Article
Ecology
Guillaume G. Cossard, Olivier Godfroy, Zofia Nehr, Corinne Cruaud, J. Mark Cock, Agnieszka P. Lipinska, Susana M. Coelho
Summary: The study reveals that the transition to co-sexuality in brown algae involves adaptive gene expression changes and rapid sequence evolution. The gene expression profiles of co-sexual species are more similar to those of ancestral females rather than males. Convergent gene expression changes are associated with the transition to co-sexuality.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Matthew M. Edwards, Michael Zuccaro, Ido Sagi, Qiliang Ding, Dan Vershkov, Nissim Benvenisty, Dieter Egli, Amnon Koren
Summary: The study found differences in DNA replication timing between haploid human embryonic stem cells and diploid cells, with unique features of delayed replication in certain genomic regions, especially the X Chromosome. The dosage effect of active X Chromosomes may affect the speed of chromosomal replication.
Review
Plant Sciences
Isidre Hooghvorst, Salvador Nogues
Summary: The doubled haploid technique aims to generate pure inbred lines through haploid plant generation and chromosome doubling. Efforts have been focused on haploid production methods such as androgenesis, gynogenesis, and parthenogenesis. Recent interest has been in optimizing chromosome doubling methods to increase rates and efficiency of doubled haploid plant production.
PLANT CELL REPORTS
(2021)
Review
Biology
Francesc Piferrer
Summary: Epigenetic mechanisms play vital roles in vertebrate sex determination, not only within individuals in a generation, but also potentially across generations to facilitate the transition of sexual systems. The article presents examples supporting these points and suggests possible ways to test this hypothesis.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Marco A. Coelho, Giuseppe Ianiri, Marcia David-Palma, Bart Theelen, Rohit Goyal, Aswathy Narayanan, Jeffrey M. Lorch, Kaustuv Sanyal, Teun Boekhout, Joseph Heitman
Summary: Fungi in the genus Malassezia, which are commonly found on the skin of humans and other warm-blooded animals, have been linked to skin diseases and systemic disorders. Analysis of Malassezia genomes suggests that their ability to adapt to the skin microenvironment is directly influenced by their genetic makeup. Despite the absence of observed sexual reproduction, the presence of mating/meiotic genes suggests a potential for sexual reproduction in Malassezia. The arrangement of mating type loci in Malassezia has been found to be different from other basidiomycetes, indicating an ancestral state of the genus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Cardiac & Cardiovascular Systems
Jasmine Nour, Fabrizia Bonacina, Giuseppe D. Norata
Summary: Epidemiological data and interventional studies suggest that women have a lower risk of cardiovascular disease compared to men until menopause. The molecular mechanisms underlying this difference are still debated, but experimental models have shown that estrogen receptor activation is atheroprotective. Additionally, the importance of sex chromosome complement on atherosclerosis beyond sex hormones is also worth investigating.
Article
Oncology
Yunpeng Liu-Lupo, James Dongjoo Ham, Swarna K. A. Jeewajee, Lan Nguyen, Toni Delorey, Azucena Ramos, David M. Weinstock, Aviv Regev, Michael T. Hemann
Summary: The study used single-cell RNA-Seq and computational inference to identify key differences between near-haploid and diploid leukemia cells. They found that RAD51B, a component of the homologous recombination pathway, is an essential gene in near-haploid leukemia. Furthermore, RAD51B and its associated genes were overexpressed in near-haploid leukemia patients, suggesting that RAD51B could be a promising target for therapy in this treatment-resistant disease.
BLOOD CANCER JOURNAL
(2023)
Article
Biology
Jack G. Rayner, Thomas J. Hitchcock, Nathan W. Bailey
Summary: Recent research suggests that dosage compensation on the X chromosome scales phenotypic effects between the sexes, with incomplete dosage compensation potentially leading to female-biased effects on X-linked alleles.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Emily C. Moore, Patrick J. Ciccotto, Erin N. Peterson, Melissa S. Lamm, R. Craig Albertson, Reade B. Roberts
Summary: For many vertebrates, a single genetic locus initiates a cascade of developmental sex differences, resulting in adults with two phenotypically distinct sexes. However, species with polygenic sex determination have multiple interacting sex determination alleles, allowing for more than two genotypic sexes. In the cichlid fish Metriaclima mbenjii, polygenic sex determination produces modular variation in morphological and behavioral traits, and the evolution or introgression of a newly acquired sex determiner creates additional axes of phenotypic variation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Othman Al-Dossary, Bader Alsubaie, Ardashir Kharabian-Masouleh, Ibrahim Al-Mssallem, Agnelo Furtado, Robert J. Henry
Summary: The genome sequences of male and female jojoba plants show significant differences in sex chromosomes, with large insertions and novel genes found in the Y chromosome compared to the X chromosome. The wide divergence of sex chromosomes suggests long-term adaptation to diverging sex-specific roles, potentially driven by factors such as differing reproductive resource allocation requirements and the stress of the desert environment. These sex-determining regions accumulate beneficial genes for each sex, leading to the evolution of many novel sex-specific genes which could be a valuable source for manipulation of reproductive performance and environmental adaptation in crops.
Article
Evolutionary Biology
Garett P. Slater, Amy L. Dapper, Brock A. Harpur
Summary: Many species have separate haploid and diploid phases, which should be influenced by evolutionary forces differently. In this study, we used a multiomic approach in honey bees to investigate the evolutionary rates of haploid-biased genes and the relative effects of sexual and haploid expression on molecular evolution. We found that the evolutionary rate of haploid-biased genes is higher compared to diploid-based genes, but when accounting for ploidy and sex, both types of genes evolve at a lower rate than expected.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Christopher R. Cooney, Judith E. Mank, Alison E. Wright
Summary: Research shows that sex differences in recombination rates are evolutionarily labile and not driven by simple neutral processes, contradicting nonadaptive explanations. While there is potential for adaptive processes in the patterns of heterochiasmy, the direct link to sexual selection or sexual conflict across species is unclear, indicating subtle or complex effects. Additionally, evidence suggests correlated rates of recombination rate evolution between males and females, suggesting genetic constraints and sexual conflict over the recombination landscape.
Review
Cell Biology
Francesca Terrin, Annachiara Tesoriere, Nicoletta Plotegher, Luisa Dalla Valle
Summary: Sex hormones and genes on sex chromosomes play a crucial role in sexual differentiation, reproduction, and brain homeostasis. They are important for brain development and function, as well as the predisposition and progression of neurodegenerative diseases. This review focuses on the impact of biological sex on brain development and its role in neurodegenerative diseases, particularly Parkinson's disease. It highlights the significance of considering sex in the study of brain physiology and pathology to better understand disease etiology and develop tailored therapeutic strategies.
Review
Biochemistry & Molecular Biology
Ewa Starosta, Justyna Szwarc, Janetta Niemann, Katarzyna Szewczyk, Dorota Weigt
Summary: Rapeseed is an important oil crop and the demand for oil requires the development of new cultivars. Double haploid technology is a convenient approach for plant breeding and genetic research. Brassica napus is a model species for double haploid production, but the molecular mechanisms are not well understood. New methods have been reported for double haploid rapeseed production, and this review covers the latest findings and advances in Brassica napus double haploid production.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Serik Eliby, Sara Bekkuzhina, Olena Kishchenko, Gulnur Iskakova, Gulnar Kylyshbayeva, Satyvaldy Jatayev, Kathleen Soole, Peter Langridge, Nikolai Borisjuk, Yuri Shavrukov
Summary: Doubled haploid production is a valuable biotechnology that accelerates the breeding of new wheat varieties and plays important roles in studying genetic control, marker-assisted selection, genomics, and genetic engineering in wheat. This paper reviews recent advances in androgenesis and gynogenesis techniques, with a focus on the in vitro culture phase, and the emerging innovative approaches in researching and producing wheat doubled haploids. The use of CRISPR-based genome editing for inducing doubled haploids in wheat is also discussed.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Plant Sciences
Haiqin Yao, Delphine Scornet, Murielle Jam, Cecile Herve, Philippe Potin, Lydie Oliveira Correia, Susana M. Coelho, J. Mark Cock
Summary: The life cycle of the filamentous brown alga Ectocarpus involves alternation between sporophyte and gametophyte generations, with deployment of the sporophyte developmental program requiring specific transcription factors. The sporophyte generation secretes a diffusible factor that may belong to the arabinogalactan proteins family.
JOURNAL OF PHYCOLOGY
(2021)
Article
Environmental Sciences
Alexander Jueterbock, Antoine J. P. Minne, J. Mark Cock, Melinda A. Coleman, Thomas Wernberg, Lydia Scheschonk, Ralf Rautenberger, Jie Zhang, Zi-Min Hu
Summary: Marine macrophytes play a crucial role in coastal ecosystems, but face threats from climate change and other human-induced stressors. Studies suggest that priming these plants with heat stress may enhance their resilience to future temperature fluctuations.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Ecology
Svenja Heesch, Martha Serrano-Serrano, Josue Barrera-Redondo, Remy Luthringer, Akira F. Peters, Christophe Destombe, J. Mark Cock, Myriam Valero, Denis Roze, Nicolas Salamin, Susana M. Coelho
Summary: A study on the evolution of life cycles in brown algae revealed that diploid growth evolves when sexual reproduction is preferred over asexual reproduction. The research also found that haploid sex determination is ancestral to diploid sex determination, and isogamous species in brown algae evolved from anisogamous ancestors, contrary to the commonly reported pattern of evolution from isogamy to anisogamy.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Biochemical Research Methods
Sarah R. Rommelfanger, Mowei Zhou, Henna Shaghasi, Shin-Cheng Tzeng, Bradley S. Evans, Ljiljana Pasa-Toli, James G. Umen, James J. Pesavento
Summary: An updated analysis of linker and core histone proteins in the green microalga Chlamydomonas reinhardtii was conducted using top-down mass spectrometry, revealing 86 proteoforms. Variants with high levels of acetylation were identified among the canonical histones, emphasizing the presence of diverse protein forms in this organism.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Plant Sciences
Inmaculada Couso, Amanda L. Smythers, Megan M. Ford, James G. Umen, Jose L. Crespo, Leslie M. Hicks
Summary: This study reveals the synergistic role of inositol pyrophosphates and TOR signaling in coordinating cell growth and lipid metabolism in green algae. The inhibitory effect of rapamycin on TOR signaling is more significant in the vip1-1 mutant compared to wild-type, highlighting the independent yet coordinated interaction between InsPs and TOR. Additionally, phosphorylation patterns of photosystem proteins are affected by light stress and other stresses, indicating a novel role for inositol pyrophosphates and TOR signaling in response to environmental cues.
Review
Genetics & Heredity
Bernard Kloareg, Yacine Badis, J. Mark Cock, Gurvan Michel
Summary: Multicellular eukaryotes have an expanded extracellular matrix that plays essential roles in tissue texture, cell screening, development, and immunity. The expansion of ECM in multicellular marine algae is crucial for the acquisition of complex multicellularity through various innovations, leading to convergences in ECM structures and functions across algae, animals, and plants.
Article
Genetics & Heredity
Yang-Tsung Lin, Tomomi Takeuchi, Brian Youk, James Umen, Barbara B. Sears, Christoph Benning
Summary: In the green alga Chlamydomonas reinhardtii, the CHT7 protein plays a critical role in regulating the cell cycle, affecting cell morphology, division, and survival. CHT7 has an opposite regulatory role to mitotic cyclin-dependent kinases, and its absence leads to abnormal expression of cell wall synthesis and remodeling genes. Furthermore, the loss of CHT7 results in the misregulation of minimally characterized kinases, some of which are related to MAP3K and Aurora-like kinases.
G3-GENES GENOMES GENETICS
(2022)
Editorial Material
Genetics & Heredity
J. Mark Cock
Article
Biochemistry & Molecular Biology
Shingo Akita, Christophe Vieira, Takeaki Hanyuda, Florence Rousseau, Corinne Cruaud, Arnaud Couloux, Svenja Heesch, J. Mark Cock, Hiroshi Kawai
Summary: Analyses of nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders provide significant support for resolving phylogenetic relationships within the studied taxa, confirming relationships seen in other sequences such as nuclear, chloroplast, and mitochondrial. This suggests that nuclear protein coding sequences may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Josselin Gueno, Michael Borg, Simon Bourdareau, Guillaume Cossard, Olivier Godfroy, Agnieszka Lipinska, Leila Tirichine, J. Mark Cock, Susana M. Coelho
Summary: In many eukaryotes, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. The regulation of sex-biased gene expression during sexual differentiation remains unclear. This study investigates the epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, finding that chromatin signatures correlated with gene expression and histone PTMs changes occurred preferentially at sex-specific genes. The chromatin landscape of UV sex chromosomes differs from autosomes, likely driven by evolutionary young genes in the pseudoautosomal regions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Ecology
Guillaume G. Cossard, Olivier Godfroy, Zofia Nehr, Corinne Cruaud, J. Mark Cock, Agnieszka P. Lipinska, Susana M. Coelho
Summary: The study reveals that the transition to co-sexuality in brown algae involves adaptive gene expression changes and rapid sequence evolution. The gene expression profiles of co-sexual species are more similar to those of ancestral females rather than males. Convergent gene expression changes are associated with the transition to co-sexuality.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Plant Sciences
Daniela Strenkert, Asli Yildirim, Juying Yan, Yuko Yoshinaga, Matteo Pellegrini, Ronan C. O'Malley, Sabeeha S. Merchant, James G. Umen
Summary: Chromatin modifications, specifically mono- and trimethylated histone H3 lysine 4 (H3K4), were investigated in different phases of the Chlamydomonas cell cycle. The study revealed that trimethylated H3K4 was enriched at transcription start sites of most protein coding genes, while mono-methylated H3K4 was the default state for histones outside of these sites. Additionally, DNA cytosine methylation was found to be enriched in regions lacking H3K4 methylation, and genes within these regions showed poor expression. The study also used H3K4me3 ChIP-seq data to validate long non-coding RNA genes.
Article
Plant Sciences
J. Mark Cock
JOURNAL OF PHYCOLOGY
(2023)
Article
Biochemical Research Methods
Simon Bourdareau, Olivier Godfroy, Josselin Gueno, Delphine Scornet, Susana M. Coelho, Leila Tirichine, J. Mark Cock
Summary: This article introduces a chromatin immunoprecipitation method for brown algal genomic research, which can reveal the importance of gene regulation in brown algae through the detection and analysis of post-translational modifications. It effectively addresses the challenge of extracting chromatin from cells protected by a resistant cell wall.
METHODS AND PROTOCOLS
(2022)
Article
Biotechnology & Applied Microbiology
Simon Bourdareau, Leila Tirichine, Berangere Lombard, Damarys Loew, Delphine Scornet, Yue Wu, Susana M. Coelho, J. Mark Cock
Summary: The study identified 47 histone post-translational modifications in brown algae, including a novel mark H2AZR38me1, while lacking H3K27me3 and major polycomb complexes. The findings show stable patterns of histone modifications throughout the life cycle, with specific chromatin marks correlating with gene expression levels. This overview sets a foundation for future research on chromatin modifications in regulating brown algal genomes.
