Centromere organization and UU/V sex chromosome behavior in a liverwort.

In 1917, sex chromosomes in plants were discovered in a liverwort with hetermorphic U and V chromosomes. Such heteromorphy is unexpected because, unlike the XY chromosomes in diploid-dominant plants, in haploid-dominant plants the female U and the male V chromosomes experience largely symmetrical potential recombination environments. Here we use molecular cytogenetics and super-resolution microscopy to study Frullania dilatata, a liverwort with one male and two female sex chromosomes. We applied a pipeline to Illumina sequences to detect abundant types of repetitive DNA and developed FISH probes to microscopically distinguish the sex chromosomes. We also determined the phenotypic population sex ratio because biased ratios have been reported from other liverworts with heteromorphic sex chromosomes. Populations had male-biased sex ratios. The sex chromosomes are monocentric, and of 14 probes studied (eight satellites, five transposable elements and one plastid region), four resulted in unique signals that differentiated the sex chromosomes from the autosomes and from each other. One FISH probe selectively marked the centromeres of both U chromosomes, so we could prove that during meiosis each U chromosome associates with one of the opposite telomeres of the V chromosome, resulting in a head-to-head trivalent. The similarity of the two U chromosomes to each other in size and in their centromere FISH signal positions points to their origin via a non-disjunction event (aneuploidy), which would fit with the general picture of sex chromosomes rarely crossing-over and being prone to suffer from non-disjunction.

Polyploidy in gymnosperms - Insights into the genomic and evolutionary consequences of polyploidy in Ephedra.

While polyploidization is recognized as a major evolutionary driver for ferns and angiosperms, little is known about its impact in gymnosperms, where polyploidy is much less frequent. We explore Ephedra to evaluate (i) the extent of genome size diversity in the genus and the influence polyploidy has had on the evolution of nuclear DNA contents, and (ii) identify where shifts in genome size and polyploidy have occurred both temporally and spatially. A phylogenetic framework of all Ephedra species together with genome sizes and karyotypes for 87% and 67% of them respectively, were used to explore ploidy evolution and its global distribution patterns. Polyploidy was shown to be extremely common, with 41 species (83%) being polyploid (up to 8×) or having polyploid cytotypes - the highest frequency and level reported for any gymnosperm. Genome size was also diverse, with values ranging ~5-fold (8.09-38.34 pg/1C) - the largest range for any gymnosperm family - and increasing in proportion to ploidy level (i.e. no genome downsizing). Our findings provide novel data which support the view that gymnosperms have a more conserved mode of genomic evolution compared with angiosperms.

Different from tracheophytes, liverworts commonly have mixed 35S and 5S arrays.

BACKGROUND AND AIMS: Unlike other nuclear genes in eukaryotes, rDNA genes (5S and 35S loci) are present in numerous copies per cell and, when stained, can therefore provide basic information about genome organization. In tracheophytes (vascular plants), they are usually located on separate chromosomes, the so-called S-type organization. An analysis of 1791 species of land plants suggested that S-type arrays might be ancestral in land plants, while linked (L-type) organization may be derived. However, no outgroup and only a handful of ferns and bryophytes were included. METHODS: We analysed genome sizes and the distribution of telomere, 5S and 35S rDNA FISH signals in up to 12 monoicous or dioicous species of liverworts from throughout a phylogeny that includes 287 of the 386 currently recognized genera. We also used the phylogeny to plot chromosome numbers and the occurrence of visibly distinct sex chromosomes. KEY RESULTS: Chromosome numbers are newly reported for the monoicous Lejeunea cavifolia and for females of the dioicous Scapania aequiloba. We detected sex-related differences in the number of rDNA signals in the dioicous Plagiochila asplenioides and Frullania dilatata. In the latter, the presence of two UU chromosomes in females and additional 5S-35S rDNA loci result in a haploid genome 0.2082 pg larger than the male genome; sex-specific genome differences in the other dioicous species were small. Four species have S-type rDNA, while five species have mixed L-S rDNA organization, and transitions may have occurred multiple times, as suggested by rDNA loci not being conserved among closely related species of Pellia. All species shared an Arabidopsis-like telomere motif, and its detection allowed verification of the chromosome number of Radula complanata and chromosome rearrangements in Aneura pinguis and P. asplenioides, the latter also showing sex-specific interstitial telomere repeats. CONCLUSIONS: The S and L rDNA arrangements appear to have evolved repeatedly within liverworts, even in the same species. Evidence for differential accumulation of rDNA between the sexes so far is limited.

Cytogenetic comparison of heteromorphic and homomorphic sex chromosomes in Coccinia (Cucurbitaceae) points to sex chromosome turnover.

Our understanding of the evolution of plant sex chromosomes is increasing rapidly due to high-throughput sequencing data and phylogenetic and molecular-cytogenetic approaches that make it possible to infer the evolutionary direction and steps leading from homomorphic to heteromorphic sex chromosomes. Here, we focus on four species of Coccinia, a genus of 25 dioecious species, including Coccinia grandis, the species with the largest known plant Y chromosome. Based on a phylogeny for the genus, we selected three species close to C. grandis to test the distribution of eight repetitive elements including two satellites, and several plastid and mitochondrial probes, that we had previously found to have distinct accumulation patterns in the C. grandis genome. Additionally, we determined C-values and performed immunostaining experiments with (peri-)centromere-specific antibodies on two species (for comparison with C. grandis). In spite of no microscopic chromosomal heteromorphism, single pairs of chromosomes in male cells of all three species accumulate some of the very same repeats that are enriched on the C. grandis Y chromosome, pointing to either old (previous) sex chromosomes or incipient (newly arising) ones, that is, to sex chromosome turnover. A 144-bp centromeric satellite repeat (CgCent) that characterizes all C. grandis chromosomes except the Y is highly abundant in all centromeric regions of the other species, indicating that the centromeric sequence of the Y chromosome diverged very recently.

Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres.

Few angiosperms have distinct Y chromosomes. Among those that do are Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae) and Coccinia grandis (Cucurbitaceae), the latter having a male/female difference of 10% of the total genome (female individuals have a 0.85 pg genome, male individuals 0.94 pg), due to a Y chromosome that arose about 3 million years ago. We compared the sequence composition of male and female C. grandis plants and determined the chromosomal distribution of repetitive and organellar DNA with probes developed from 21 types of repetitive DNA, including 16 mobile elements. The size of the Y chromosome is largely due to the accumulation of certain repeats, such as members of the Ty1/copia and Ty3/gypsy superfamilies, an unclassified element and a satellite, but also plastome- and chondriome-derived sequences. An abundant tandem repeat with a unit size of 144 bp stains the centromeres of the X chromosome and the autosomes, but is absent from the Y centromere. Immunostaining with pericentromere-specific markers for anti-histone H3Ser10ph and H2AThr120ph revealed a Y-specific extension of these histone marks. That the Y centromere has a different make-up from all the remaining centromeres raises questions about its spindle attachment, and suggests that centromeric or pericentromeric chromatin might be involved in the suppression of recombination.

Chromosome number reduction in the sister clade of Carica papaya with concomitant genome size doubling.

PREMISE OF THE STUDY: Caricaceae include six genera and 34 species, among them papaya, a model species in plant sex chromosome research. The family was held to have a conserved karyotype with 2n = 18 chromosomes, an assumption based on few counts. We examined the karyotypes and genome size of species from all genera to test for possible cytogenetic variation. METHODS: We used fluorescent in situ hybridization using standard telomere, 5S, and 45S rDNA probes. New and published data were combined with a phylogeny, molecular clock dating, and C values (available for ∼50% of the species) to reconstruct genome evolution. KEY RESULTS: The African genus Cylicomorpha, which is sister to the remaining Caricaceae (all neotropical), has 2n = 18, as do the species in two other genera. A Mexican clade of five species that includes papaya, however, has 2n = 18 (papaya), 2n = 16 (Horovitzia cnidoscoloides), and 2n = 14 (Jarilla caudata and J. heterophylla; third Jarilla not counted), with the phylogeny indicating that the dysploidy events occurred ∼16.6 and ∼5.5 million years ago and that Jarilla underwent genome size doubling (∼450 to 830-920 Mbp/haploid genome). Pericentromeric interstitial telomere repeats occur in both Jarilla adjacent to 5S rDNA sites, and the variability of 5S rDNA sites across all genera is high. CONCLUSIONS: On the basis of outgroup comparison, 2n = 18 is the ancestral number, and repeated chromosomal fusions with simultaneous genome size increase as a result of repetitive elements accumulating near centromeres characterize the papaya clade. These results have implications for ongoing genome assemblies in Caricaceae.

Transposable elements in a clade of three tetraploids and a diploid relative, focusing on Gypsy amplification.

BACKGROUND: Polyploidization can activate specific transposable elements, leading to their accumulation. At the same time, the preferential loss of repetitive elements in polyploids may be central to diploidization. The paucity of studies of transposable element (TE) dynamics in closely related diploid and polyploid species, however, prevents generalizations about these patterns. Here, we use low-coverage Illumina sequencing data for a clade of three tetraploid Orobanche species and a diploid relative to quantify the abundance and relative frequencies of different types of TEs. We confirmed tetraploidy in the sequenced individuals using standard cytogenetic methods and inferred the time of origin of the tetraploid clade with a rate-calibrated molecular clock. FINDINGS: The sequenced individuals of Orobanche austrohispanica, Orobanche densiflora, and Orobanche gracilis have 2n = 76 chromosomes, are tetraploid, and shared a most recent common ancestor some 6.7 Ma ago. Comparison of TE classifications from the Illumina data with classification from 454 data for one of the species revealed strong effects of sequencing technology on the detection of certain types of repetitive DNA. The three tetraploids show repeat enrichment especially of Gypsy TE families compared to eight previously analyzed Orobanchaceae. However, the diploid Orobanche rapum-genistae genome also has a very high proportion (30%) of Gypsy elements. CONCLUSIONS: We had earlier suggested that tetraploidization might have contributed to an amplification of Gypsy elements, particularly of the Tekay clade, and that O. gracilis underwent genome downsizing following polyploidization. The new data reveal that Gypsy amplification in Orobanchaceae does not consistently relate to tetraploidy and that more species sampling is required to generalize about Tekay accumulation patterns.

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms.

BACKGROUND AND AIMS: Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined. METHODS: Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes. KEY RESULTS: Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of <100 Mbp were almost exclusively found in a derived lineage of South American species. The ancestral haploid chromosome number was inferred to be n = 8. Chromosome numbers in Genlisea ranged from 2n = 2x = 16 to 2n = 4x = 32. Ascendant dysploid series (2n = 36, 38) are documented for three derived taxa. The different ploidy levels corresponded to the two subgenera, but were not directly correlated to differences in genome size; the three different karyotype ranges mirrored the different sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported, but in G. tuberosa (1C ≈ 61 Mbp) and some strains of G. aurea (1C ≈ 64 Mbp). CONCLUSIONS: Genlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.

Combining FISH and model-based predictions to understand chromosome evolution in Typhonium (Araceae).

BACKGROUND AND AIMS: Since the advent of molecular phylogenetics, numerous attempts have been made to infer the evolutionary trajectories of chromosome numbers on DNA phylogenies. Ideally, such inferences should be evaluated against cytogenetic data. Towards this goal, we carried out phylogenetic modelling of chromosome number change and fluorescence in situ hybridization (FISH) in a medium sized genus of Araceae to elucidate if data from chromosomal markers would support maximum likelihood-inferred changes in chromosome numbers among close relatives. Typhonium, the focal genus, includes species with 2n = 65 and 2n = 8, the lowest known count in the family. METHODS: A phylogeny from nuclear and plastid sequences (96 taxa, 4252 nucleotides) and counts for all included species (15 of them first reported here) were used to model chromosome number evolution, assuming discrete events, such as polyploidization and descending or ascending dysploidy, occurring at different rates. FISH with three probes (5S rDNA, 45S rDNA and Arabidopsis-like telomeres) was performed on ten species with 2n = 8 to 2n = 24. KEY RESULTS: The best-fitting models assume numerous past chromosome number reductions. Of the species analysed with FISH, the two with the lowest chromosome numbers contained interstitial telomeric signals (Its), which together with the phylogeny and modelling indicates decreasing dysploidy as an explanation for the low numbers. A model-inferred polyploidization in another species is matched by an increase in rDNA sites. CONCLUSIONS: The combination of a densely sampled phylogeny, ancestral state modelling and FISH revealed that the species with n = 4 is highly derived, with the FISH data pointing to a Robertsonian fusion-like chromosome rearrangement in the ancestor of this species.

Complicações obstétricas em adolescentes de uma maternidade / Obstetric complications in teens of a maternity

Objetivo: identificar as complicações obstétricas em adolescentes atendidas em uma maternidade. Método:trata-se de estudo documental, retrospectivo, realizado a partir da coleta de 45 prontuários do serviço dearquivo médico e estatístico (Same) do Hospital Regional de Cajazeiras, em março e abril de 2011. Os dadosforam analisados com enfoque no método quantitativo, o qual tende a enfatizar o raciocínio dedutivo, asregras da lógica e atributos mensuráveis de experiência humana. A pesquisa foi aprovada pelo Comitê de Éticaem Pesquisa da Faculdade Santa Maria (FSM), sob o CAAE n. 43102/2010. Resultados: 31,1% das adolescentesapresentaram bebês com baixo peso ao nascer; 22,2% com pré-eclampsia; 20% com prematuridade; 13,3% comruptura do colo do útero; e 8,8% com infecções urogenitais e eclampsia. Conclusão: diante dos achados, fazsenecessária uma melhor atuação dos profissionais e gestores de saúde, pois a adolescência é um desafiopara pais, educadores e profissionais da saúde e demanda, assim, apoio, compreensão, participação e diálogo.

Ribosomal DNA distribution and a genus-wide phylogeny reveal patterns of chromosomal evolution in Alstroemeria (Alstroemeriaceae).

PREMISE OF THE STUDY: Understanding the flexibility of monocot genomes requires a phylogenetic framework, which so far is available for few of the ca. 2800 genera. Here we use a molecular tree for the South American genus Alstroemeria to place karyological information, including fluorescent in situ hybridization (FISH) signals, in an explicit evolutionary context. METHODS: From a phylogeny based on plastid, nuclear, and mitochondrial sequences for most species of Alstroemeria, we selected early-branching (Chilean) and derived (Brazilian) species for which we obtained 18S-25S and 5S rDNA FISH signals; we also analyzed chromosome numbers, 1C-values, and telomere FISH signals (in two species). KEY RESULTS: Chromosome counts for Alstroemeria cf. rupestris and A. pulchella confirm 2n = 16 as typical of the genus, which now has chromosomes counted for 29 of its 78 species. The rDNA sites are polymorphic both among and within species, and interstitial telomeric sites in Alstroemeria cf. rupestris suggest chromosome fusion. CONCLUSIONS: In spite of a constant chromosome number, closely related species of Alstroemeria differ drastically in their rDNA, indicating rapid increase, decrease, or translocations of these genes. Previously proposed Brazilian and Chilean karyotype groups are not natural, and the n = 8 chromosomes in Alstroemeria compared to n = 9 in its sister genus Bomarea may result from a Robertsonian fusion.

Maximum likelihood inference implies a high, not a low, ancestral haploid chromosome number in Araceae, with a critique of the bias introduced by 'x'.

BACKGROUND AND AIMS: For 84 years, botanists have relied on calculating the highest common factor for series of haploid chromosome numbers to arrive at a so-called basic number, x. This was done without consistent (reproducible) reference to species relationships and frequencies of different numbers in a clade. Likelihood models that treat polyploidy, chromosome fusion and fission as events with particular probabilities now allow reconstruction of ancestral chromosome numbers in an explicit framework. We have used a modelling approach to reconstruct chromosome number change in the large monocot family Araceae and to test earlier hypotheses about basic numbers in the family. METHODS: Using a maximum likelihood approach and chromosome counts for 26 % of the 3300 species of Araceae and representative numbers for each of the other 13 families of Alismatales, polyploidization events and single chromosome changes were inferred on a genus-level phylogenetic tree for 113 of the 117 genera of Araceae. KEY RESULTS: The previously inferred basic numbers x = 14 and x = 7 are rejected. Instead, maximum likelihood optimization revealed an ancestral haploid chromosome number of n = 16, Bayesian inference of n = 18. Chromosome fusion (loss) is the predominant inferred event, whereas polyploidization events occurred less frequently and mainly towards the tips of the tree. CONCLUSIONS: The bias towards low basic numbers (x) introduced by the algebraic approach to inferring chromosome number changes, prevalent among botanists, may have contributed to an unrealistic picture of ancestral chromosome numbers in many plant clades. The availability of robust quantitative methods for reconstructing ancestral chromosome numbers on molecular phylogenetic trees (with or without branch length information), with confidence statistics, makes the calculation of x an obsolete approach, at least when applied to large clades.