Evolution of ribosomal DNA unit on the X chromosome independent of autosomal units in the liverwort Marchantia polymorpha

Sex Determination in Dioscorea dumetorum: Evidence of Heteromorphic Sex Chromosomes and Sex-Linked NORs

Yams (Dioscorea spp.) are a pantropical genus located worldwide that constitute an important source of nutrients and pharmaceutical substances. Some Dioscorea crop species are widely grown in West Africa. One species that is mainly cultivated in Cameroon is Dioscorea dumetorum. This is a dioecious root crop whose sex-determining system was unknown until now. To address the possible presence of sex chromosomes in D. dumetorum, we performed a karyotype characterization of male and female individuals using classical and molecular cytogenetic approaches. It was determined that 2n = 40 was the most common number of chromosomes in all of the investigated samples. One chromosome pair was longer than the others in the chromosome set and was a heteromorph in male and homomorph in female individuals. This pair corresponded to sex chromosomes, and we also confirmed this with molecular cytogenetic experiments. The results of chromomycin banding revealed the presence of strong positive signals on this chromosome pair. The signals, corresponding to GC-rich DNA regions, were similar in size on the chromosomes of the female individuals, whereas they were different in size in the male individuals. This size difference in the GC-rich heterochromatin regions was also apparent in the interphase nuclei as one small and one large fluorescent spot. The results of the in situ hybridization experiment showed that these chromomycin positive signals on the sex chromosomes also corresponded to the 35S rDNA cluster. The mean 2C DNA value (genome size) obtained for D. dumentorum was 0.71 pg (±0.012), which represents a small genome size. We found no difference in the genome size between the male and female individuals. The results of this study contribute to increasing our knowledge of sex determination in D. dumetorum (standard sex-determining XX/XY system) and may have some agronomic applications.

The renaissance and enlightenment of Marchantia as a model system

The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.

Identification of 45S rDNA in Passiflora using low coverage sequencing: analysis of GC content and chromosomal localization

BACKGROUND

The 45S rDNA is considered the most useful chromosomal marker for cytogenetic analysis of Passiflora. Amplification of 45S rDNA sequence via PCR are more advantageous than sequence maintenance in vectors for chromosomal hybridization via FISH. We aimed both to identify 45S rDNA by sequencing data for chromosomal localization and to verify the relationship between GC content and CMA₃/DAPI banding.

METHODS AND RESULTS

Low-coverage sequencing of Passiflora alata, P. cincinnata, and P. edulis was performed, and 45S rDNA units were identified using RepeatExplorer. The 45S rDNA units were used to construct a neighbor-joining tree to verify the similarities between the three species' 18S and 26S rDNA sequences. Clusters (CL)116 (P. alata), CL71 (P. cincinnata), and CL116 (P. edulis) were remarkably similar among the three species, and the 26S rDNA sequences of the clusters were similar to those of Populus tremuloides, Salix interior, and Averrhoa carambola (98% identity). The 26S rDNA was cytologically localized in the chromosomes of P. edulis, P. bahiensis, and the backcrossed hybrid (P. sublanceolata vs. HD13). The hybridization transfer capacity was evaluated in Citrus sunki and Cucumis melo. Finally, a chromosomal pair with a heteromorphic 26S rDNA site was observed in P. edulis, which was the same to that observed for CMA₃.

CONCLUSION

The amplification of the 26S rDNA in Passiflora via PCR and the chromosomal localization in Passiflora and other plant species was successfully achieved. The CMA₃ bands were found to be related not only to the amount of GC but also to its structure and the number of repetitions.

The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies

The ubiquitous presence of rRNA genes in nuclear, plastid, and mitochondrial genomes has provided an opportunity to use genomic markers to infer patterns of molecular and organismic evolution as well as to assess systematic issues throughout the tree of life. The number, size, location, and activity of the 35S rDNA cistrons in plant karyotypes have been used as conventional cytogenetic landmarks. Their scrutiny has been useful to infer patterns of chromosomal evolution and the data have been used as a proxy for assessing species discrimination, population differentiation and evolutionary relationships. The correct interpretation of rDNA markers in plant taxonomy and evolution is not free of drawbacks given the complexities derived from the lability of the genetic architecture, the diverse patterns of molecular change, and the fate and evolutionary dynamics of the rDNA units in hybrids and polyploid species. In addition, the terminology used by independent authors is somewhat vague, which often complicates comparisons. To date, no efforts have been reported addressing the potential problems and limitations involved in generating, utilizing, and interpreting the data from the 35S rDNA in cytogenetics. This review discusses the main technical and conceptual limitations of these rDNA markers obtained by cytological and karyological experimental work, in order to clarify biological and evolutionary inferences postulated in a systematic and phylogenetic context. Also, we provide clarification for some ambiguity and misconceptions in terminology usually found in published work that may help to improve the usage of the 35S ribosomal world in plant evolution.

Development and Molecular Genetics of Marchantia polymorpha

Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.

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.

Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin

Genome packaging by nucleosomes is a hallmark of eukaryotes. Histones and the pathways that deposit, remove, and read histone modifications are deeply conserved. Yet, we lack information regarding chromatin landscapes in extant representatives of ancestors of the main groups of eukaryotes, and our knowledge of the evolution of chromatin-related processes is limited. We used the bryophyte Marchantia polymorpha, which diverged from vascular plants circa 400 mya, to obtain a whole chromosome genome assembly and explore the chromatin landscape and three-dimensional genome organization in an early diverging land plant lineage. Based on genomic profiles of ten chromatin marks, we conclude that the relationship between active marks and gene expression is conserved across land plants. In contrast, we observed distinctive features of transposons and other repetitive sequences in Marchantia compared with flowering plants. Silenced transposons and repeats did not accumulate around centromeres. Although a large fraction of constitutive heterochromatin was marked by H3K9 methylation as in flowering plants, a significant proportion of transposons were marked by H3K27me3, which is otherwise dedicated to the transcriptional repression of protein-coding genes in flowering plants. Chromatin compartmentalization analyses of Hi-C data revealed that repressed B compartments were densely decorated with H3K27me3 but not H3K9 or DNA methylation as reported in flowering plants. We conclude that, in early plants, H3K27me3 played an essential role in heterochromatin function, suggesting an ancestral role of this mark in transposon silencing.

UV Chromosomes and Haploid Sexual Systems

The evolution of sex determination continues to pose major questions in biology. Sex-determination mechanisms control reproductive cell differentiation and development of sexual characteristics in all organisms, from algae to animals and plants. While the underlying processes defining sex (meiosis and recombination) are conserved, sex-determination mechanisms are highly labile. In particular, a flow of new discoveries has highlighted several fascinating features of the previously understudied haploid UV sex determination and related mating systems found in diverse photosynthetic taxa including green algae, bryophytes, and brown algae. Analyses integrating information from these systems and contrasting them with classical XY and ZW systems are providing exciting insights into both the universality and the diversity of sex-determining chromosomes across eukaryotes.

Living together and living apart: the sexual lives of bryophytes

Haploid gametophytes of bryophytes spread by clonal growth but mate locally, within an area defined by the range of sperm movement. Rarity of establishment from spores or vegetative competition can result in unisexual populations unable to reproduce sexually. Females typically outcompete males, probably because females expend fewer resources than males on the production of gametes. Extreme sexual dimorphism-tiny males growing as epiphytes on much larger females-has evolved many times. Haploid selfing is common in bryophytes with bisexual gametophytes, and results in completely homozygous sporophytes. Spores from these sporophytes recapitulate the genotype of their single haploid parent. This process can be considered analogous to 'asexual' reproduction with 'sexual' reproduction occurring after rare outcrossing between haploid parents. Ferns also produce bisexual haploid gametophytes but, unlike bryophytes, haploid outcrossing predominates over haploid selfing. This difference is probably related to clonal growth and vegetative competition occurring in the haploid but not the diploid phase in bryophytes, but the reverse in ferns. Ferns are thereby subject to stronger inbreeding depression than bryophytes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

Conserved Organisation of 45S rDNA Sites and rDNA Gene Copy Number among Major Clades of Early Land Plants

Genes encoding ribosomal RNA (rDNA) are universal key constituents of eukaryotic genomes, and the nuclear genome harbours hundreds to several thousand copies of each species. Knowledge about the number of rDNA loci and gene copy number provides information for comparative studies of organismal and molecular evolution at various phylogenetic levels. With the exception of seed plants, the range of 45S rDNA locus (encoding 18S, 5.8S and 26S rRNA) and gene copy number variation within key evolutionary plant groups is largely unknown. This is especially true for the three earliest land plant lineages Marchantiophyta (liverworts), Bryophyta (mosses), and Anthocerotophyta (hornworts). In this work, we report the extent of rDNA variation in early land plants, assessing the number of 45S rDNA loci and gene copy number in 106 species and 25 species, respectively, of mosses, liverworts and hornworts. Unexpectedly, the results show a narrow range of ribosomal locus variation (one or two 45S rDNA loci) and gene copies not present in vascular plant lineages, where a wide spectrum is recorded. Mutation analysis of whole genomic reads showed higher (3-fold) intragenomic heterogeneity of Marchantia polymorpha (Marchantiophyta) rDNA compared to Physcomitrella patens (Bryophyta) and two angiosperms (Arabidopsis thaliana and Nicotiana tomentosifomis) suggesting the presence of rDNA pseudogenes in its genome. No association between phylogenetic position, taxonomic adscription and the number of rDNA loci and gene copy number was found. Our results suggest a likely evolutionary rDNA stasis during land colonisation and diversification across 480 myr of bryophyte evolution. We hypothesise that strong selection forces may be acting against ribosomal gene locus amplification. Despite showing a predominant haploid phase and infrequent meiosis, overall rDNA homogeneity is not severely compromised in bryophytes.

Non-Random Distribution of 5S rDNA Sites and Its Association with 45S rDNA in Plant Chromosomes

5S and 45S rDNA sites are the best mapped chromosome regions in eukaryotic chromosomes. In this work, a database was built gathering information about the position and number of 5S rDNA sites in 784 plant species, aiming to identify patterns of distribution along the chromosomes and its correlation with the position of 45S rDNA sites. Data revealed that in most karyotypes (54.5%, including polyploids) two 5S rDNA sites (a single pair) are present, with 58.7% of all sites occurring in the short arm, mainly in the proximal region. In karyotypes of angiosperms with only 1 pair of sites (single sites) they are mostly found in the proximal region (52.0%), whereas in karyotypes with multiple sites the location varies according to the average chromosome size. Karyotypes with multiple sites and small chromosomes (<3 µm) often display proximal sites, while medium-sized (between 3 and 6 µm) and large chromosomes (>6 µm) more commonly show terminal or interstitial sites. In species with holokinetic chromosomes, the modal value of sites per karyotype was also 2, but they were found mainly in a terminal position. Adjacent 5S and 45S rDNA sites were often found in the short arm, reflecting the preferential distribution of both sites in this arm. The high frequency of genera with at least 1 species with adjacent 5S and 45S sites reveals that this association appeared several times during angiosperm evolution, but it has been maintained only rarely as the dominant array in plant genera.

Gene content, organization and molecular evolution of plant organellar genomes and sex chromosomes: insights from the case of the liverwort Marchantia polymorpha

The complete nucleotide sequence of chloroplast DNA (121,025 base pairs, bp) from a liverwort, Marchantia polymorpha, has made clear the entire gene organization of the chloroplast genome. Quite a few genes encoding components of photosynthesis and protein synthesis machinery have been identified by comparative computer analysis. We also determined the complete nucleotide sequence of the liverwort mitochondrial DNA and deduced 96 possible genes in the sequence of 186,608 bp. The complete chloroplast genome encodes twenty introns (19 group II and 1 group I) in 18 different genes. One of the chloroplast group II introns separates a ribosomal protein gene in a trans-position. The mitochondrial genome contains thirty-two introns (25 group II and 7 group I) in the coding regions of 17 genes. From the evolutionary point of view, we describe the origin of organellar introns and give evidence for vertical and horizontal intron transfers and their intragenomic propagation. Furthermore, we describe the gene organization of the Y chromosome in the dioecious liverwort M. polymorpha, the first detailed view of a Y chromosome in a haploid organism. On the 10 megabase (Mb) Y chromosome, 64 genes are identified, 14 of which are detected only in the male genome. These 14 genes are expressed in reproductive organs but not in vegetative thalli, suggesting their participation in male reproductive functions. These findings indicate that the Y and X chromosomes share the same ancestral autosome and support the prediction that in a haploid organism essential genes on sex chromosomes are more likely to persist than in a diploid organism.

Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system

Y chromosomes are different from other chromosomes because of a lack of recombination. Until now, complete sequence information of Y chromosomes has been available only for some primates, although considerable information is available for other organisms, e.g., several species of Drosophila. Here, we report the gene organization of the Y chromosome in the dioecious liverwort Marchantia polymorpha and provide a detailed view of a Y chromosome in a haploid organism. On the 10-Mb Y chromosome, 64 genes are identified, 14 of which are detected only in the male genome and are expressed in reproductive organs but not in vegetative thalli, suggesting their participation in male reproductive functions. Another 40 genes on the Y chromosome are expressed in thalli and male sexual organs. At least six of these genes have diverged X-linked counterparts that are in turn expressed in thalli and sexual organs in female plants, suggesting that these X- and Y-linked genes have essential cellular functions. These findings indicate that the Y and X chromosomes share the same ancestral autosome and support the prediction that in a haploid organism essential genes on sex chromosomes are more likely to persist than in a diploid organism.

Differentiating sex chromosomes of the dioecious Spinacia oleracea L. (spinach) by FISH of 45S rDNA

Spinacia oleracea L. (spinach) is a dioecious species with both male and female plants having 2n = 2x = 12 chromosomes, consisting of two large metacentrics, two long subtelocentrics, two short subtelocentrics, two acrocentrics, and four submetacentrics. The location of 45S rDNA was investigated on metaphase chromosomes using fluorescence in situ hybridization (FISH). The numbers of 45S rDNA foci in diploid sets of chromosomes from females was six and from males was five. All the fluorescent foci lay in secondary constrictions and the satellites. Our results indicate that an XY-type sex chromosome system could be present in spinach where the Y chromosome lacks a 45S RNA focus.