Biology subjects

Pedrosa-Harand, A.

Publications and source records attributed to Pedrosa-Harand, A..

11 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

A holocentric pangenome links karyotype evolution to meiotic recombination

Chromosomal fissions, fusions and whole-genome duplications propel genome evolution, yet their impact on meiotic recombination is obscured by the centromere constraint, since in monocentric species most large rearrangements are lethal1-4. Holocentric organisms, which distribute kinetochore activity along the entire chromosome, overcome this barrier and therefore offer a unique window onto the interplay between karyotype change and crossover control2. We assembled chromosome-scale genomes for 20 holocentric Rhynchospora species (including 56 haplotypes), representing all major clades of the genus, featuring satellite-based holocentromeres5,6, and integrated single-gamete crossover maps, high-resolution meiotic synapsis immunocytochemistry and Hi-C chromatin architecture. Breakpoint analysis shows that holocentromeric Tyba satellite arrays6,7 are recurrent hotspots for both chromosome fusions and fissions, contributing to the genuss extraordinary chromosome number variation from 2n = 4 to 36. Crossover landscapes group into two apparent modes: strongly distal-biased versus irregularly distributed, which is correlated with divergent patterns of synapsis elongation. Moreover, crossover number scales with chromosome count and meiotic axis length. In contrast, crossover density per megabase is inversely related to chromosome length and to chromatin-loop size. We propose that chromosome fissions create karyotypes with smaller chromosomes folded into shorter loops, thereby increasing the axial substrate accessible for double-strand break formation and elevating recombination frequency. Together, our results provide a structural link between large-scale structural chromosome evolution and meiotic recombination through coupled changes in chromosome number, size, loop geometry, and synapsis dynamics.

genomics↗

bioRxiv2025

Cytogenetic Insights of C. argentinana Yunk. and C. parodiana Yunk., two species from section Subulatae (Cuscuta L. - Convolvulaceae)

The genus Cuscuta exhibits remarkable cytogenetic diversity, strongly influenced by heterochromatin dynamics. The genus is divided into four subgenera, the subgenus Grammica is almost exclusively found in the Americas, and South America is the first major diversification center. The section Subulatae consists of species primarily found in Argentina. To cytogenetically characterize the Cuscuta species of Subulatae and investigate the chromosomal evolution of the subgenus Grammica, CMA/DAPI banding, FISH with 5S and 35S rDNA, and flow cytometry were performed on C. argentinana and C. parodiana. Both species exhibited 2n = 30 with differences in chromosome size, heterochromatic banding patterns, and genome size. Cuscuta argentinana has smaller chromosomes and genome (1C = 1.49 Gbp) and a higher number of metacentric chromosomes and CMA/DAPI- bands, whereas C. parodiana (1C = 2.79 Gbp) exhibits heterochromatin accumulation and a higher number of submetacentric chromosomes and heterochromatin accumulation. While the number of 5S rDNA sites was the same (six sites), C. parodiana presented one more pair of 35S rDNA sites. The results suggest that genome variation in Cuscuta section Subulatae is associated with heterochromatin amplification. These findings contribute to understanding of Grammica diversification and the role of heterochomatin in the chromosomal evolution of the genus.

plant 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↗

bioRxiv2024

Cytogenetic comparison of Cuscuta psorothamnensis and C. veatchii (Convolvulaceae), two species originated from recurrent hybridization between the same diploid parents

Genus Cuscuta L. (Convolvulaceae) exhibits cases of hybridization and allopolyploidy. Section Denticulatae, subg. Grammica, includes four species: the allopolyploids, C. veatchii and C. psorothamnensis (2n = 60), which originated from two independent reticulation events between the diploids, C. denticulata and C. nevadensis (2n = 30). The allopolyploids are morphologically similar, but are differing in their geographical distribution and host specificity. While cytogenetic data have been reported for C. veatchii, this study aims to provide a comparative analysis with C. psorothamnensis. To characterize the chromosomal complement of C. psorothamnensis and compare it with C. veatchii, we used CMA/DAPI banding, FISH, and GISH. The karyotypes of both species displayed similarity in chromosome number, size, and symmetry, and interphase nucleus organization. Both species exhibited a pair of 5S and 35S rDNA sites adjacent on the same chromosome. The number of 5S rDNA sites in C. psorothamnensis is variable, with some individuals displaying four, five, and six sites. Our results show: 1) the chromosomal pair carrying adjacent 5S and 35S rDNA in C. denticulata is retained in the polyploids; 2) the loss of C. nevadensis rDNA sites occurred in both tetraploids; 3) C. psorothamnensis and C. veatchii are allopolyploids part of a species complex, originated from successive independent hybridization events between C. denticulata and C. nevadensis; and 4) C. psorothamnensis is probably more recent in origin than C. veatchii based on the degree of diploidization. This cytogenetic comparison allows us to understand the processes involved in the emergence of new polyploid species by hybridization. Main ConclusionCuscuta psorothamnensis and C. veatchii form a complex of allopolyploid species originating from independent, successive hybridization events between C. denticulata and C. nevadensis.

plant biology↗

bioRxiv2024

Repeat-based holocentromeres of the woodrush Luzula sylvatica reveal new insights into the evolutionary transition from mono- to holocentricity

Although the centromere is restricted to a single region of the chromosome in most studied eukaryotes, members of the rush family (Juncaceae) harbor either monocentric (Juncus) or holocentric (Luzula) chromosomes. This provides an opportunity to study the evolutionary mechanisms involved in the transition to holocentricity. Here by combining chromosome-scale genome assembly, epigenetic analyses, immuno-FISH, and super-resolution microscopy, we report the occurrence of repeat-based holocentromeres in L. sylvatica. We found an irregular distribution of genes, centromeric units, and most repeats along the chromosomes. We determined the centromere function predominantly associated with two satellite DNA repeats, Lusy1 and Lusy2 of 124- and 174-bp monomer length, respectively, while CENH3 also binds satellite-free gene-poor regions. Comparative repeat analysis revealed that Lusy1 is present in most Luzula species, suggesting a conserved centromere role of this repeat. Synteny between L. sylvatica (n = 6) and J. effusus (n = 21) genomes further evidenced a chromosome number reduction in Luzula derived from multiple chromosome fusions of ancestral J. effusus-like chromosomes. We propose that the transition to holocentricity in Luzula involves: (i) fusion of small chromosomes resembling Juncus-like centromeres; (ii) expansion of atypical centromeric units; and (iii) colonization of satellite DNA for centromere stabilization.

genomics↗

bioRxiv2023

Oligo-barcodes illuminate holocentric karyotype evolution in Rhynchospora (Cyperaceae)

Holocentric karyotypes are assumed to rapidly evolve through chromosome fusions and fissions due to the diffuse nature of their centromeres. Here, we took advantage of the recent availability of a chromosome-scale reference genome for Rhynchospora breviuscula, a model species of this holocentric genus, and developed the first set of oligo-based barcode probes for a holocentric plant. These probes were applied to 13 additional species of the genus, aiming to investigate the evolutionary dynamics driving the karyotype evolution in Rhynchospora. The two sets of probes were composed of 27,392 (green) and 23,968 (magenta) oligonucleotides, and generated 15 distinct FISH signals as a unique barcode pattern for the identification of all five chromosome pairs of the R. breviuscula karyotype. Oligo-FISH comparative analyzes revealed different types of rearrangements, such as fusions, fissions, putative inversions and translocations, as well as genomic duplications among the analyzed species. Two rounds of whole genome duplication (WGD) were demonstrated in R. pubera, but both analyzed accessions differed in the complex chain of events that gave rise to its large, structurally diploidized karyotypes with 2n = 10 or 12. Considering the phylogenetic relationships and divergence time of the species, the specificity and synteny of the probes were maintained up to species with a divergence time of [~]25 My. However, karyotype divergence in more distant species hindered chromosome mapping and the inference of specific events. This barcoding system is a powerful tool to study chromosomal variations and genomic evolution in holocentric chromosomes of Rhynchospora species.

genomics↗

bioRxiv2021

Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition

Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 89-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta. HighlightsCuscuta subgenus Pachystigma contains species with strikingly bimodal karyotypes. The emergence of these karyotypes is linked to the enrichment of varied repetitive sequences in the largest chromosomal pairs.

plant biology↗

bioRxiv2021

Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae

The tribe Phaseoleae (Leguminosae; Papilionoideae) includes several legume crops with assembled genomes. Comparative genomic studies indicate the preservation of large genomic blocks among legumes, however, the chromosome dynamics during Phaseoleae evolution has not been investigated yet. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We defined the GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata genomes. We searched for these GBs in different genome species belonging to the Phaseolinae (P. lunatus) and Glycininae subtribes (Amphicarpaea edgeworthii and Spatholobus suberectus), and in the Medicago truncaluta outgroup. To support our in silico analysis, we used oligo-FISH probes of P. vulgaris chromosomes 2 and 3 to paint the orthologous chromosomes of two non-sequenced Phaseolinae species (Macroptilium atropurpureum and Lablab purpureus). We inferred the APK with n = 11 and 19 GBs (A to S). We hypothesized five chromosome fusions that reduced the ancestral legume karyotype with n = 16 to n = 11 in APK. Furthermore, we identified the main rearrangements within Phaseolinae and observed an extensive centromere repositioning resulting from evolutionary new centromeres (ENC) in the Phaseolus lineage. Additionally, we demonstrated that the A. edgeworthii genome is more reshuffled than the dysploid S. suberectus genome, in which we could reconstruct the main events that lead the chromosome number reduction. The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.

genomics↗

bioRxiv2020

Aiming off the target: studying repetitive DNA using target capture sequencing reads

O_LIWith the advance of high-throughput sequencing (HTS), reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information. As the off-target reads from such sequencing are expected to be similar to genome skims (GS), we assessed the quality of repeat characterization using this data. C_LIO_LIFor this, repeat composition from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. C_LIO_LIAll the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01% in the GS data. Rank correlation between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS was also reliable to develop a cytogenetic probe and solve phylogenetic relationships of Rhynchospora species with high support. C_LIO_LIIn light of our results, TCS data can be effectively used for cyto- and phylogenomic investigations of repetitive DNA. Given the growing availability of HTS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity. C_LI

genomics↗

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↗