Most cited article - PubMed ID 38606901
Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus
The centromere has a conserved function across eukaryotes; however, the associated DNA sequences exhibit remarkable diversity in both size and structure. In plants, some species possess well-defined centromeres dominated by tandem satellite repeats and centromeric retrotransposons, while others have centromeric regions composed almost entirely of retrotransposons. Using a combination of bioinformatic, molecular, and cytogenetic approaches, we analyzed the centromeric landscape of Humulus lupulus. We identified novel centromeric repeats and characterized two types of centromeric organization. Cytogenetic localization on metaphase chromosomes confirmed the genomic distribution of the major repeats and revealed unique centromeric organization specifically on chromosomes 2, 8, and Y. Two centromeric types are composed of the major repeats SaazCEN and SaazCRM1 (Ty3/Gypsy) which are further accompanied by chromosome-specific centromeric satellites, Saaz40, Saaz293, Saaz85, and HuluTR120. Chromosome 2 displays unbalanced segregation during mitosis and meiosis, implicating an important role for its centromere structure in segregation patterns. Moreover, chromosome 2-specific centromeric repeat Saaz293 is a new marker for studying aneuploidy in hops. Our findings provide new insights into chromosome segregation in hops and highlight the diversity and complexity of the centromere organization in H. lupulus.
- Keywords
- Cannabaceae, asymmetric cell division, centromere, retrotransposons, sex chromosomes,
- MeSH
- Centromere * genetics MeSH
- Chromosomes, Plant genetics MeSH
- Humulus * genetics MeSH
- Meiosis genetics MeSH
- Repetitive Sequences, Nucleic Acid * genetics MeSH
- Retroelements * genetics MeSH
- Chromosome Segregation genetics MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Retroelements * MeSH
INTRODUCTION: Satellite DNA (satDNA) is a rapidly evolving component of plant genomes, typically found in (peri)centromeric, (sub)telomeric, and other heterochromatic regions. Due to their variability and species- or population-specific distribution, satDNA serves as valuable cytogenetic markers for studying chromosomal rearrangements and karyotype evolution among closely related species. Previous studies have identified species-specific subtelomeric repeats CS-1 in Cannabis sativa, HSR1 in Humulus lupulus, and HJSR in Humulus japonicus. These satellites have been used to differentiate sex chromosomes from autosomes, however, their evolutionary origins, sequence variation and conservation pattern across related species remain largely unexplored. METHODS: In this study, we analyze sequence similarity among these satellites and assess their interspecific chromosomal localization using fluorescence in situ hybridization (FISH). RESULTS: Our results reveal that the HSR1 and HJSR satellites are shared across all studied species, suggesting their common origin from a shared pool of satDNA in their common ancestor. In contrast, the CS-1 satellite exhibits higher sequence divergence. DISCUSSION: Although all three satellites are predominantly localized in subtelomeric regions, we identified species-specific exceptions. These findings provide new insight into the evolutionary dynamics of satDNA within the Cannabaceae family and offer further support for the divergence of Humulus species.
- Keywords
- Humulus, metaphase chromosomes, phylogenetics, satellite divergence, subtelomeric repeats,
- Publication type
- Journal Article MeSH
Reproduction is a fundamental aspect of life that affects all levels of biology, from genomes and development to population dynamics and diversification. The first Tree of Sex database synthesized a vast diversity of reproductive strategies and their intriguing distribution throughout eukaryotes. A decade on, we are reviving this initiative and greatly expanding its scope to provide the most comprehensive integration of knowledge on eukaryotic reproduction to date. In this perspective, we first identify important gaps in our current knowledge of reproductive strategies across eukaryotes. We then highlight a selection of questions that will benefit most from this new Tree of Sex project, including those related to the evolution of sex, modes of sex determination, sex chromosomes, and the consequences of various reproductive strategies. Finally, we outline our vision for the new Tree of Sex database and the consortium that will create it (treeofsex.org). The new database will cover all Eukaryota and include a wide selection of biological traits. It will also incorporate genomic data types that were scarce or non-existent at the time of the first Tree of Sex initiative. The new database will be publicly accessible, stable, and self-sustaining, thus greatly improving the accessibility of reproductive knowledge to researchers across disciplines for years to come. Lastly, the consortium will persist after the database is created to serve as a collaborative framework for research, prioritizing ethical standards in the collection, use, and sharing of reproductive data. The new Tree of Sex consortium is open, and we encourage all who are interested in this topic to join us.
Sex chromosomes have evolved in many plant species with separate sexes. Current plant research is shifting from examining the structure of sex chromosomes to exploring their functional aspects. New studies are progressively unveiling the specific genetic and epigenetic mechanisms responsible for shaping distinct sexes in plants. While the fundamental methods of molecular biology and genomics are generally employed for the analysis of sex chromosomes, it is often necessary to modify classical procedures not only to simplify and expedite analyses but sometimes to make them possible at all. In this review, we demonstrate how, at the level of structural and functional genetics, cytogenetics, and bioinformatics, it is essential to adapt established procedures for sex chromosome analysis.
- Keywords
- Bioinformatics, chromosome dissection, cytogenetics, dioecious plants, epigenetics, functional genetics, sex chromosomes, tandem repeats, transposable elements,
- MeSH
- Chromosomes, Plant * genetics MeSH
- Sex Chromosomes * genetics MeSH
- Plants genetics MeSH
- Computational Biology methods MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
