PMEL is involved in snake colour pattern transition from blotches to stripes

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Сен. 3, 2024

Abstract Corn snakes are emerging models for animal colouration studies. Here, we focus on the Terrazzo morph, whose skin pattern is characterized by stripes rather than blotches. Using genome mapping, discover a disruptive mutation in coding region of Premelanosome protein ( PMEL ) gene. Our transcriptomic analyses reveal that expression significantly downregulated embryonic tissues. We produce corn snake knockouts, which present comparable phenotype to and subcellular structure their melanosomes xanthosomes also similarly impacted. single-cell wild-type dorsal demonstrate all chromatophore progenitors express at varying levels. Finally, show embryos -expressing cells initially uniformly spread before forming aggregates eventually blotches, as seen adults. In embryos, fail form. results provide insights into mechanisms governing patterning reptiles.

Язык: Английский

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Conserved features of recombination control in vertebrates

PLoS Biology, Год журнала: 2025, Номер 23(1), С. e3002959 - e3002959

Опубликована: Янв. 7, 2025

A recent study in PLOS Biology on the epigenetic recombination regulator PRDM9 salmonid fish reveals that its function has been preserved across vertebrates for hundreds of millions years, with rapidly evolving DNA-binding domains being a defining attribute.

Язык: Английский

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Regulatory and disruptive variants in the CLCN2 gene are associated with modified skin color pattern phenotypes in the corn snake

Genome biology, Год журнала: 2025, Номер 26(1)

Опубликована: Март 26, 2025

Abstract Background Snakes exhibit a broad variety of adaptive colors and color patterns, generated by the spatial arrangement chromatophores, but little is known mechanisms responsible for these spectacular traits. Here, we investigate mono-locus trait with two recessive alleles, motley stripe , that both cause pattern aberrations in corn snake. Results We use mapping-by-sequencing to identify genomic interval where causal mutations reside. With our differential gene expression analyses, find CLCN2 (Chloride Voltage-Gated Channel 2), within interval, significantly downregulated Motley embryonic skin. Furthermore, allele as insertion an LTR-retrotransposon resulting disruptive mutation protein. confirm involvement formation producing knock-out snakes present phenotype similar Stripe. In humans mice, disruption results leukoencephalopathy, well retinal testes degeneration. Our single-cell transcriptomic analyses reveal indeed expressed chromatophores during embryogenesis adult brain, behavior fertility Stripe are not impacted. Conclusions genomic, transcriptomic, functional plasma membrane anion channel be involved development show active might key driver diversification snakes.

Язык: Английский

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Germline mutation rates and fine-scale recombination parameters in zebra finch

PLoS Genetics, Год журнала: 2025, Номер 21(4), С. e1011661 - e1011661

Опубликована: Апрель 15, 2025

Most of our understanding the fundamental processes mutation and recombination stems from a handful disparate model organisms pedigree studies mammals, with little known about other vertebrates. To gain broader comparative perspective, we focused on zebra finch ( Taeniopygia castanotis ), which, like birds, differs mammals in its karyotype (which includes many micro-chromosomes), mechanism by which is directed to genome, aspects ontogenesis. We collected genome sequences three generation pedigrees that provide information 80 meioses, inferring 202 single-point de novo mutations, 1,088 crossovers, 275 non-crossovers. On basis, estimated sex-averaged rate 5.0 × 10 -9 per base pair generation, par have similar time (~2–3 years). Also as found paternal germline bias at later stages gametogenesis (of 1.7:1) but no discernible difference between sexes early development. Examining patterns, crossover macro-chromosomes 0.93 cM/Mb, pronounced enrichment crossovers near telomeres. In contrast, non-crossover rates are more uniformly distributed. micro-chromosomes, substantially higher (3.96 cM/Mb), accordance homeostasis, both events At finer scale, overlap CpG islands often than expected chance, absence PRDM9. Estimates degree GC-biased gene conversion (59%), mean tract length (~32 bp), non-crossover-to-crossover ratio (5.4:1) all comparable those reported primates mice. Therefore, properties resolutions remain over large phylogenetic distances.

Язык: Английский

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Unraveling the tempo and mode of horizontal gene transfer in bacteria

Trends in Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: Английский

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Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko

Evolution, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 26, 2024

Abstract Variation of recombination rate along the genome is crucial importance to rapid adaptation and organismal diversification. Many unknowns remain regarding how why landscapes evolve in nature. Here, we reconstruct maps based on linkage disequilibrium use subsampling simulations derive a new measure landscape evolution: Population Recombination Divergence Index (PRDI). Using PRDI, show that fine-scale differ substantially between two cichlid fish ecotypes Astatotilapia calliptera diverged only ~2,500 generations ago. Perhaps surprisingly, differences are not driven by divergence terms allele frequency (FST) nucleotide diversity (Δ(π)): although there some association, observe positive PRDI regions where FST Δ(π) zero. We found stronger association evolution 47 large haplotype blocks polymorphic Lake Masoko, cover 21% genome, appear include multiple inversions. Among blocks, strong clear degree heterozygosity, consistent with suppression heterozygotes. Overall, our work provides holistic view changes population during early stages speciation gene flow.

Язык: Английский

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Keeping it safe: control of meiotic chromosome breakage

Trends in Genetics, Год журнала: 2024, Номер unknown

Опубликована: Дек. 1, 2024

Язык: Английский

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2023 ASHG Scientific Achievement Award

The American Journal of Human Genetics, Год журнала: 2024, Номер 111(3), С. 425 - 427

Опубликована: Март 1, 2024

This article is based on the address given by author at 2023 meeting of The American Society Human Genetics (ASHG) in Washington, D.C. A video original can be found ASHG website. Thank you for kind introduction. I am deeply honored to receive this award, and occasion even more than usual, grateful many people who have helped me along way. Most obviously, Jay Shendure, wrote out blue say that he had nominated wish luck, Awards committee. would also like thank my letter writers, Sally Otto, Andy Clark, Aravinda Chakravarti, years wise counsel unstinting support. My research group interested exploring evolutionary roots genetic variation: how differences among humans arose, why they are maintained. For over a century now, we known variation arises from two processes, mutation recombination, shaped population demographic history our ancestors selective pressures which were subject.1Provine W.B. Origins theoretical genetics. University Chicago Press, Chicago, IL2001Crossref Google Scholar Over past 20 years, begun data finally characterize these different forces evaluate their relative importance.2Przeworski M. Hudson R.R. Di Rienzo A. Adjusting focus human variation.Trends Genet. 2000; 16: 296-302Abstract Full Text PDF PubMed Scopus (230) means aim build ground-up, comprehensive understanding instance, understand not just how, but why, trait often so polygenic3Boyle E.A. Li Y.I. Pritchard J.K. An Expanded View Complex Traits: From Polygenic Omnigenic.Cell. 2017; 169: 1177-1186Abstract (1651) Scholar,4Sella G. Barton N.H. Thinking About Evolution Traits Era Genome-Wide Association Studies.Annu. Rev. Genomics Hum. 2019; 20: 461-493Crossref (117) Scholar; some disease mutations frequent populations others5Amorim C.E.G. Gao Z. Baker Diesel J.F. Simons Y.B. Haque I.S. Pickrell J. Przeworski genetics disease: case recessive, lethal mutations.PLoS 13e1006915Crossref (29) or what fraction heritable under selection.6Chakravarti Commentary: central questions genetics: Richard Lewontin's 1968 senior lecture Victor McKusick's Bar Harbor short course.Int. Epidemiol. 2016; 45: 668-672Crossref (1) decade, lab has been especially processes new variants arise: recombination. What particularly exciting about working area basic remain unanswered.7Ségurel L. Wyman M.J. Determinants rate germline.Annu. 2014; 15: 47-70Crossref (198) Scholar,8Moorjani P. Germline Mutation Erratic Evolutionary Clock.PLoS Biol. 14e2000744Crossref (40) To give one example, it was long believed sex bias germline mutation—the fact fathers transmit point mothers—reflects cell divisions rise sperm older fathers.9Crow origins, patterns implications spontaneous mutation.Nat. 1: 40-47Crossref (683) Yet, as showed, actually very similar parents ages,10Gao Moorjani Sasani T.A. Pedersen B.S. Quinlan A.R. Jorde L.B. Amster Overlooked roles DNA damage maternal age generating mutations.Proc. Natl. Acad. Sci. USA. 116: 9491-9500Crossref (107) across mammals with drastically reproductive lifespans.11Wu F.L. Strand A.I. Cox L.A. Ober C. Wall J.D. comparison baboons suggests rates do track divisions.PLoS 2020; 18e3000838Crossref Scholar,12de Manuel Wu paternal widespread amniotes arise independently division numbers.Elife. 2022; 11Crossref (13) More generally, analyses suggest contrary believed, most divisions, instead incorrectly repaired.13Spisak N. de Milligan W. Sella Disentangling sources clock-like soma.bioRxiv. 2023; https://doi.org/10.1101/2023.09.07.556720v1Crossref Along Bernard Massy, Peter Donnelly, Anjali Hinch, Gil McVean, Simon Myers, others, worked toward recombination events directed genome during meiosis. We now know humans, binding PRDM9 specifies location almost all events, turnover affinity drives rapid evolution hotspots within between species.14Baudat F. Buard Grey Fledel-Alon Coop Massy B. major determinant meiotic mice.Science. 2010; 327: 836-840Crossref (721) Scholar,15Myers S. Bowden R. Tumian Bontrop R.E. Freeman MacFie T.S. McVean Donnelly Drive against hotspot motifs primates implicates gene recombination.Science. 876-879Crossref (493) Scholar,16Hinch A.G. Zhang Becker P.W. Moralli D. Hinch Davies Factors influencing revealed whole-genome sequencing single sperm.Science. 363https://doi.org/10.1126/science.aau8861Crossref (64) Scholar,17Auton Pfeifer Venn O. Ségurel Street T. Leffler E.M. Aneas I. Broxholme et al.A fine-scale chimpanzee map sequencing.Science. 2012; 336: 193-198Crossref (210) Scholar,18Altemose Noor Bitoun E. Imbeault Chapman J.R. Aricescu Myers S.R. provides evidence novel behaviors other zinc-finger proteins meiosis.Elife. 6https://doi.org/10.7554/eLife.28383Crossref (55) learned vertebrates, such dogs birds, lack use strategies, result stable landscapes.19Singhal Sannareddy K. Turner Hooper D.M. Q. Raney Balakrishnan C.N. al.Stable birds.Science. 2015; 350: 928-932Crossref (183) Scholar,20Auton Rui Y. Kidd Oliveira Nadel Holloway Hayward J.J. Cohen P.E. Greally J.M. Wang al.Genetic targeted towards promoter regions dogs.PLoS 2013; 9e1003984Crossref (136) In yet species, snakes, turns strategies co-exist.21Hoge Mahgoub Okami Fuller Banerjee McNulty Andolfatto Macfarlan al.Patterns snakes reveal tug war promoter-like features.bioRxiv. https://doi.org/10.1101/2023.07.11.548536v1Crossref parallel, better dynamics natural selection humans. Together Graham Coop, Joe Pickrell, Jonathan Pritchard, Guy Sella, showed adaptations act large effect rapidly frequency until fix population.22Hernandez R.D. Kelley J.L. Elyashiv Melton S.C. Auton 1000 Genomes ProjectClassic sweeps rare recent evolution.Science. 2011; 331: 920-924Crossref (317) Scholar,23Pritchard adaptation: hard sweeps, soft polygenic adaptation.Curr. R208-R215Abstract (627) Instead, traits interest likely involved concomitant alleles much smaller effect. These findings shifted adaptation motivated current efforts GWAS elucidate played globe.24Harpak changing environments.PLoS 2021; 19e3001072Crossref (24) Scholar,25Mostafavi H. Berisa Day F.R. Perry J.R.B. Identifying affect viability cohorts.PLoS 15e2002458Crossref (47) Scholar,26Berg signal adaptation.PLoS 10e1004412Crossref (315) Scholar,27Edge M.D. Reconstructing History Scores Using Coalescent.Trees. Genetics. 211: 235-262Google Scholar,28Sanjak J.S. Sidorenko Robinson M.R. Thornton K.R. Visscher P.M. Evidence directional stabilizing contemporary humans.Proc. 2018; 115: 151-156Crossref (69) Scholar,29Field Boyle Telis Gaulton K.J. Golan Yengo Rocheleau Froguel McCarthy M.I. al.Detection 2000 years.Science. 354: 760-764Crossref (241) Scholar,30Speidel Forest Shi method genome-wide genealogy estimation thousands samples.Nat. 51: 1321-1329Crossref (199) Scholar,31Mathieson 40,000 years.Curr. Opin. Dev. 62: 97-104Crossref (18) Much work describe done since moved Columbia University, 10 ago. But I'd take opportunity go back time acknowledge contributed professional fortunes—and beyond that, highlight role solidarity, scientific success. never studied reached Brian Charlesworth, took chance when knew no biology, thanks whom accepted into exactly six graduate programs applied. Ecology Department entered PhD student turned an unrivaled environment introduced quantitative genetics, part because Deborah advisor Hudson, Marty Kreitman, faculty members, amazing cohort students postdocs landed, including Andolfatto, Magnus Nordborg, Jeff Wall. particular, owe entrance genetics; him few key pep talks, more. good luck continued last year PhD, came through talk, encouraged join him, Matthew Stephens, others postdoc Oxford. That too exceptional constellation people—including time, started member, more—and statistical intellectual experience community thinking ever since. later reunited member where ran labs side several years. department founded Nancy Cox, Anna Rienzo, Carole Ober, quarter start, fostered unique conversation Yet again, lucky: myself vibrant, collegial high standards real sense excitement. nurtured protected chairs, Conrad Gilliam Ober. Now longer managed pull off granted, realize fortune starting career there, particular Anna. being inspiring colleague loyal friend decades now; it's imagine path accompanied it. huge influences great friends Finally, immense debt gratitude 40 world somehow made way lab. As sometimes well appreciated, science fundamentally social activity: its best, offers every background common language shared mysteries solve. enjoyed aspect all, present members countless discussions, arguments, explanations—and else failed, senses humor.

Язык: Английский

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Competition between sites of meiotic recombination in snakes

Nature Reviews Genetics, Год журнала: 2024, Номер 25(5), С. 304 - 304

Опубликована: Март 12, 2024

Язык: Английский

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Rapid evolution of fine-scale recombination during domestication

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 6, 2024

ABSTRACT Recombination serves as a central force driving the evolution of genomic diversity in sexually reproducing organisms. Despite its fundamental role, evolutionary dynamics recombination rates remain largely elusive. The domestication animals, characterized by dynamic selective pressures, provides unique lens through which to investigate these phenomena. Here, we constructed fine-scale map using whole-genome data from domestic chickens, including both contemporary commercial breeds and their wild progenitor, Red Junglefowl (RJF). Our analysis reveals rapid landscape within between chicken populations, find that average rate decreased during domestication. Remarkably, this trend is further corroborated re-analysis genomes several species ducks, goats, pigs, sheep. Contrary hypothesis leads an increase rates, our results provide no support for such scenario. We suggest low beneficial maintaining uniform stable phenotypes inbreeding. Furthermore, significant variation hotspots across particularly pronounced despite recent divergence. turnover coldspots appears be closely linked sweeps. Interestingly, contrast prevailing observations most species, long-term inbreeding negative correlation frequency introgressed ancestry other RJF subspecies. insights into complex interplay forces shaping recombination.

Язык: Английский

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