Gene Gain and Loss from the Asian Corn Borer W Chromosome DOI Open Access
Wenting Dai, Judith E. Mank, Liping Ban

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 21, 2022

Abstract We built a chromosome-level genome assembly of the Asian corn borer, Ostrinia furnacalis Guenée (Lepidoptera: Pyralidae, Pyraloidea), an economically important pest in corn, from female, including both Z and W chromosome. Despite deep conservation chromosome across Lepidoptera, our reveals little with available sequence related species or chromosome, consistent non-canonical origin The has accumulated significant repetitive elements experienced rapid gene gain remainder genome, most genes exhibiting pseudogenization after duplication to W. that retain expression are largely enriched for functions DNA recombination, nucleosome, chromatin binding, likely meiotic mitotic processes within female gonad.

Language: Английский

Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data DOI Creative Commons
Vivak Soni, Jeffrey D. Jensen

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

Published: Sept. 22, 2024

The demographic history of a population, and the distribution fitness effects (DFE) newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation evolutionary trajectories. Although DFE inference has been performed extensively humans, these approaches have generally either limited to simple models involving single or, where complex population inferred, without accounting for potentially confounding selection at linked sites. Taking advantage coding-sparse nature genome, we propose 2-step approach which coalescent simulations first used infer multi-population model, utilizing large non-functional regions that likely free from background selection. We then use forward-in-time perform conditional on demography inferred expected estimation procedure. Throughout, recombination mutation rate maps were account underlying empirical heterogeneity across human genome. Importantly, within this framework it is possible utilize fit multiple aspects data, scheme represents generalized such large-scale species with genomes.

Language: Английский

Citations

6
Rapid gene content turnover on the germline-restricted chromosome in songbirds DOI Creative Commons
Stephen A. Schlebusch, Jakub Rídl, Manon Poignet

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: July 29, 2023

The germline-restricted chromosome (GRC) of songbirds represents a taxonomically widespread example programmed DNA elimination. Despite its apparent indispensability, we still know very little about the GRC's genetic composition, function, and evolutionary significance. Here assemble GRC in two closely related species, common thrush nightingale. In total identify 192 genes across GRCs, with many them present multiple copies. Interestingly, appears to be under selective pressure, content differing dramatically between species appearing pseudogenized fragments. Only one gene, cpeb1, has complete coding region all examined individuals shows no copy number variation. acquisition this gene by corresponds earliest estimates origin, making it good candidate for functional indispensability songbirds.

Language: Английский

Citations

11
The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus) DOI Creative Commons

John McAuley,

Bertrand Servin, Hamish A. Burnett

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)

Published: Aug. 24, 2024

Abstract Meiotic recombination through chromosomal crossing-over is a fundamental feature of sex and an important driver genomic diversity. It ensures proper disjunction, allows increased selection responses, prevents mutation accumulation; however, it also mutagenic can break up favorable haplotypes. This cost–benefit dynamic likely to vary depending on mechanistic evolutionary contexts, indeed, rates show huge variation in nature. Identifying the genetic architecture this key understanding its causes consequences. Here, we investigate individual rate wild house sparrows (Passer domesticus). We integrate pedigree data identify autosomal crossover counts (ACCs) intrachromosomal allelic shuffling (r¯intra) 13,056 gametes transmitted from 2,653 individuals their offspring. Females had 1.37 times higher ACC, 1.55 r¯intra than males. ACC were heritable females males (ACC h2 = 0.23 0.11; 0.12 0.14), but cross-sex additive correlations low (rA 0.29 0.32 for r¯intra). Conditional bivariate analyses showed that all measures remained after accounting values opposite sex, indicating sex-specific evolve somewhat independently. Genome-wide models are polygenic driven by many small-effect loci, which act trans as global modifiers. Our findings have different potential birds, providing compelling mechanism evolution sexual dimorphism recombination.

Language: Английский

Citations

4
The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus) DOI Creative Commons

John McAuley,

Bertrand Servin, Hamish A. Burnett

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 27, 2023

Abstract Meiotic recombination through chromosomal crossing-over is a fundamental feature of sex and an important driver genomic diversity. It ensures proper disjunction, allows increased selection responses, prevents mutation accumulation; however, it also mutagenic can break up favourable haplotypes. This cost/benefit dynamic likely to vary depending on mechanistic evolutionary contexts, indeed, rates show huge variation in nature. Identifying the genetic architecture this key understanding its causes consequences. Here, we investigate individual rate wild house sparrows ( Passer domesticus ). We integrate pedigree data identify autosomal crossover counts (ACC) intra-chromosomal allelic shuffling r̅ intra ) 13,056 gametes. Females had 1.37 times higher ACC, 1.55 than males. ACC were heritable females males (ACC h 2 = 0.23 0.11; 0.12 0.14), but cross-sex additive correlations low (r A 0.29 0.32 for Conditional bivariate analyses showed that all measures remained after accounting values opposite sex, indicating sex-specific evolve somewhat independently. Genome-wide models are polygenic driven by many small-effect loci, which act trans as global modifiers. Our findings have different potential birds, providing compelling mechanism evolution sexual dimorphism recombination.

Language: Английский

Citations

7
Gene gain and loss from the Asian corn borer W chromosome DOI Creative Commons
Wenting Dai, Judith E. Mank, Liping Ban

et al.

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

Published: May 1, 2024

Sex-limited chromosomes Y and W share some characteristics, including the degeneration of protein-coding genes, enrichment repetitive elements, heterochromatin. However, although many studies have suggested that retain genes related to male function, far less is known about whether they female-specific function.

Language: Английский

Citations

2
Songbird germline-restricted chromosome as a potential arena of genetic conflicts DOI Creative Commons

Niki Vontzou,

Yifan Pei, Jakob C. Mueller

et al.

Current Opinion in Genetics & Development, Journal Year: 2023, Volume and Issue: 83, P. 102113 - 102113

Published: Sept. 19, 2023

Genetic conflicts can arise between components of the genome with different inheritance strategies. The germline-restricted chromosome (GRC) songbirds shows unusual mitotic and meiotic transmission compared rest genome. It is excluded from somatic cells maintained only in germline. usually present one copy male germline eliminated during spermatogenesis, while female germline, it occurs two copies behaves as a regular chromosome. Here, we review what known about GRC's evolutionary history, genetic content, expression discuss how may be involved types conflicts. Finally, interrogate potential role GRC songbird development, highlighting several unsolved mysteries.

Language: Английский

Citations

6
Germline-restricted chromosomes of the songbirds DOI Creative Commons
Pavel M. Borodin

Vavilov Journal of Genetics and Breeding, Journal Year: 2023, Volume and Issue: 27(6), P. 641 - 650

Published: Nov. 2, 2023

Germline-restricted chromosomes (GRCs) are present in the genomes of germline cells and absent from somatic cells. A GRC is found all species songbirds (Passeri) none other bird orders studied to date. This indicates that originated common ancestor songbirds. The germline-restricted chromosome permanently songbird, while female usually contain two copies male ones have one copy. In females, GRCs undergo synapsis restricted recombination their terminal regions during meiotic prophase. males, it almost always eliminated spermatocytes. Thus, inherited exclusively through maternal lineage. a necessary genomic element To date, genetic composition has been four only. Some genes actively expressed gonads, controlling development synthesis proteins involved organization chromosomes. Songbird vary size composition. each consists amplified modified basic genome species. level homology between different relatively low, indicating high rate evolution this chromosome. Transmission lineage suppression contribute significantly accelerated GRCs. One may suggest rapid coordinated might be responsible for explosive speciation adaptive radiation most species-rich diverse infraorder birds.Хромосомы, ограниченные зародышевой линией (germline-restricted – GRC), присутствуют в геномах герминативных клеток и запрограммированно элиминируются из соматических ходе развития. Они крайне редко возникают эволюции. Еще реже они становятся необходимыми элементами геномов крупных таксонов. Такая хромосома, ограниченная линией, была обнаружена у всех исследованных представителей подотряда воробьинообразных певчих птиц. Ни одного других отрядов птиц не выявлено. Это свидетельствует о том, что возникла общего предка У этого присутствует, как правило, двух копиях клетках самок одной копии самцов отсутствует клетках. синаптируют рекомбинируют профазе мейоза. почти всегда сперматоцитов. Таким образом, наследуется исключительно по материнской линии. Хромосомы, необходимый элемент генома На сегодняшний день исследованы геномы четырех видов. Некоторые гены активно экспрессируются гонадах самок, контролируют развитие клеток, синтез белков, вовлеченных организацию мейотических хромосом. разных видов различаются размерам генетическому составу. Геном каждого вида состоит амплифицированных перестроенных копий генов основного данного вида. Уровень гомологии между довольно низок. указывает на высокую скорость эволюции генетического состава хромосомы. Значительный вклад ускорение вносят передача этой хромосомы линии подавление рекомбинации ней. Можно считать, быстрая согласованная эволюция набора играет важную роль видообразовании адаптивной радиации самого богатого видами разнообразного

Language: Русский

Citations

2
Host genotype shapes root mycobiota in durum wheat DOI Creative Commons
Margot Trinquier, Michel Colombo, Hélène Fréville

et al.

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

Published: Oct. 29, 2024

Summary In addition to environmental factors, plant genetics play a key role in shaping the root microbiota; however, extent of this genetic control remains underexplored. Using collection 181 wheat lines derived from genetically diverse population, we investigated influence genotypes on composition endophytic mycobiota and explored determinants driving these relationships. We first characterized associated with roots field-grown Evolutionary Prebreeding pOpulation (EPO) using Internal Transcribed Spacer 2 (ITS2) barcoding. Fungal diversity was then correlated by quantitative methods, including heritability analysis Genome Wide Association Studies (GWAS), identify novel influencing composition. species richness showed positive correlation across most fungal clades, except between Mortierellomycotina Glomeromycotina . Some specific such as Olpidiomycota or Chytridiomycota , underscored their potential endophytes. Additionally, observed higher clades ( i.e. at phylum subphylum rank) that exhibit homogenous trophic mode, biotrophic Arbuscular Mycorrhizal Fungi (AMF). This study identifies 11 QTLs clade level. By shedding light uncovering associations, work enhances our understanding plant-microbiota interactions highlights for breeding strategies optimize

Language: Английский

Citations

0
Gene Gain and Loss from the Asian Corn Borer W Chromosome DOI Open Access
Wenting Dai, Judith E. Mank, Liping Ban

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 21, 2022

Abstract We built a chromosome-level genome assembly of the Asian corn borer, Ostrinia furnacalis Guenée (Lepidoptera: Pyralidae, Pyraloidea), an economically important pest in corn, from female, including both Z and W chromosome. Despite deep conservation chromosome across Lepidoptera, our reveals little with available sequence related species or chromosome, consistent non-canonical origin The has accumulated significant repetitive elements experienced rapid gene gain remainder genome, most genes exhibiting pseudogenization after duplication to W. that retain expression are largely enriched for functions DNA recombination, nucleosome, chromatin binding, likely meiotic mitotic processes within female gonad.

Language: Английский

Citations

2