Convergent genomic signatures associated with vertebrate viviparity

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Feb. 8, 2024

Abstract Background Viviparity—live birth—is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree Life. Viviparous species exhibit remarkable levels reproductive diversity, both in amount care provided by parent during gestation, ways which is delivered. The genetic basis viviparity garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, thus not able to address changes occurring broader scale. Using whole genome data, we investigated molecular this innovation diversity vertebrates answer long held question biology: evolution convergent traits driven genomic changes? Results We reveal protein family sizes, protein-coding regions, introns, untranslated regions (UTRs) number distantly related viviparous lineages. Specifically, identify 15 families showing evidence contraction or expansion associated with viviparity. additionally elevated substitution rates coding noncoding sequences several However, did find any changes—be it at nucleotide level—common all Conclusions Our results highlight value macroevolutionary comparative genomics determining transitions. While may be vertebrates, there does appear signature shared vertebrates. Ultimately, our findings indicate trait as likely evolves multiple different pathways.

Language: Английский

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Comparative molecular landscapes of immature neurons in the mammalian dentate gyrus across species reveal special features in humans

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species specialized features in humans remain poorly understood. Here we performed machine learning-augmented analysis of published single-cell RNA-sequencing datasets identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs, mice showed few shared (such as DPYSL5), mostly species-specific gene expression that converged onto common biological processes regulating development. We further human-specific transcriptomic demonstrated functional roles human imGC-enriched a family proton-transporting vacuolar-type ATPase subtypes development derived pluripotent stem cells. study reveals divergent patterns convergent the molecular characteristics species, highlighting importance conducting independent analyses for different species.

Language: Английский

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Trophoblast Fusion in Hypertensive Disorders of Pregnancy and Preeclampsia

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(7), P. 2859 - 2859

Published: March 21, 2025

Trophoblast fusion into the multinucleated syncytiotrophoblast (SCT) appears as an inescapable feature of placentation in mammals and other viviparous species. The trophoblast cells underlying syncytium are considered a reservoir for restoration aging peripheric structure. transition from trophoblasts to SCTs has be tightly regulated, could altered by genetic anomalies or environmental exposure. resulting defective placental function one causes major diseases, such preeclampsia (PE) Intra-Uterine Growth Restriction (IUGR). This review attempts take stock current knowledge about mechanisms their deregulations.

Language: Английский

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Genome‐Wide Mining of lncRNAs Reveals Their Potential Regulatory Role in the Evolution of Viviparity

Integrative Zoology, Journal Year: 2025, Volume and Issue: unknown

Published: April 28, 2025

ABSTRACT Reproduction in vertebrates usually involves egg‐laying (oviparity) or live‐bearing (viviparity). Oviparity is the ancestral trait from which viviparity has independently evolved more than 100 times squamate reptiles. This transition a series of physiological and structural changes, including degeneration eggshell evolution placenta differences temporal spatial expression patterns some functional genes that drive transformation. Long non‐coding RNAs (lncRNAs) play important roles regulation gene expression, yet it remains unclear whether they participate shifts during oviparity to viviparity, if so how. Therefore, we employ deep mining identify novel lncRNAs closely related oviparous‐viviparous pair lizards ( Phrynocephalus przewalskii P. vlangalii ). We construct cis‐ trans‐regulatory networks between target using transcriptomic data oviduct uteri tissues across reproductive periods. Results show regulate gland developmental oviparous lizard are lost less expressed viviparous lizard. A number involved placental development embryo attachment species have no orthologs species, others little expression. Accordingly, may regulatory changes viviparity. These results open doors further elucidation genetic networks.

Language: Английский

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Egg Yolk Protein Homologs Identified in Live-Bearing Sharks: Co-Opted in the Lecithotrophy-to-Matrotrophy Shift?

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(3)

Published: Feb. 20, 2023

Abstract Reproductive modes of vertebrates are classified into two major embryonic nutritional types: yolk deposits (i.e., lecithotrophy) and maternal investment matrotrophy). Vitellogenin (VTG), a egg protein synthesized in the female liver, is one molecules relevant to lecithotrophy-to-matrotrophy shift bony vertebrates. In mammals, all VTG genes lost following shift, it remains be elucidated whether nonmammalians also associated with repertoire modification. this study, we focused on chondrichthyans (cartilaginous fishes)—a vertebrate clade that underwent multiple shifts. For an exhaustive search homologs, performed tissue-by-tissue transcriptome sequencing for viviparous chondrichthyans, frilled shark Chlamydoselachus anguineus spotless smooth-hound Mustelus griseus, inferred molecular phylogeny its receptor very low-density lipoprotein (VLDLR), across diverse As result, identified either three or four orthologs including species. We showed had additional VLDLR previously unrecognized their unique lineage (designated as VLDLRc2 VLDLRc3). Notably, gene expression patterns differed species studied depending reproductive mode; VTGs broadly expressed tissues, uterus, sharks, addition liver. This finding suggests do not only function nutrient but matrotrophic factor. Altogether, our study indicates was achieved through distinct evolutionary process from mammals.

Language: Английский

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Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 22(5), P. 1282 - 1298

Published: Dec. 20, 2023

The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly power natural selection. underlying genetic mechanisms have important implications to understand how genome evolves under environmental challenges. In cereal crops, both rice barley can develop black-coloured husk/pericarp due melanin accumulation. However, it unclear if this shares a common origin. Here, we fine-mapped HvBlp gene controlling black confirmed its function by silencing. result was further supported yellow mutant with deletion gene, derived from gamma ray radiation wild-type W1. encodes putative tyrosine transporter homologous husk OsBh4 rice. Surprisingly, synteny phylogenetic analyses showed that belonged different lineages resulted dispersed tandem duplications, respectively, suggesting has emerged independently. duplication (dated at 21.23 MYA) yielding occurred exclusively ancestor Triticeae. displayed converged transcription tissues, contributing trait. Further transcriptome metabolome data identified critical candidate genes metabolites related production barley. Taken together, our study described compelling case convergent evolution transcriptional convergence after duplication, providing valuable insights into phenotypic evolution. identification also great potential breeding for stress-resilient varieties higher nutritional values.

Language: Английский

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Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(10)

Published: Oct. 1, 2023

The transition from oviparity to viviparity has occurred independently over 150 times across vertebrates, presenting one of the most compelling cases phenotypic convergence. However, whether repeated, independent evolution is driven by redeployment similar genetic mechanisms and these leave a common signature in genomic divergence remains largely unknown. Although recent investigations into have demonstrated striking similarity among genes molecular pathways involved disparate vertebrate groups, quantitative tests for genome-wide convergent provided ambivalent answers. Here, we investigate potential role convergence during transitions an order ray-finned freshwater fish (Cyprinodontiformes). We assembled de novo genomes utilized publicly available viviparous oviparous species test both coding noncoding regions. found no evidence excess amino acid substitutions rates sequence divergence, implying changes are associated with transitions. statistical power biological confounds could constrain our ability detect significant correlated evolution. therefore identified candidate signatures Cyprinodontiformes lineages. Motif enrichment gene ontology analyses suggest transcriptional early morphogenesis, brain development, immunity alongside viviparity. Overall, however, findings indicate that not strongly convergence, but few show convincing

Language: Английский

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Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts

Science China Life Sciences, Journal Year: 2023, Volume and Issue: 66(11), P. 2629 - 2645

Published: May 31, 2023

Language: Английский

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Adaptive structural and functional evolution of the placenta protects fetal growth in high-elevation deer mice

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(25)

Published: June 12, 2023

Environmental hypoxia challenges female reproductive physiology in placental mammals, increasing rates of gestational complications. Adaptation to high elevation has limited many these effects humans and other offering potential insight into the developmental processes that lead protect against hypoxia-related However, our understanding adaptations been hampered by a lack experimental work linking functional, regulatory, genetic underpinnings development locally adapted populations. Here, we dissect high-elevation adaptation deer mice (Peromyscus maniculatus), rodent species with an exceptionally broad elevational distribution emerged as model for adaptation. Using acclimations, show lowland experience pronounced fetal growth restriction when challenged hypoxia, while highland maintain normal expanding compartment placenta facilitates nutrient gas exchange between parent fetus. We then use compartment-specific transcriptome analyses adaptive structural remodeling is coincident widespread changes gene expression within this same compartment. Genes associated significantly overlap genes involved human development, pointing conserved or convergent pathways underlying processes. Finally, overlay results data from natural populations identify candidate genomic features contribute adaptations. Collectively, experiments advance hypoxic environments revealing physiological mechanisms shape trajectories under maternal hypoxia.

Language: Английский

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Functional characterization of luciferase in a brittle star indicates parallel evolution influenced by genomic availability of haloalkane dehalogenase

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

Published: Oct. 17, 2024

Determining why convergent traits use distinct versus shared genetic components is crucial for understanding how evolutionary processes generate and sustain biodiversity. However, the factors dictating underpinnings of remain incompletely understood. Here, we heterologous protein expression, biochemical assays, phylogenetic analyses to confirm origin a luciferase gene from haloalkane dehalogenases in brittle star

Language: Английский

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