Analysis of the small chromosomal Prionium serratum (Cyperid) demonstrates the importance of reliable methods to differentiate between mono- and holocentricity

Báez, Mariana; Kuo, Yi‐Tzu; Dias, Yhanndra; Souza, Thaíssa Boldieri de; Boudichevskaia, Anastassia; Fuchs, Joerg; Schubert, Veit; Vanzela, André Luís Laforga; Pedrosa‐Harand, Andrea

doi:10.1007/s00412-020-00745-6

Cited by 12 publications

(17 citation statements)

References 81 publications

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“…Prionium serratum (L.f.) Drège had a 2C value of 0.70 pg (Tables 1, 2; Fig. 1), which is consistent with 670 Mbp (≈ 0.69 pg) previously recorded for this species, also using FCM with PI as uorescent dye (Baez et al 2020). The ploidy level of P. serratum (2n = 46) and therefore the monoploid genome size (1Cx) are not known, but the chromosomes are comparatively small (MC 0.02 pg) and have a localized centromere (monocentric chromosomes).…”

Section: Characteristics Of the Familiessupporting

confidence: 88%

Genome size variation and whole-genome duplications in the monocot order Poales

Winterfeld,

Tkach,

Röser

2023

Preprint

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Nuclear genome sizes of 54 representative species from 44 genera of the monocot order Poales were investigated by flow cytometry (FCM). Small holoploid genomes with < 2 pg/2C are characteristic of the Poales, only some families have larger 2C values, although this is not consistently the case. The sizes of monoploid genomes as well as mean DNA content per chromosome (MC) show a similar pattern. A comparison of the genome size data with current molecular phylogenetic data suggests that small monoploid genomes (1Cx < 0.4 pg) and small chromosomes (MC ≤ 0.05 pg), as found in some families, are likely the ancestral features of the order Poales. Conspicuous increases in genome size occurred particularly in the Poaceae (grasses) and to a lesser extent in the xyrid clade and the restios. According to previous phylogenomic studies, the Poaceae are characterized by a whole-genome duplication (WGDs) called ρ, which is absent in all other Poales families. However, it is clear from the 1Cx values, that the ρ event is not, or no longer, associated with a significant increase in the minimum 1Cx genome sizes of grasses compared to other Poales families. Future studies need to clarify whether the smallest 1Cx values in the Poaceae are due to a secondary reduction of the nuclear genome after the ρ event and whether the relatively large minimal 1Cx values of the xyrid clade were caused by a further WGD within Poales.

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Section: Characteristics Of the Familiessupporting

confidence: 88%

Genome size variation and whole-genome duplications in the monocot order Poales

Winterfeld,

Tkach,

Röser

2023

Preprint

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“…Immuno-FISH was performed following Baez et al (2020). The best slides obtained from immunostaining, as described above, were selected for FISH using a telomeric probe.…”

Section: Sequential Immunostaining and Fluorescence In Situ Hybridisa...mentioning

confidence: 99%

Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

Castellani

Zhang

Thangavel

et al. 2023

Preprint

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Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics influencing the overall distribution and frequency of crossovers. Here, we studied how recombination is regulated and distributed in the holocentric plant Rhynchospora breviuscula, a species lacking localised centromeres. Combining immunocytochemistry, chromatin analysis and high-throughput single-pollen sequencing, we discovered that crossover frequency is higher at ends related to centred chromosomal regions. Contrasting the diffused distribution of (epi)genetic features and hundreds of repeat-based centromeric units. Remarkably, we found that crossovers were abolished at core centromeric units but not at their vicinity indicating the absence of a centromere effect across repeat-based holocentromeres. We further show that telomere-led pairing and synapsis of homologous chromosomes appear to be the primary force determining the observed U-shaped recombination landscape. While centromere and (epi)genetic properties only affect crossover positioning locally. Our results suggest that the conserved U-shaped crossover distribution of eukaryotes is independent of chromosome compartmentalisation and centromere organisation.

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“…chromosomes were counted in 1,140 species (~20%; Rice et al, 2015) and more closely inspected regarding chromosome structure in roughly 100 species (~1.8%; 78 species listed by Melters et al, 2012 plus some other inspected later). Contrary to the previous report (Zedek et al, 2016), monocentric chromosomes were recently proven by CenH3 and microtubule immunolabeling in mitosis of Prionium serratum from a small related cyperid family Thurniaceae (Baez et al, 2020). Monocentric chromosomes were also suggested in four species of the genus Juncus from the sister family Juncaceae (Guerra et al, 2019), although the authors base their conclusions on DAPI and CMA staining and histone phosphorylation patterns (Guerra et al, 2019), none of which are reliable markers for holo-or monocentricity (Kolodin et al, 2018;Neumann et al, 2020).…”

Section: Discussionmentioning

confidence: 62%

Holocentric Chromosomes Probably Do Not Prevent Centromere Drive in Cyperaceae

et al. 2021

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Centromere drive model describes an evolutionary process initiated by centromeric repeats expansion, which leads to the recruitment of excess kinetochore proteins and consequent preferential segregation of an expanded centromere to the egg during female asymmetric meiosis. In response to these selfish centromeres, the histone protein CenH3, which recruits kinetochore components, adaptively evolves to restore chromosomal parity and counter the detrimental effects of centromere drive. Holocentric chromosomes, whose kinetochores are assembled along entire chromosomes, have been hypothesized to prevent expanded centromeres from acquiring a selective advantage and initiating centromere drive. In such a case, CenH3 would be subjected to less frequent or no adaptive evolution. Using codon substitution models, we analyzed 36 CenH3 sequences from 35 species of the holocentric family Cyperaceae. We found 10 positively selected codons in the CenH3 gene [six codons in the N-terminus and four in the histone fold domain (HFD)] and six branches of its phylogeny along which the positive selection occurred. One of the positively selected codons was found in the centromere targeting domain (CATD) that directly interacts with DNA and its mutations may be important in centromere drive suppression. The frequency of these positive selection events was comparable to the frequency of positive selection in monocentric clades with asymmetric female meiosis. Taken together, these results suggest that preventing centromere drive is not the primary adaptive role of holocentric chromosomes, and their ability to suppress it likely depends on their kinetochore structure in meiosis.

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Analysis of the small chromosomal Prionium serratum (Cyperid) demonstrates the importance of reliable methods to differentiate between mono- and holocentricity

Cited by 12 publications

References 81 publications

Genome size variation and whole-genome duplications in the monocot order Poales

Genome size variation and whole-genome duplications in the monocot order Poales

Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

Holocentric Chromosomes Probably Do Not Prevent Centromere Drive in Cyperaceae

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