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• Chromosome number and genome variation in flowering plants have stimulated growing speculation about the ancestral chromosome number of angiosperms, but estimates so far remain equivocal. • We used a probabilistic approach to model haploid chromosome number (n) changes along a phylogeny embracing more than 10 000 taxa, to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms and the most recent common ancestor for single angiosperm families. Independently, we carried out an analysis of 1C genome size evolution, including over 5000 taxa. • Our analyses revealed an ancestral haploid chromosome number for angiosperms of n = 7, a diploid status, and an ancestral 1C of 1.73 pg. For 160 families, inferred ancestral n are provided for the first time. • Both descending dysploidy and polyploidy played crucial roles in chromosome number evolution. While descending dysploidy is equally distributed early and late across the phylogeny, polyploidy is detected mainly towards the tips. Similarly, 1C genome size also increases (or decreases) significantly in late-branching lineages. Therefore, no evidence exists of a clear link between ancestral chromosome numbers and ancient polyploidization events, suggesting that further insights are needed to elucidate the organization of genome packaging into chromosomes.

Why women live longer than men is still an open question in human biology. Sex chromosomes have been proposed to play a role in the observed sex gap in longevity, and the Y male chromosome has been suspected of having a potential toxic genomic impact on male longevity. It has been hypothesized that transposable element (TE) repression declines with age, potentially leading to detrimental effects such as somatic mutations and disrupted gene expression, which may accelerate the aging process. Given that the Y chromosome is rich in repeats, age-related increases in TE expression could be more pronounced in males, likely contributing to their reduced longevity compared to females. In this work, we first studied whether TE expression is associated with the number of sex chromosomes in humans. We analyzed blood transcriptomic data obtained from individuals of different karyotype compositions: 46,XX females (normal female karyotype), 46,XY males (normal male karyotype), as well as males with abnormal karyotypes, such as 47,XXY, and 47,XYY. We found that sex chromosomes might be associated to TE expression, with the presence and number of Y chromosomes particularly associated with a global increase in TE expression. This tendency was also observed across several TE subfamilies. We also tested whether TE expression is higher in older males than in older females using published human blood transcriptomic data from the Genotype-Tissue Expression (GTEx) project. However, we did not find increased TE expression in older males compared to older females probably due to the heterogeneity of the dataset. Our findings suggest an association between sex chromosome content and TE expression and open a new window to study the toxic effect of the Y chromosome in human longevity.

Evolution of chromosome complements can be resolved by genome sequencing, comparative genetic mapping, and comparative chromosome painting. Previously, comparison of genetic maps and gene-based phylogenies suggested that the karyotypes of Arabidopsis thaliana (n = 5) and of related species with six or seven chromosome pairs were derived from an ancestral karyotype with eight chromosome pairs. To test this hypothesis, we applied multicolor chromosome painting using contiguous bacterial artificial chromosome pools of A. thaliana arranged according to the genetic maps of Arabidopsis lyrata and Capsella rubella (both n = 8) to A. thaliana, A. lyrata, Neslia paniculata, Turritis glabra, and Hornungia alpina. This approach allowed us to map the A. lyrata centromeres as a prerequisite to defining a putative ancestral karyotype (n = 8) and to elucidate the evolutionary mechanisms that shaped the karyotype of A. thaliana and its relatives. We conclude that chromosome \"fusions\" in A. thaliana resulted from (I) generation of acrocentric chromosomes by pericentric inversions, (ii) reciprocal translocation between two chromosomes (one or both acrocentric), and (iii) elimination of a minichromosome that arose in addition to the \"fusion chromosome.\" Comparative chromosome painting applied to N. paniculata (n = 7), T. glabra (n = 6), and H. alpina (n = 6), for which genetic maps are not available, revealed chromosomal colinearity between all species tested and allowed us to reconstruct the evolution of their chromosomes from a putative ancestral karyotype (n = 8). Although involving different ancestral chromosomes, chromosome number reduction followed similar routes as found within the genus Arabidopsis.

Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of Aegilops tauschii, the diploid source of the wheat D genome. Comparisons of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and 40 were assigned respectively to the rice, sorghum, and Ae. tauschii lineages, showing greatly accelerated genome evolution in the large Triticeae genomes. The reduction of the basic chromosome number from 12 to 7 in the Triticeae has taken place by a process during which an entire chromosome is inserted by its telomeres into a break in the centromeric region of another chromosome. The original centromere-telomere polarity of the chromosome arms is maintained in the new chromosome. An intrachromosomal telomere-telomere fusion resulting in a pericentric translocation of a chromosome segment or an entire arm accompanied or preceded the chromosome insertion in some instances. Insertional dysploidy has been recorded in three grass subfamilies and appears to be the dominant mechanism of basic chromosome number reduction in grasses. A total of 64% and 66% of Ae. tauschii genes were syntenic with sorghum and rice genes, respectively. Synteny was reduced in the vicinity of the termini of modern Ae. tauschii chromosomes but not in the vicinity of the ancient termini embedded in the Ae. tauschii chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere-telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated.

We announce the release of chromEvol version 2.0, a software tool for inferring the pattern of chromosome number change along a phylogeny. The software facilitates the inference of the expected number of polyploidy and dysploidy transitions along each branch of a phylogeny and estimates ancestral chromosome numbers at internal nodes. The new version features a novel extension of the model accounting for general multiplication events, other than doubling of the number of chromosomes. This allows the monoploid number (commonly referred to as x, or the base-number) of a group of interest to be inferred in a statistical framework. In addition, we devise an inference scheme, which allows explicit categorization of each terminal taxon as either diploid or polyploid. The new version also supports intraspecific variation in chromosome number and allows hypothesis testing regarding the root chromosome number. The software, alongside a detailed usage manual, is available at http://www.tau.ac.il/∼itaymay/cp/chromEvol/.

Background Frequent interspecific hybridization, unclear genetic backgrounds, and ambiguous evolutionary relationships within the genus Lycoris pose significant challenges to the identification and classification of hybrids, thereby impacting the application and development of Lycoris . This study utilizes karyotype structure, genome size, and fluorescent in situ hybridization (FISH) technology to explore the chromosomal evolution and hybrid identification of Lycoris employing three approaches at the cytogenetic level. Results The findings indicate that species with a smaller basic chromosome number exhibit less asymmetry than those with a larger basic chromosome number, suggesting that species with different basic chromosome numbers may have followed different evolutionary pathways. Lycoris aurea has a more symmetrical karyotype, which may be the plesiomorphic state, reflecting an evolutionary transition from symmetry to asymmetry in Lycoris chromosomes. Systematic clustering of 18 Lycoris species is consistent with chromosomal karyotype classification, primarily dividing into two groups: species with M + T + A type an M + T type as one group, and A type as another group. The average nuclear genome size (C-value) of the Lycoris genus is 22.99 Gb, with the smallest genome being that of L. wulingensis (17.10 Gb) and the largest being L. squamigera (33.06 Gb). Chromosome length is positively correlated with the C-value, and the haploid genome size (Cx-value) decreases with an increase in basic chromosome number (x). The FISH technique can quickly identify and authenticate artificial hybrids, thus inferring the parentage of natural hybrids. Conclusion The study reveals the genetic background and interspecific relationships of 18 Lycoris species, identifies the authenticity of artificial Lycoris hybrids, and infers the possible parentage of natural hybrids, offering technical insights for the identification, classification, and genomic projects of Lycoris .

Karyotypes are characterized by traits such as chromosome number, which can change through whole-genome duplication and dysploidy. In the parasitic plant genus Cuscuta (Convolvulaceae), chromosome numbers vary more than 18-fold. In addition, species of this group show the highest diversity in terms of genome size among angiosperms, as well as a wide variation in the number and distribution of 5S and 35S ribosomal DNA (rDNA) sites. To understand its karyotypic evolution, ancestral character state reconstructions were performed for chromosome number, genome size, and position of 5S and 35S rDNA sites. Previous cytogenetic data were reviewed and complemented with original chromosome counts, genome size estimates, and rDNA distribution assessed via fluorescence in situ hybridization (FISH), for two, seven, and 10 species, respectively. Starting from an ancestral chromosome number of x  = 15, duplications were inferred as the prevalent evolutionary process. However, in holocentric clade (subgenus Cuscuta ), dysploidy was identified as the main evolutionary mechanism, typical of holocentric karyotypes. The ancestral genome size of Cuscuta was inferred as approximately 1C = 12 Gbp, with an average genome size of 1C = 2.8 Gbp. This indicates an expansion of the genome size relative to other Convolvulaceae, which may be linked to the parasitic lifestyle of Cuscuta . Finally, the position of rDNA sites varied mostly in species with multiple sites in the same karyotype. This feature may be related to the amplification of rDNA sites in association to other repeats present in the heterochromatin. The data suggest that different mechanisms acted in different subgenera, generating the exceptional diversity of karyotypes in Cuscuta .

Whole‐genome duplication (WGD) is central to the evolution of many eukaryotic genomes, in particular rendering angiosperm (flowering plant) genomes much less stable than those of animals. Following repeated duplication/triplication(s), angiosperm chromosome numbers have usually been restored to a narrow range, as one element in a ‘diploidization’ process that re‐establishes diploid heredity. In several angiosperms affected by WGD, we show that chromosome number reduction (CNR) is best explained by intra‐ and/or inter‐chromosomal crossovers to form new chromosomes that utilize the existing telomeres of ‘invaded’ and centromeres of ‘invading’ chromosomes, the alternative centromeres and telomeres being lost. Comparison with the banana (Musa acuminata) genome supports a ‘fusion model’ for the evolution of rice (Oryza sativa) chromosomes 2 and 3, implying that the grass common ancestor had seven chromosomes rather than the five implied by a ‘fission model.’ The ‘invading’ and ‘invaded’ chromosomes are frequently homoeologs, originating from duplication of a common ancestral chromosome and with greater‐than‐average DNA‐level correspondence to one another. Telomere‐centric CNR following recursive WGD in plants is also important in mammals and yeast, and may be a general mechanism of restoring small linear chromosome numbers in higher eukaryotes.

Background Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica . This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x  = 8, BB: x  = 9) and their allopolyploid derivatives on several ploidy levels (from 3 x to 6 x ). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation. Results The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2 n  = 16 and 18 (2 n  = 25 with the presence of supernumerary B chromosomes), and from 2 n  = 26 to 51 in polyploids on four different ploidy levels (3 x , 4 x , 5 x , and 6 x ). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels. Conclusions This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.

Recent molecular systematic studies have significantly improved our understanding of the large, complex, and cosmopolitan plant family Rubiaceae, comprising about 13,000 species. Besides the obvious importance of DNA phylogenetic data, cytological studies have long added important basic information on the circumscription of clades and relationships within the family. In light of recent changes affecting a large number of tribes and genera, the current knowledge on the systematics of Neotropical Rubiaceae is reviewed with a focus on Costa Rica, which harbors an exceptionally rich Rubiaceae flora including most of the genera and biogeographic elements present in the Neotropics. Based on this systematic framework, previously published chromosome counts on Costa Rican taxa are reviewed and 49 new chromosome counts are reported. In total, 110 accessions of 75 species or infraspecific taxa representing 36 genera of Costa Rican Rubiaceae are discussed and supplemented by new counts for extraterritorial taxa when appropriate. Altogether the present study includes the first chromosome counts reported for the tribes Cordiereae and Hillieae, as well as for 10 genera and 27 species, providing new aspects of Rubiaceae systematics.