Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary classification of sexes DOI Open Access
Chen Xie, Sven Künzel, Diethard Tautz

et al.

Published: Aug. 16, 2024

The phenotypic differences between the sexes are generated by genes with sex-biased expression. These range from a few major regulators to large numbers of organ-specific effector in sexually mature individuals. We explore variation and evolutionary patterns these dataset natural populations sub-species species mice across an distance 2 million years. Intriguingly, even within short phylogenetic distances, we find extremely fast turnover gene expression adaptive protein evolution. To capture individual variances expression, have developed index (SBI) that represents cumulative all for each organ. SBI distributions often overlapping do not correlate organs, thus defying simple binary sex distinction given Comparison data humans shows fewer most organs strongly sexes. conclude subject particularly evolution, no long-term stability male or female characteristics sex-related characters is usually

Language: Английский

Recent progress in understanding the genomic architecture of sexual conflict DOI Creative Commons
Peter D. Price,

Sylvie M Parkus,

Alison E. Wright

et al.

Current Opinion in Genetics & Development, Journal Year: 2023, Volume and Issue: 80, P. 102047 - 102047

Published: May 8, 2023

Genomic conflict between the sexes over shared traits is widely assumed to be resolved through evolution of sex-biased expression and subsequent emergence sexually dimorphic phenotypes. However, while there support for a broad relationship genome-wide patterns level sexual conflict, recent studies suggest that sex differences in nature strength interactions loci are instead key resolution. Furthermore, advent new technologies measuring perturbing means we now have much more power detect genomic signatures conflict. Here, review our current understanding architecture light these highlight potential novel approaches address outstanding knowledge gaps.

Language: Английский

Citations

6
Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues DOI Creative Commons
Bryan B. Teefy, Aaron J.J. Lemus, Ari Adler

et al.

Cell Reports, Journal Year: 2023, Volume and Issue: 42(10), P. 113237 - 113237

Published: Oct. 1, 2023

The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, spleen. We annotate 22 cell types, define marker genes, infer differentiation trajectories. find pervasive sex-dimorphic across types. Sex-dimorphic genes tend to linked lipid metabolism, consistent with clear differences storage vs. livers. use machine learning predict sex using identify potential markers molecular identity. As proof principle, show our used deconvolute existing bulk RNA sequencing (RNA-seq) data obtain accurate estimates type proportions. This resource community could leveraged develop cell-type-specific transgenic animals.

Language: Английский

Citations

4
Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle DOI Creative Commons

Shreya Ramakanth,

Taylor Kennedy,

Berk Yalcinkaya

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 27, 2024

Abstract The life cycle of biomedical and agriculturally relevant eukaryotic microorganisms involves complex transitions between proliferative non-proliferative states such as dormancy, mating, meiosis, cell division. New drugs, pesticides, vaccines can be created by targeting specific stages parasites pathogens. However, defining the structure a microbial often relies on partial observations that are theoretically assembled in an ideal path. To create more quantitative approach to studying complete cycles, we generated deep learning-driven imaging framework track across sexually reproducing generations. Our combines microfluidic culturing, stage-specific segmentation microscopy images using convolutional neural networks, novel tracking algorithm, FIEST, based enhancing overlap single masks consecutive through learning video frame interpolation. As proof principle, used this quantitatively image compare growth regulation sexual Saccharomyces cerevisiae . We developed fluorescent reporter system fluorescently labeled Whi5 protein, yeast analog mammalian Rb, new High-Cdk1 activity sensor, LiCHI, designed report during DNA replication, mitosis, meiotic homologous recombination, meiosis I, II. found preceded exit from mitotic G1, pre-meiotic G0 spore state germination. A decrease total concentration characterized states, which is consistent with dilution model. nuclear accumulation was developmentally regulated, being at its highest formation. temporal coordination division not significantly different three could characterize other single-cell cycles remain incompletely described. An off-the-shelf user interface Yeastvision provides free access our processing algorithms.

Language: Английский

Citations

1
Sex-biased gene expression across tissues reveals unexpected differentiation in the gills of the threespine stickleback DOI Creative Commons
Florent Sylvestre, Nadia Aubin‐Horth, Louis Bernatchez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 9, 2024

Abstract Sexual dimorphism can evolve through sex-specific regulation of the same gene set. However, sex chromosomes also facilitate this by directly linking expression to sex. Moreover, differences in content between heteromorphic contributes sexual dimorphism. Understanding patterns sex-biased across organisms is important for gaining insight about evolution and chromosomes. studying species with recently established help understand evolutionary dynamics loss dosage compensation. The three-spined stickleback known its strong dimorphism, especially during reproductive period. Sex determined a young XY chromosome pair non-recombining region divided three strata, which have started degenerate. Using high multiplexing capability 3′ QuantSeq sequence transcriptome liver, gills brain, we provide first characterization transcriptomes from ∼80 (40 males 40 females) collected natural population We find that liver extremely differentiated sexes (36% autosomal genes) reflects ongoing reproduction, while brain shows very low levels differentiation (0.78%) no functional enrichment. Finally, exhibit (5%), suggesting should be considered physiological ecotoxicological studies gill responses fishes. hemizygous genes mainly driven lack conserved copies on both likely degeneration Y allele down-regulation male-beneficial mutations X chromosome.

Language: Английский

Citations

1
Molecular Mechanisms of Temperature Tolerance Plasticity in an Arthropod DOI Creative Commons
Anne Aagaard, Jesper Bechsgaard, Jesper Givskov Sørensen

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(8)

Published: July 26, 2024

How species thrive in a wide range of environments is major focus evolutionary biology. For many species, limited genetic diversity or gene flow among habitats means that phenotypic plasticity must play an important role their capacity to tolerate environmental heterogeneity and colonize new habitats. However, we have understanding the molecular components govern ecologically relevant phenotypes. We examined this hypothesis spider (Stegodyphus dumicola) with extremely low species-wide nevertheless occupies broad thermal environments. determined responses temperature stress individuals from four climatic zones using common garden acclimation experiments disentangle adaptations. Simultaneously, created data sets on multiple modalities: genome, transcriptome, methylome, metabolome, bacterial microbiome determine associations responses. Analyses reveal transcriptome metabolome correlate patterns tolerance. Surprisingly, genes whose expression seemed be involved tolerance were generally highly methylated contradicting idea DNA methylation stabilizes expression. This suggests function invertebrates varies not only but also genes. The was stable across period; combined our previous demonstrations temporally wild populations, convincing evidence does facilitate Our results suggest population-specific variation temperatures appears result evolution mainly

Language: Английский

Citations

1
Machine learning based analysis of single-cell data reveals evidence of subject-specific single-cell gene expression profiles in acute myeloid leukaemia patients and healthy controls DOI Creative Commons
Andreas C. Chrysostomou,

Cristina Furlan,

Edoardo Saccenti

et al.

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Journal Year: 2024, Volume and Issue: unknown, P. 195062 - 195062

Published: Oct. 1, 2024

Language: Английский

Citations

1
Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant DOI Creative Commons
Lei Zhao,

Wei Zhou,

Jun He

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Sept. 1, 2023

Sex-biased genes offer insights into the evolution of sexual dimorphism. genes, especially those with male bias, show elevated evolutionary rates protein sequences driven by positive selection and relaxed purifying in animals. Although rapid sequence sex-biased forces have been investigated animals brown algae, less is known about dioecious angiosperms. In this study, we separately compared expression between female floral buds flowers at anthesis Trichosanthes pilosa (Cucurbitaceae). buds, gene was pervasive, had significantly different roles dimorphism such as physiology. We observed higher for male-biased to female-biased unbiased genes. Male-biased under were mainly associated functions abiotic stress immune responses, suggesting that high are adaptive evolution. Additionally, may contribute accelerated generated duplication. Our findings, first time angiosperms, suggest evident advance our understanding patterns driving plants.

Language: Английский

Citations

3
Why is measuring and predicting fitness under genomic conflict so hard? DOI Creative Commons
Jessica K. Abbott, Katrine K. Lund‐Hansen, Colin Olito

et al.

Current Opinion in Genetics & Development, Journal Year: 2023, Volume and Issue: 81, P. 102070 - 102070

Published: June 25, 2023

Genomic conflict between the sexes is caused by differences in optimal male and female reproductive strategies, a major contributor to genetic, phenotypic, life history variation. While early experimental work appeared strongly support sexual paradigm, recent has produced more ambiguous results. Recent advances evolution studies combined with theoretical arguments can shed light on why measuring fitness under so challenging, including incidental alteration of mating dynamics, demographic effects, inherent complexity what quantity selection maximizes. We stress that non-intuitive results do not necessarily mean absence conflict, follow-up experiments determine priori predictions failed ultimately teach us than if they had been confirmed.

Language: Английский

Citations

2
Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant DOI Open Access
Lei Zhao,

Wei Zhou,

Jun He

et al.

Published: Jan. 8, 2024

Sex-biased genes offer insights into the evolution of sexual dimorphism. genes, especially those with male bias, show elevated evolutionary rates protein sequences driven by positive selection and relaxed purifying in animals. Although rapid sequence sex-biased forces have been investigated animals brown algae, less is known about dioecious angiosperms. In this study, we separately compared expression between female floral buds flowers at anthesis Trichosanthes pilosa (Cucurbitaceae). buds, gene was pervasive, had significantly different roles dimorphism such as physiology. We observed higher for male-biased to female-biased unbiased genes. Male-biased under were mainly associated functions abiotic stress immune responses, suggesting that high are adaptive evolution. Additionally, may contribute accelerated generated duplication. Our findings, first time angiosperms, suggest evident advance our understanding patterns driving plants.

Language: Английский

Citations

0
Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant DOI Open Access
Lei Zhao,

Wei Zhou,

Jun He

et al.

Published: Jan. 29, 2024

Sex-biased genes offer insights into the evolution of sexual dimorphism. genes, especially those with male bias, show elevated evolutionary rates protein sequences driven by positive selection and relaxed purifying in animals. Although rapid sequence sex-biased forces have been investigated animals brown algae, less is known about dioecious angiosperms. In this study, we separately compared expression between female floral buds flowers at anthesis Trichosanthes pilosa (Cucurbitaceae). buds, gene was pervasive, had significantly different roles dimorphism such as physiology. We observed higher for male-biased to female-biased unbiased genes. Male-biased under were mainly associated functions abiotic stress immune responses, suggesting that high are adaptive evolution. Additionally, may contribute accelerated generated duplication. Our findings, first time angiosperms, suggest evident advance our understanding patterns driving plants.

Language: Английский

Citations

0