaceae: contrasting repeat organisation in Mapanioideae and Cyperoideae

Centromeres ensure accurate chromosome segregation and are typically confined to a single, localised region in monocentric chromosomes. In contrast, holocentric chromosomes exhibit kinetochore activity distributed along the chromosome length. Although holocentricity is widespread in Cyperaceae, the composition and organisation of these centromeres, as well as their evolutionary diversification, remain poorly understood. Here, we investigated centromere organisation in representatives of the subfamilies Mapanioideae (Hypolytrum schraderianum Nees) and Cyperoideae (Cladium mariscus (L.) Pohl) by combining genome assemblies, repeatome characterisation (RepeatExplorer), fluorescence in situ hybridisation (FISH), and immunolocalisation. Comparative synteny analyses incorporating the genomes of Rhynchospora breviuscula (n = 5) and Carex littledalei (n = 29) identified conserved blocks, eventually expanding almost whole chromosomes of H. schraderianum (n = 30) and Cl. mariscus (n = 39), despite divergent chromosome numbers and deep evolutionary distances within Cyperaceae. Mobile elements showed very low abundances and were uniformly dispersed, with Ty1/Copia Angela being the most abundant in both species. In Cl. mariscus, holocentromeres showed an extended distribution of centromere- and kinetochore-associated proteins along the chromosomes, largely colocalised with two satellite DNA repeats that form dispersed clusters. In contrast, H. schraderianum also displayed kinetochore signals along chromatids, but the most abundant satellite DNA family was enriched in distal and interstitial chromosomal regions rather than interspersed along the chromatids. Together, these results reveal different genomic architectures underlying holocentric organisation in phylogenetically distinct Cyperaceae lineages, suggesting that holocentromeres in this family have diversified with variation in centromere organisation in regard to its association with repetitive DNA.

evolutionary biology↗

bioRxiv2026

Genomic instability within a sympatric complex of South American garlics (Nothoscordum spp., Amaryllidaceae)

Background and AimsThe evolution of reproductive isolation between previously interbreeding populations is a fundamental driver of plant speciation. Within Amaryllidaceae, Nothoscordum represents an evolutionarily complex genus, characterized by an unusually high incidence of chromosomal rearrangements. During fieldwork, Nothoscordum montevidense and Nothoscordum bonariense were found growing in sympatry, along with individuals exhibiting intermediate morphological traits, suggesting a putative hybrid origin. To test this hypothesis, we employed an integrative approach to characterize the morphologically intermediate specimens and the two sympatric populations. Materials and methodsTo characterize the putative hybrids we have combined morphological, cytogenetic analyses (chromosome counts, CMA/DAPI banding, and FISH) and flow cytometry-based genome size estimation. Phylogenetic relationships and genomic structure were also investigated through Genotyping-by-Sequencing (GBS), complete chloroplast genome assembly, and comparative repetitive DNA analysis. We also performed species distribution modeling and phenological analyses of the putative parental species. Key ResultsMultiple lines of evidence confirm the hybrid origin of the studied plants. Cytogenetic analyses revealed specimens with 2n = 21 (1C {approx} 33 pg = 32.274 Mbp) and 2n = 25 (1C {approx} 37 pg = 36.186 Mbp), accompanied by meiotic irregularities consistent with interspecific hybridization. Chloroplast genome phylogeny identified N. montevidense (2n = 16, 1C {approx} 25 pg) as the maternal lineage, while GBS data confirmed N. bonariense (2n = 26, 1C {approx} 41 pg) as the paternal contributor and revealed evidence of subsequent backcrossing. Comparative analysis of repetitive DNA showed reduced 35S rDNA diversity in the hybrid, indicative of post-hybridization genomic restructuring. Despite the observed genomic complexity, no clear morphological differentiation was detected among hybrid individuals. Phenological analyses and species distribution models demonstrated broad overlap between parental species. ConclusionsOur findings highlight the role of hybridization in shaping genome architecture in cytogenetically labile plant lineages. Furthermore, our results underscore that morphological similarity can mask profound genomic complexity, reinforcing the value of integrative approaches to understand genera characterized by reticulate evolution and genomic instability.

plant biology↗

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

Kinetochore mutations and histone phosphorylation pattern changes preceded holo- and macro-monocentromere evolution

Centromeres are essential for kinetochore assembly and spindle attachment. While chromosomes of most species are monocentric with a single centromere, a minority exhibit holocentricity, with a centromere along the chromatid length. Sporadic emergence of holocentricity suggests multiple independent transitions. To explore this, we compared the centromere and (epi)genome organization of two sister genera with contrasting centromere types: Chamaelirium luteum with large "macro-monocentromeres" and Chionographis japonica with holocentromeres. Both exhibit chromosome-wide histone phosphorylation patterns distinct from typical monocentric species. Kinetochore analysis revealed similar chimeric Borealin in both species, with additional KNL2 loss and NSL1 chimerism in Cha. luteum. The broad-scale synteny between both genomes supports de novo holocentromere formation in Chi. japonica. Despite sharing features with both centromere types, macro-monocentromeres do not represent a direct link between mono- and holocentromeres. We propose a model for the divergent evolution involving kinetochore gene mutations, altered histone phosphorylation patterns, and centromeric satellite DNA amplification.

evolutionary biology↗

bioRxiv2024

Two species and two karyotypes? Cytogenetic differentiation between Passiflora foetida L. and P. vesicaria L. (Passifloraceae)

The genus Passiflora L. (Passifloraceae) is widely distributed, primarily in the Neotropics, and comprises over 500 species divided into four main subgenera. The subgenus Passiflora is the most economically relevant and has a basic chromosome number of x = 9, with P. foetida L. being the sole species in the subgenus having a chromosome number of n = 10. However, P. foetida exhibits substantial morphological variation among its varieties, and recently, two of these varieties were reclassified as Passiflora vesicaria L. and P. vesicaria var. galapagensis. This study aimed to cytogenetically characterise both species by estimating genome sizes using flow cytometry, mapping heterochromatic regions by CMA/DAPI staining, and identifying 5S and 35S ribosomal DNA sites using fluorescent in situ hybridization (FISH). The genome sizes were similar across the three accessions analyzed, varying from 2C = 1.00 {+/-} 0.03 pg for P. vesicaria var. galapagensis to 2C = 1.16 {+/-} 0.01 pg for P. vesicaria, indicating small genomes. All three accessions showed 2n = 20, confirming the count for P. foetida and revealing the chromosome numbers of the two P. vesicaria accessions for the first time. Six CMA+ bands were observed in P. foetida, four in P. vesicaria var. galapagensis, and two in P. vesicaria, all co-localised with the 35S rDNA sites. FISH with 5S and 35S rDNA showed six pericentromeric 35S sites of different intensities in P. foetida and four interstitial 5S sites, with one individual having only two interstitial 5S sites, demonstrating a polymorphism at the intrapopulation level not yet recorded for the genus or the species. Passiflora vesicaria exhibited four 35S sites also pericentromeric, as well as two 5S sites, while P. vesicaria var. galapagensis presented four pericentromeric 35S sites and two 5S sites. Therefore, despite these species having the same chromosome number (n = 10) and similar genome sizes, there are karyotypic variations in the number of CMA+ bands and rDNA sites, allowing their discrimination.

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↗