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BackgroundEukaryotic genomes are packaged by Histone proteins in a structure called chromatin. There are different chromatin types. Euchromatin is typically associated with decondensed, transcriptionally active regions and heterochromatin to more condensed regions of the chromosomes. Methylation of Lysine 9 of Histone H3 (H3K9me) is a conserved biochemical marker of heterochromatin. In many organisms, heterochromatin is usually localized at telomeric as well as pericentromeric regions but can also be found at interstitial chromosomal loci. This distribution may vary in different species depending on their general chromosomal organization. Holocentric species such as Spodoptera frugiperda (Lepidoptera: Noctuidae) possess dispersed centromeres instead of a monocentric one and thus no observable pericentromeric compartment. To identify the localization of heterochromatin in such species we performed ChIP-Seq experiments and analyzed the distribution of the heterochromatin marker H3K9me2 in the Sf9 cell line and whole 4th instar larvae (L4) in relation to RNA-Seq data.ResultsIn both samples we measured an enrichment of H3K9me2 at the (sub) telomeres, rDNA loci, and satellite DNA sequences, which could represent dispersed centromeric regions. We also observed that density of H3K9me2 is positively correlated with transposable elements and protein-coding genes. But contrary to most model organisms, H3K9me2 density is not correlated with transcriptional repression.ConclusionThis is the first genome-wide ChIP-Seq analysis conducted in S. frugiperda for H3K9me2. Compared to model organisms, this mark is found in expected chromosomal compartments such as rDNA and telomeres. However, it is also localized at numerous dispersed regions, instead of the well described large pericentromeric domains, indicating that H3K9me2 might not represent a classical heterochromatin marker in Lepidoptera.

Made available in DSpace on 2022-04-28T19:46:42Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-03-01 Agencia Nacional de Investigación e Innovación American University University of Arizona University of Vermont Junta de Andalucía Comisión Sectorial de Investigación Científica Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Ministerio de Educación y Cultura The subfamily Triatominae (Hemiptera-Reduviidae) includes more than 150 blood-sucking species, potential vectors of the protozoan Trypanosoma cruzi, causative agent of Chagas disease. A distinctive cytogenetic characteristic of this group is the presence of extremely stable chromosome numbers. Unexpectedly, the analyses of the chromosomal location of ribosomal gene clusters and other repetitive sequences place Triatominae as a significantly diverse hemipteran subfamily. Here, we advance the understanding of Triatominae chromosomal evolution through the analysis of the 45S rDNA cluster chromosomal location in 92 Triatominae species. We found the 45S rDNA clusters in one to four loci per haploid genome with different chromosomal patterns: On one or two autosomes, on one, two or three sex chromosomes, on the X chromosome plus one to three autosomes. The movement of 45S rDNA clusters is discussed in an evolutionary context. Our results illustrate that rDNA mobility has been relatively common in the past and in recent evolutionary history of the group. The high frequency of rDNA patterns involving autosomes and sex chromosomes among closely related species could affect genetic recombination and the viability of hybrid populations, which suggests that the mobility of rDNA clusters could be a driver of species diversification. Sección Genética Evolutiva Facultad de Ciencias Universidad de la República Department of Experimental Biology Genetics University of Jaén Department of Biomedicine and Biotechnology University of Alcalá Laboratório de Entomologia em Saúde Pública Departamento de Epidemiologia Faculdade de Saúde Pública Universidade de São Paulo Faculdade de Ciências Farmacêuticas Universidade Estadual Paulista “Júlio de Mesquita Filho” (Unesp) Fundação Oswaldo Cruz Laboratorio de Investigación en Genética Evolutiva – LIGE Universidad Pedagógica y Tecnológica de Colombia Programa de Biología Celular y Molecular ICBM Facultad de Medicina Universidad de Chile Laboratorio de Entomología Aplicada y Parasitología Escuela de Biología Facultad de Farmacia Universidad de San Carlos de Guatemala Department of Biological Sciences Loyola University New Orleans Departamento de Microbiología y Parasitología Facultad de Medicina Universidad Nacional Autónoma de México Faculdade de Ciências Farmacêuticas Universidade Estadual Paulista “Júlio de Mesquita Filho” (Unesp) Comisión Sectorial de Investigación Científica: 160 FAPESP: 17/05015-7 FAPESP: 19/02145-2 FAPESP: 307 398/2018-8 Ministerio de Educación y Cultura: II/FVF/2019/054

Ultraviolet-B radiation (UV-B, wavelength 280-315 nm) is a clastogen (chromosome-breaking factor) that has accompanied life on Earth throughout its entire history (Lomax, 2012). Plants need to cope with UV-B almost permanently, as they are sessile organisms whose survival is directly dependent on solar radiation. The susceptibility to clastogens may depend on the type of chromosomes (Zedek and Bures, 2018).

Previous studies on grass species suggested that the total centromere size (sum of all centromere sizes in a cell) may be determined by the genome size, possibly because stable scaling is important for proper cell division. However, it is unclear whether this relationship is universal. Here we analyze the total centromere size using the CenH3-immunofluorescence area as a proxy in 130 taxa including plants, animals, fungi, and protists. We verified the reliability of our methodological approach by comparing our measurements with available ChIP-seq-based measurements of the size of CenH3-binding domains. Data based on these two independent methods showed the same positive relationship between the total centromere size and genome size. Our results demonstrate that the genome size is a strong predictor (R-squared = 0.964) of the total centromere size universally across Eukaryotes. We also show that this relationship is independent of phylogenetic relatedness and centromere type (monocentric, metapolycentric, and holocentric), implying a common mechanism maintaining stable total centromere size in Eukaryotes.

The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.

Centromeres are essential for chromosome movement. In independent taxa, species with holocentric chromosomes exist. In contrast to monocentric species, where no obvious dispersion of centromeres occurs during interphase, the organization of holocentromeres differs between condensed and decondensed chromosomes. During interphase, centromeres are dispersed into a large number of CENH3-positive nucleosome clusters in a number of holocentric species. With the onset of chromosome condensation, the centromeric nucleosomes join and form line-like holocentromeres. Using polymer simulations, we propose a mechanism, relying on the interaction between centromeric nucleosomes and Structural Maintenance of Chromosomes (SMC) proteins. All simulations represented a ~20 Mbp-long chromosome, corresponding to ~100,000 nucleosomes. Different sets of molecular dynamic simulations were evaluated by testing four parameters: 1) the concentration of Loop Extruders (LEs) corresponding to SMCs; 2) the distribution and number of centromeric nucleosomes; 3) the effect of centromeric nucleosomes on interacting LEs; and 4) the assembly of kinetochores bound to centromeric nucleosomes. We observed the formation of a line-like holocentromere, due to the aggregation of the centromeric nucleosomes when the chromosome was compacted into loops. A groove-like holocentromere structure formed after a kinetochore complex was simulated along the centromeric line. Similar mechanisms may also organize a monocentric chromosome constriction, and its regulation may cause different centromere types during evolution.

Graphical abstract, Repeat-rich regions of higher plant genomes are usually associated with constitutive heterochromatin, a specific type of chromatin that forms tightly packed nuclear chromocenters and chromosome bands. There is a large body of cytogenetic evidence that these chromosome regions are often composed of tandemly organized satellite DNA. However, comparatively little is known about the sequence arrangement within heterochromatic regions, which are difficult to assemble due to their repeated nature. Here, we explore long-range sequence organization of heterochromatin regions containing the major satellite repeat CUS-TR24 in the holocentric plant Cuscuta europaea. Using a combination of ultra-long read sequencing with assembly-free sequence analysis, we reveal the complex structure of these loci, which are composed of short arrays of CUS-TR24 interrupted frequently by emerging simple sequence repeats and targeted insertions of a specific lineage of LINE retrotransposons. These data suggest that the organization of satellite repeats constituting heterochromatic chromosome bands can be more complex than previously envisioned, and demonstrate that heterochromatin organization can be efficiently investigated without the need for genome assembly.

In this paper, we present new cytogenetic data for three species of the family Pentatomidae: Dichelops melacanthus (Dallas, 1851), Loxa viridis (Palisot de Beauvois, 1805), and Edessa collaris (Dallas, 1851). All studied species presented holocentric chromosomes and inverted meiosis for the sex chromosomes. D. melacanthus has 2n = 12 (10A + XY); L. viridis showed 2n = 14 (12A + XY); and E. collaris showed 2n = 14 (12A + XY). C-banding was performed for the first time in these species and revealed terminal and interstitial heterochromatic regions on the autosomes; DAPI/CMA3 staining showed different fluorescent patterns. In all species, fluorescence in situ hybridization (FISH) with 18S rDNA probe identified signals on one autosomal bivalent, this being the first report of FISH application in the species D. melacanthus and L. viridis. The results obtained add to those already existing in the literature, enabling a better understanding of the meiotic behavior of these insects.

SummaryThe parasitic genus Cuscuta (Convolvulaceae) is exceptional among plants with respect to centromere organization, including both monocentric and holocentric chromosomes, and substantial variation in genome size and chromosome number. We investigated 12 species representing the diversity of the genus in a phylogenetic context to reveal the molecular and evolutionary processes leading to diversification of their genomes.We measured genome sizes and investigated karyotypes and centromere organization using molecular cytogenetic techniques. We also performed low-pass whole genome sequencing and comparative analysis of repetitive DNA composition.A remarkable 102-fold variation in genome sizes (342–34,734 Mbp/1C) was detected for monocentric Cuscuta species, while genomes of holocentric species were of moderate sizes (533–1,545 Mbp/1C). The genome size variation was primarily driven by the differential accumulation of repetitive sequences. The transition to holocentric chromosomes in the subgenus Cuscuta was associated with loss of histone H2A phosphorylation and elimination of centromeric retrotransposons. In addition, the basic chromosome number (x) decreased from 15 to 7, presumably due to chromosome fusions.We demonstrated that the transition to holocentricity in Cuscuta was accompanied by significant changes in epigenetic marks, chromosome number and the repetitive DNA sequence composition.

Made available in DSpace on 2021-06-25T10:33:44Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-12-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Satellite DNAs (satDNA) are fast-evolving repetitive sequences organized in large tandem arrays, with characteristic enrichment in heterochromatin. Knowledge about evolutionary dynamics of this genome fraction is mostly restricted to its characterization in species with monocentric chromosomes, i.e., localized centromeres. In holocentric species, with non-localized centromeres, satDNAs have been largely ignored. Here we advance the understanding of satDNA evolution among holocentric species by characterization of the most abundant satDNAs in the hemipteran Holhymenia histrio, integrating genomic and chromosomal analyses. High plasticity at chromosomal and molecular levels was noticed for 34 satDNAs populating H. histrio genome. One satDNA family in particular (HhiSat01-184) was highly amplified on multiple chromosomes and also highly polymorphic. Our data support the emergence of a new satDNA family from this abundant satDNA, confined to a single chromosome. Moreover, we present new information about composition of a peculiar chromosome in Coreidae, the m-chromosome, and of the X chromosome. Overall, the molecular and chromosomal patterns for satDNAs in the holocentric species H. histrio seem to be similar to those observed in monocentric species. Departamento de Biologia Geral e Aplicada Instituto de Biociências/IB UNESP - Universidade Estadual Paulista, Rio Claro Departamento de Biologia Geral e Aplicada Instituto de Biociências/IB UNESP - Universidade Estadual Paulista, Rio Claro FAPESP: 2018/21772-5 FAPESP: 2019/19069-7

Previous studies suggested that holocentric chromosomes may confer a selective advantage under high ionizing or UV-B radiation due to their tolerance of fragmentation, and that the first plant and animal colonizers of land in the Palaeozoic were or may have been holocentric. Holocentric chromosomes could have, therefore, aided terrestrialization of Earth’s biota half a billion years ago, because leaving water meant facing a sharp increase of UV-B. Because we cannot go back in time, the hypothesis needs to be tested with present-day species using an indicator of UV-B stress. We took advantage of the fact that UV-B intensity increases with elevation and tested whether holocentric plants (six species of Cyperaceae and Juncaceae) are less stressed with increasing elevation than monocentric plants (six species of Poaceae). Phylogenetically corrected regression showed that the proxy for UV-B stress (endopolyploidy index from 671 samples measured by flow cytometry) increased with elevation in holocentric and monocentric species, but the increase was more rapid in monocentric species. Although half a billion year elapsed since terrestrialization, holocentric Cyperaceae and Juncaceae still appear less stressed by UV-B than monocentric Poaceae, despite the other counter UV-B adaptations they both have evolved (graminoid morphology, silica bodies).

The Polyommatus butterflies have holocentric chromosomes, which are characterized by kinetic activity distributed along the entire chromosome length, and the highest range of haploid chromosome numbers (n) known within a single eukaryotic genus (from n = 10 to n = 226). Previous analyses have shown that these numbers most likely evolved gradually from an ancestral karyotype, in accordance with the Brownian motion model of chromosome change accumulation. Here we studied chromosome sets within a monophyletic group of previously non-karyotyped Polyommatus species. We demonstrate that these species have a limited interspecific chromosome number variation from n = 16 to n = 25, which is consistent with the Brownian motion model prediction. We also found intra- and interpopulation variation in the chromosome numbers. These findings support the model of karyotype evolution through the gradual accumulation of neutral or weakly underdominant rearrangements that can persist in the heterozygous state within a population. For Polyommatus poseidonides we report the phenomenon of flexible meiosis in which the chromosome multivalents are able to undergo either conventional or inverted meiosis within the same individual. We hypothesise that the ability to invert the order of the meiotic events may be adaptive and can facilitate proper chromosome segregation in chromosomal heterozygotes, thus promoting rapid karyotype evolution.

Background and Aims Ultraviolet-B radiation (UV-B) radiation damages the DNA, cells and photosynthetic apparatus of plants. Plants commonly prevent this damage by synthetizing UV-B-protective compounds. Recent laboratory experiments in Arabidopsis and cucumber have indicated that plants can also respond to UV-B stress with endopolyploidy. Here we test the generality of this response in natural plant populations, considering their monocentric or holocentric chromosomal structure. Methods We measured the endopolyploidy index (flow cytometry) and the concentration of UV-B-protective compounds in leaves of 12 herbaceous species (1007 individuals) from forest interiors and neighbouring clearings where they were exposed to increased UV-B radiation (103 forest + clearing populations). We then analysed the data using phylogenetic mixed models. Key Results The concentration of UV-B protectives increased with UV-B doses estimated from hemispheric photographs of the sky above sample collection sites, but the increase was more rapid in species with monocentric chromosomes. Endopolyploidy index increased with UV-B doses and with concentrations of UV-B-absorbing compounds only in species with monocentric chromosomes, while holocentric species responded negligibly. Conclusions Endopolyploidy seems to be a common response to increased UV-B in monocentric plants. Low sensitivity to UV-B in holocentric species might relate to their success in high-UV-stressed habitats and corroborates the hypothesized role of holocentric chromosomes in plant terrestrialization.

Centromere protein A (CENP-A) is a histone H3 variant that defines centromeric chromatin and is essential for centromere function. In most eukaryotes, CENP-A-containing chromatin is epigenetically maintained, and centromere identity is inherited from one cell cycle to the next. In the germ line of the holocentric nematode Caenorhabditis elegans, this inheritance cycle is disrupted. CENP-A is removed at the mitosis-to-meiosis transition and is reestablished on chromatin during diplotene of meiosis I. Here, we show that the N-terminal tail of CENP-A is required for the de novo establishment of centromeres, but then its presence becomes dispensable for centromere maintenance during development. Worms homozygous for a CENP-A tail deletion maintain functional centromeres during development but give rise to inviable offspring because they fail to reestablish centromeres in the maternal germ line. We identify the N-terminal tail of CENP-A as a critical domain for the interaction with the conserved kinetochore protein KNL-2 and argue that this interaction plays an important role in setting centromere identity in the germ line. We conclude that centromere establishment and maintenance are functionally distinct in C. elegans., This study of the nematode Caenorhabditis elegans shows that centromere identity is set in the maternal germ line and passed on to the progeny via an epigenetic mechanism that requires the N-terminal tail of the centromeric histone H3 variant CENP-A.

The purpose of this article is to review the genetic basis of mulberry silkworm to understand the mystery of silk production and the silkworm’s role as a model organism. Data regarding mulberry silkworm’s genetic diversity, genetic bases of silk production, gene mapping and chromosomal properties was reviewed. Findings illustrated that genetic variability exists among mulberry silkworms of different geographical regions. Hence, it acts as an indicator of the genetic bases of silk production since it is higher in males, although sex is primarily determined by females. Studies have revealed that chromosomes in mulberry silkworm are holocentric and gene mapping provides an insight into the accurate location of silk genes on chromosomes. It is concluded that the genetic study of silkworm is useful due to its commercial and economic significance and it is the crucial need of sericulture industry to enhance its output by collecting information about superior silkworm breeds. Hence, further research should be carried out to explore the hidden facts about mulberry silkworm.

Differently from the common monocentric organization of eukaryotic chromosomes, the so-called holocentric chromosomes present many centromeric regions along their length. This chromosomal organization can be found in animal and plant lineages, whose distribution suggests that it has evolved independently several times. Holocentric chromosomes present an advantage: even broken chromosome parts can be correctly segregated upon cell division. However, the evolution of holocentricity brought about consequences to nuclear processes and several adaptations are necessary to cope with this new organization. Centromeres of monocentric chromosomes are involved in a two-step cohesion release during meiosis. To deal with that holocentric lineages developed different adaptations, like the chromosome remodeling strategy inCaenorhabditis elegansor the inverted meiosis in plants. Furthermore, the frequency of recombination at or around centromeres is normally very low and the presence of centromeric regions throughout the entire length of the chromosomes could potentially pose a problem for recombination in holocentric organisms. However, meiotic recombination happens, with exceptions, in those lineages in spite of their holocentric organization suggesting that the role of centromere as recombination suppressor might be altered in these lineages. Most of the available information about adaptations to meiosis in holocentric organisms is derived from the animal modelC. elegans. As holocentricity evolved independently in different lineages, adaptations observed inC. elegansprobably do not apply to other lineages and very limited research is available for holocentric plants. Currently, we still lack a holocentric model for plants, but good candidates may be found among Cyperaceae, a large angiosperm family. Besides holocentricity, chiasmatic and achiasmatic inverted meiosis are found in the family. Here, we introduce the main concepts of meiotic constraints and adaptations with special focus in meiosis progression and recombination in holocentric plants. Finally, we present the main challenges and perspectives for future research in the field of chromosome biology and meiosis in holocentric plants.

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.

Centromere protein A (CENP-A) is a histone H3 variant that defines centromeric chromatin and is essential for centromere function. In most eukaryotes CENP-A-containing chromatin is epigenetically maintained, and centromere identity is inherited from one cell cycle to the next. In the germ line of the holocentric nematodeCaenorhabditis elegans, this inheritance cycle is disrupted. CENP-A is removed at the mitosis-to-meiosis transition and is establishedde novoon chromatin during diplotene of meiosis I. Here we show that the N-terminal tail of CENP-A is required for thede novoestablishment of centromeres, but dispensable for centromere maintenance during embryogenesis. Worms homozygous for a CENP-A tail deletion maintain a functional centromere during development, but give rise to inviable offspring because they fail to re-establish centromeres in the maternal germ line. We identify the N-terminal tail of CENP-A as a critical domain for the interaction with the conserved kinetochore protein KNL-2, and argue that this interaction plays an important role in setting centromere identity in the germ line. We conclude that centromere establishment and maintenance are functionally distinct inC. elegans.

Despite the fundamental role of centromeres two different types are observed across plants and animals. Monocentric chromosomes possess a single region that function as the centromere while in holocentric chromosomes centromere activity is spread across the entire chromosome. Proper segregation may fail in species with monocentric chromosomes after a fusion or fission, which may lead to chromosomes with no centromere or multiple centromeres. In contrast, species with holocentric chromosomes should still be able to safely segregate chromosomes after fusion or fission. This along with the observation of high chromosome number in some holocentric clades has led to the hypothesis that holocentricity leads to higher rates of chromosome number evolution. To test for differences in rates of chromosome number evolution between these systems, we analyzed data from 4,393 species of insects in a phylogenetic framework. We found that insect orders exhibit striking differences in rates of fissions, fusions, and polyploidy. However, across all insects we found no evidence that holocentric clades have higher rates of fissions, fusions, or polyploidy than monocentric clades. Our results suggest that holocentricity alone does not lead to higher rates of chromosome number changes. Instead, we suggest that other co-evolving traits must explain striking differences between clades., Author summary One of the most basic features of the genome is its division into chromosomes. When we look across clades, we find a striking pattern where almost all species in some groups exhibit the same number of chromosomes, while in other groups, there is great variation in chromosome number even between closely related species. One possible explanation for these differences is the type of centromeres that a clade possesses. Monocentric chromosomes must have a single region that functions as the centromere, while in holocentric chromosomes, centromere activity is present across the entire chromosome. For this reason, it has been hypothesized that holocentric species should tolerate structural changes in chromosomes (fusions, fission, etc.) better than monocentric species. To test this hypothesis, we estimated the rate of fusion, fission, and polyploidy using data from 4,393 species of insects spanning 22 orders. We found that insect orders exhibit striking differences in rates of chromosome evolution. However, across all insects, we found no evidence that holocentric orders have higher rates of fissions, fusions, or polyploidy than monocentric orders. Our results suggest that holocentricity alone does not lead to higher rates of chromosome number changes.

Heterozygotes for major chromosomal rearrangements such as fusions and fissions are expected to display a high level of sterility due to problems during meiosis. However, some species, especially plants and animals with holocentric chromosomes, are known to tolerate chromosomal heterozygosity even for multiple rearrangements. Here, we studied male meiotic chromosome behavior in four hybrid generations (F1–F4) between two chromosomal races of the Wood White butterfly Leptidea sinapis differentiated by at least 24 chromosomal fusions/fissions. Previous work showed that these hybrids were fertile, although their fertility was reduced as compared to crosses within chromosomal races. We demonstrate that (i) F1 hybrids are highly heterozygous with nearly all chromosomes participating in the formation of trivalents at the first meiotic division, and (ii) that from F1 to F4 the number of trivalents decreases and the number of bivalents increases. We argue that the observed process of chromosome sorting would, if continued, result in a new homozygous chromosomal race, i.e., in a new karyotype with intermediate chromosome number and, possibly, in a new incipient homoploid hybrid species. We also discuss the segregational model of karyotype evolution and the chromosomal model of homoploid hybrid speciation., Support for this research was provided by the Russian Science Foundation No. 19-14-00202 to VL, by the Academy of Finland to VD (decision no. 328895), by the Royal Swedish Academy of Sciences to MF, and by the Spanish AEI/FEDER, UE (CGL2016-76322-P and PID2019-107078GB-I00) to RV.

Eukaryotic chromosomes have phylogenetic persistence. In many taxa, the number of chromosomes is related to the number of centromeres. However, in some groups, such as rhabditid nematodes, centromeric function is distributed across multiple sites on each chromosome. These holocentric chromosomes might, a priori, be expected to be permissive of large-scale chromosomal rearrangement, as chromosomal fragments could still partition correctly and fusions would not generate lethal conflict between multiple centromeres. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematode Oscheius tipulae generated from nanopore long reads. The 60 Mb O. tipulae genome is resolved into six chromosomal molecules. We find evidence of specific chromatin diminution at all telomeres. Comparing this chromosomal O. tipulae assembly with chromosomal assemblies of diverse rhabditid nematodes we identify seven ancestral chromosomal elements (Nigon elements), and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex-chromosome associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.

Cyperaceae is a family of Monocotyledons comprised of species with holocentric chromosomes that are associated with intense dysploidy and polyploidy events. Within this family the genus Rhynchospora has recently become the focus of several studies that characterize the organization of the holocentric karyotype and genome structures. To broaden our understanding of genome evolution in this genus, representatives of Rhynchospora were studied to contrast chromosome features, C-CMA/DAPI band distribution and genome sizes. Here, we carried out a comparative analysis for 35 taxa of Rhynchospora, and generated new genome size estimates for 20 taxa. The DNA 2C-values varied up to 22-fold, from 2C = 0.51 pg to 11.32 pg, and chromosome numbers ranged from 2n = 4 to 61. At least 37% of our sampling exhibited 2n different from the basic number x = 5, and chromosome rearrangements were also observed. A large variation in C-CMA/DAPI band accumulation and distribution was observed as well. We show that genome variation in Rhynchospora is much larger than previously reported. Phylogenetic analysis showed that most taxa were grouped in clades corresponding to previously described taxonomic sections. Basic chromosome numbers are the same within every section, however, changes appeared in all the clades. Ancestral chromosome number reconstruction revealed n = 5 as the most likely ancestral complements, but n = 10 appears as a new possibility. Chromosome evolution models point to polyploidy as the major driver of chromosome evolution in Rhynchospora, followed by dysploidy. A negative correlation between chromosome size and diploid number open the discussion for holokinetic drive-based genome evolution. This study explores relationships between karyotype differentiation and genome size variation in Rhynchospora, and contrasts it against the phylogeny of this holocentric group.

Holocentric chromosomes possess multiple kinetochores along their length rather than the single centromere typical of other chromosomes [1]. They have been described for the first time in cytogenetic experiments dating from 1935 and, since this first observation, the term holocentric chromosome has referred to chromosomes that: i. lack the primary constriction corresponding to centromere observed in monocentric chromosomes [2]; ii. possess multiple kinetochores dispersed along the chromosomal axis so that microtubules bind to chromosomes along their entire length and move broadside to the pole from the metaphase plate [3]. These chromosomes are also termed holokinetic, because, during cell division, chromatids move apart in parallel and do not form the classical V-shaped figures typical of monocentric chromosomes [4–6]. Holocentric chromosomes evolved several times during both animal and plant evolution and are currently reported in about eight hundred diverse species, including plants, insects, arachnids and nematodes [7,8]. As a consequence of their diffuse kinetochores, holocentric chromosomes may stabilize chromosomal fragments favouring karyotype rearrangements [9,10]. However, holocentric chromosome may also present limitations to crossing over causing a restriction of the number of chiasma in bivalents [11] and may cause a restructuring of meiotic divisions resulting in an inverted meiosis [12].

Brandt et al. establish mechanisms that target Polo-like kinase during meiotic prophase in C. elegans. CDK-1 phosphorylates a synaptonemal complex component, SYP-1, to generate docking sites for PLK-2, whose association is prevented until crossover formation to ensure homologue pairing, synapsis, and chromosome remodeling., Polo-like kinases (PLKs) play widely conserved roles in orchestrating meiotic chromosome dynamics. However, how PLKs are targeted to distinct subcellular localizations during meiotic progression remains poorly understood. Here, we demonstrate that the cyclin-dependent kinase CDK-1 primes the recruitment of PLK-2 to the synaptonemal complex (SC) through phosphorylation of SYP-1 in C. elegans. SYP-1 phosphorylation by CDK-1 occurs just before meiotic onset. However, PLK-2 docking to the SC is prevented by the nucleoplasmic HAL-2/3 complex until crossover designation, which constrains PLK-2 to special chromosomal regions known as pairing centers to ensure proper homologue pairing and synapsis. PLK-2 is targeted to crossover sites primed by CDK-1 and spreads along the SC by reinforcing SYP-1 phosphorylation on one side of each crossover only when threshold levels of crossovers are generated. Thus, the integration of chromosome-autonomous signaling and a nucleus-wide crossover-counting mechanism partitions holocentric chromosomes relative to the crossover site, which ultimately defines the pattern of chromosome segregation during meiosis I.

Centromeres are essential for proper chromosome segregation to the daughter cells during mitosis and meiosis. Chromosomes of most eukaryotes studied so far have regional centromeres that form primary constrictions on metaphase chromosomes. These monocentric chromosomes vary from point centromeres to so-called “meta-polycentromeres”, with multiple centromere domains in an extended primary constriction, as identified in Pisum and Lathyrus species. However, in various animal and plant lineages centromeres are distributed along almost the entire chromosome length. Therefore, they are called holocentromeres. In holocentric plants, centromere-specific proteins, at which spindle fibers usually attach, are arranged contiguously (line-like), in clusters along the chromosomes or in bands. Here, we summarize findings of ultrastructural investigations using immunolabeling with centromere-specific antibodies and super-resolution microscopy to demonstrate the structural diversity of plant centromeres. A classification of the different centromere types has been suggested based on the distribution of spindle attachment sites. Based on these findings we discuss the possible evolution and advantages of holocentricity, and potential strategies to segregate holocentric chromosomes correctly.

Polyploidy and hybridization are key events in plant evolution. Due to these events, complexes of species can be formed. Dysploidy, a frequent chromosome change in holocentric organisms, may add some difficulties to species delimitation, especially in Cyperaceae. The Eleocharis montana complex is known for its members with overlapping morpho-anatomical features and unclear circumscription. To understand its biological history, several tools were used to investigate different American populations, including morpho-anatomical analysis, genome size estimates, cytogenomic analysis, molecular marker characterization, and genomic in situ hybridization (GISH). Despite overlapping morphological features, it was possible to separate two groups, the first containing E. parodii and E. subarticulata, presenting diploid and dysploid karyotypes, respectively, and small DNA C-values. The second contained E. elegans, E. contracta, and E. montana, with large genomes created by polyploidy. All analyses suggest that E. montana with 2n = 40 is a cytotype of E. contracta with 2n = 20, and both evolved from a natural hybridization involving E. parodii (2n = 10) and a second progenitor that is yet unknown. Furthermore, the GISH results indicated that E. parodii may be an ancestor of E. elegans. All species occur in the probable center of diversification in Austral South America, where the hybridization zone is identified. Fieldwork and information obtained from herbaria indicate that diploid and dysploid species (E. subarticulata and E. parodii) do not occur beyond the center of diversification. However, E. elegans and specially E. montana occur more widely, occupying different flooded environments and landscapes.

Centromeres are chromosomal domains essential for kinetochore assembly and correct chromosome segregation. Inconsistent in their underlying DNA sequences, centromeres are defined epigenetically by the presence of the centromere-specific histone H3 variant CenH3. Most of the analyzed eukaryotes have monocentric chromosomes in which CenH3 proteins deposit into a single, primary constriction visible at metaphase chromosomes. Contrary to monocentrics, evolutionary sporadic holocentric chromosomes lack a primary constriction and have kinetochore activity distributed along the entire chromosome length. In this work, we identified cCENH3 protein, the centromeric H3 histone of the coleopteran model beetle Tribolium castaneum. By ChIP-seq analysis we disclosed that cCENH3 chromatin assembles upon a repertoire of repetitive DNAs. cCENH3 in situ mapping revealed unusually elongated T. castaneum centromeres that comprise approximately 40% of the chromosome length. Being the longest insect regional centromeres evidenced so far, T. castaneum centromeres are characterized by metapolycentric structure composed of several individual cCENH3-containing domains. We suggest that the model beetle T. castaneum with its metapolycentromeres could represent an excellent model for further studies of non-canonical centromeres in insects., Author summary Centromeres are specialized chromosome regions that mark a chromosomal “attaching site” from which the microtubules of the mitotic spindle pull the sister chromatids apart, ensuring accurate segregation of genetic material during cell division. Eukaryotic species studied to date mostly possess monocentric chromosomes with a functional centromere sited at a single locus, but there are also species with holocentric (polycentric) chromosomes whose centromeres stretch throughout the entire length of the chromosome. By investigating centromere-specific variant of the histone protein H3 and its associated centromeric DNA in the model beetle Tribolium castaneum, we discovered that T. castaneum centromeres comprise several functional domains merged into one remarkably extended region classified as a metapolycentromere. T. castaneum metapolycentromeres occupy approximately 40% of chromosome length, and emerge as the longest centromeres documented in insects to date. We believe that T. castaneum, as the representative species of the most numerous eukaryotic order Coleoptera could be a valuable model for future studies addressing atypical centromere structures.

Canonical meiosis is characterized by two sequential rounds of nuclear divisions following one round of DNA replication-reductional segregation of homologous chromosomes during the first division and equational segregation of sister chromatids during the second division. Meiosis in an inverted order of two nuclear divisions-inverted meiosis has been observed in several species with holocentromeres as an adaptive strategy to overcome the obstacle in executing a canonical meiosis due to the holocentric chromosome structure. Recent findings of co-existence of inverted and canonical meiosis in two monocentric organisms, human and fission yeast, suggested that inverted meiosis could be common and also lead to the puzzle regarding the mechanistic feasibility for executing two meiosis programs simultaneously. Here, we discuss apparent conflicts for concurrent canonical meiosis and inverted meiosis. Furthermore, we attempt to provide a working model that may be compatible for both forms of meiosis.

Holocentric chromosomes have evolved in various plant and animal taxa, which suggests they may confer a selective advantage in certain conditions, yet their adaptive potential has scarcely been studied. One of the reasons may reside in our insufficient knowledge of the phylogenetic distribution of holocentric chromosomes across eukaryotic phylogeny. In the present study, we focused on Droseraceae, a carnivorous plant family with an unknown chromosomal structure in monotypic genera Dionaea and Aldrovanda, and a closely related monotypic family Drosophyllaceae. We used flow cytometry to detect holocentric chromosomes by measuring changes in the ratio of the number of G2 nuclei to the number of G1 nuclei in response to gamma irradiation and determined chromosomal structures in Aldrovanda vesiculosa, Dionaea muscipula, Drosera tokaiensis, and Drosera ultramafica from Droseraceae and Drosophyllum lusitanicum from Drosophyllaceae. We confirmed monocentric chromosomes in D. lusitanicum and detected holocentric chromosomes in all four Droseraceae. Our novel finding of holocentric chromosomes in monotypic genera Aldrovanda and Dionaea suggests that all Droseraceae may be holocentric, but to confirm that further research is needed due to previously reported conflicting results in Drosera rotundifolia.

Background and Aims Long terminal repeat-retrotransposons (LTR-RTs) comprise a large portion of plant genomes, with massive repeat blocks distributed across the chromosomes. Eleocharis species have holocentric chromosomes, and show a positive correlation between chromosome numbers and the amount of nuclear DNA. To evaluate the role of LTR-RTs in karyotype diversity in members of Eleocharis (subgenus Eleocharis), the occurrence and location of different members of the Copia and Gypsy superfamilies were compared, covering interspecific variations in ploidy levels (considering chromosome numbers), DNA C-values and chromosomal arrangements. Methods The DNA C-value was estimated by flow cytometry. Genomes of Eleocharis elegans and E. geniculata were partially sequenced using Illumina MiSeq assemblies, which were a source for searching for conserved proteins of LTR-RTs. POL domains were used for recognition, comparing families and for probe production, considering different families of Copia and Gypsy superfamilies. Probes were obtained by PCR and used in fluorescence in situ hybridization (FISH) against chromosomes of seven Eleocharis species. Key Results A positive correlation between ploidy levels and the amount of nuclear DNA was observed, but with significant variations between samples with the same ploidy levels, associated with repetitive DNA fractions. LTR-RTs were abundant in E. elegans and E. geniculata genomes, with a predominance of Copia Sirevirus and Gypsy Athila/Tat clades. FISH using LTR-RT probes exhibited scattered and clustered signals, but with differences in the chromosomal locations of Copia and Gypsy. The diversity in LTR-RT locations suggests that there is no typical chromosomal distribution pattern for retrotransposons in holocentric chromosomes, except the CRM family with signals distributed along chromatids. Conclusions These data indicate independent fates for each LTR-RT family, including accumulation between and within chromosomes and genomes. Differential activity and small changes in LTR-RTs suggest a secondary role in nuclear DNA variation, when compared with ploidy changes.

Meiotic drive, the class of meiotic mechanisms that drive unequal segregation of alleles among gametes, may be an important force in karyotype evolution. Its role in holocentric organisms, whose chromosomes lack localized centromeres, is poorly understood. We crossed two individuals of Carex scoparia (Cyperaceae) with different chromosome numbers (2n = 33II = 66 × 2n = 32II = 64) to obtain F1 individuals, which we then self-pollinated to obtain second-generation (F2) crosses. RAD-seq was performed for 191 individuals (including the parents, five F1 individuals and 184 F2 individuals). Our F2 linkage map based on stringent editing of the RAD-seq data set yielded 32 linkage groups. In the final map, 865 loci were located on a linkage map of 3966.99 cM (linkage groups ranged from 24.39 to 193.31 cM in length and contained 5-51 loci each). Three linkage groups exhibit more loci under segregation distortion than expected by chance; within linkage groups, loci exhibiting segregation distortion are clustered. This finding implicates meiotic drive in the segregation of chromosome variants, suggesting that selection of chromosome variants in meiosis may contribute to the establishment and fixation of chromosome variants in Carex, which is renowned for high chromosomal and species diversity. This is an important finding as previous studies demonstrate that chromosome divergence may play a key role in differentiation and speciation in Carex.

Made available in DSpace on 2018-11-26T17:44:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Spittlebugs, which belong to the family Cercopidae (Auchenorrhyncha, Hemiptera), form a large group of xylemfeeding insects that are best known for causing damage to plantations and pasture grasses. The holocentric chromosomes of these insects remain poorly studied in regards to the organization of different classes of repetitive DNA. To improve chromosomal maps based on repetitive DNAs and to better understand the chromosomal organization and evolutionary dynamics of multigene families in spittlebugs, we physically mapped the U1 snRNA gene with fluorescence in situ hybridization ( FISH) in 10 species of Cercopidae belonging to three different genera. All the U1 snDNA clusters were autosomal and located in interstitial position. In seven species, they were restricted to one autosome per haploid genome, while three species of the genus Mahanarva showed two clusters in two different autosomes. Although it was not possible to precisely define the ancestral location of this gene, it was possible to observe the presence of at least one cluster located in a small bivalent in all karyotypes. The karyotype stability observed in Cercopidae is also observed in respect to the distribution of U1 snDNA. Our data are discussed in light of possible mechanisms for U1 snDNA conservation and compared with the available data from other species. Univ Estadual Paulista, Inst Biociencias, Dept Biol, Rio Claro, SP, Brazil Univ Fed Santa Maria, Dept Ecol & Evolucao, Santa Maria, RS, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Biol, Rio Claro, SP, Brazil FAPESP: 2014/11763-8 FAPESP: 2014/06226-3 CNPq: 304758/2014-0

Chromosomes that have undergone crossing over in meiotic prophase must maintain sister chromatid cohesion somewhere along their length between the first and second meiotic divisions. Although many eukaryotes use the centromere as a site to maintain cohesion, the holocentric organism Caenorhabditis elegans instead creates two chromosome domains of unequal length termed the short arm and long arm, which become the first and second site of cohesion loss at meiosis I and II. The mechanisms that confer distinct functions to the short and long arm domains remain poorly understood. Here, we show that phosphorylation of the synaptonemal complex protein SYP-1 is required to create these domains. Once crossover sites are designated, phosphorylated SYP-1 and PLK-2 become cooperatively confined to short arms and guide phosphorylated histone H3 and the chromosomal passenger complex to the site of meiosis I cohesion loss. Our results show that PLK-2 and phosphorylated SYP-1 ensure creation of the short arm subdomain, promoting disjunction of chromosomes in meiosis I., 正常な卵子を生み出す細胞分裂に必須の分子メカニズムを解明. 京都大学プレスリリース. 2017-12-28.

The present study reports the chromosome counts and meiotic analysis including microsporogenesis and pollen fertility in 7 species in the family Cyperaceae from North Indian states. We here add the chromosome record for four species of Cyperaceae. During the present investigation, in some meiotic cells of Cyperus difformis and Isolepis setacea, chromatin threads were found which were typical for the species with inverted meiosis. So present investigation gives the idea of the presence of inverted meiosis in these two genera. Pseudomonad formation, the special feature of the family Cyperaceae where three nuclei out of four degenerate and gives the final product of one pollen per PMC. The course of meiosis in most of the accessions was observed to be regular except for some individuals of Cyperus paniceus, Scirpus mucronatua and Isolepis setacea which showed certain meiotic abnormalities in meiocytes involving cytomixis, chromatin stickiness, chromatin bridges, lagging chromosomes, and interchromosomal connections of bivalents. Being a holocentric family agmatoploidy, symploidy, and polyploidy can play important role in karyotype evolution. The Family shows considerable heterogeneity in chromosome numbers ranging from n = 2 to 60. The family exhibits several base numbers (x=5-14, 16, 20-23, 26, 27, 29, 30, 36, 38, 60) and x=5 is regarded as the most relevant base number for the family. Other base numbers have supposed to be secondarily derived from the ancestral number x=5.