Contribution of GC content to differentiated region formation along a speciation continuum DOI
Fushi Ke, Liette Vasseur

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

Опубликована: Сен. 4, 2024

Abstract Genome features can interact with external evolutionary processes and are involved in the formation of highly differentiated regions (i.e., genomic islands) potentially containing adaptation speciation loci. However, GC content that elevate both regional recombination mutation has not been investigated evolving lineages to test its effects on heterozygous differentiation landscape. Here, we employed genomes 499 Asian honey bee ( Apis cerana ), a widely-distributed central lineage diverged admixed peripheral at population genetic phylogenetic levels, investigate accumulation divergence along continuum. We find islands generally low lower-than-average), lower-than-average d xy ) initially higher-than-average ones deeper divergence, corresponding suggested evolution models transforming from linked selection divergent selection. When comparing high-GC however, higher load indicating inefficient natural low-GC regions, which thus support important role instead process (e.g., selection) island formation. Finally, possess proportion lineage-specific polymorphisms than due limited admixture under gene-flow scenario, reconciliate discordance between mitochondrial nuclear phylogenies A. . Our results shed light contribution region continuum their application reconstruction intraspecific phylogeny, especially gene flow.

Язык: Английский

Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding DOI Creative Commons
Yongfa Wang, Zi-Hao Wang, Yongming Chen

и другие.

Plant Communications, Год журнала: 2024, Номер 5(5), С. 100883 - 100883

Опубликована: Март 16, 2024

Spelt (Triticum aestivum ssp. spelta) is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern breeding as a valuable genetic resource. However, relatively little known about origins and maintenance of spelt populations. Here, using resequencing data from 416 worldwide accessions, including representative wheat, we demonstrate European emerged when primitive hexaploid spread west hybridized with pre-settled domesticated emmer, putative maternal donor. Genomic introgression regions emmer confer spelt's morphological characters used for species taxonomy, such tenacious glumes later flowering. We propose haplotype-based "spelt index" identify spelt-type varieties quantify utilization gene pool cultivars. This study reveals basis establishment specific ecological niche vital role unique germplasm resource breeding.

Язык: Английский

Процитировано

5
The evolutionary dynamics of locally adaptive chromosome inversions inMimulus guttatus DOI Open Access
Leslie M. Kollar, Lauren E. Stanley, Sunil K. Kenchanmane Raju

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 8, 2023

Abstract Chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a significant role in evolution adaptations those species. Inversions thought to operate as supergenes by trapping adaptive alleles at multiple linked loci through suppression recombination. While there is now considerable support for supergene mechanism evolution, extent which inversions trap pre-existing genetic variation versus accumulate new variants over time remains unclear. In this study, we report insights into evolutionary dynamics locally chromosomal polymorphism (inv_chr8A), contributes divergence between coastal perennial inland annual ecotypes yellow monkeyflower, Mimulus guttatus . This research was enabled sequencing, assembly, annotation genomes M. using Oxford Nanopore long-read sequencing technology. addition inv_chr8A inversion, identified three other large polymorphisms, including previously unknown (inv_chr8B) nested within inv_chr8A. Through population genomic analyses comparative genomics, determined that inv_chr8B significantly older than larger it resides. We also evaluated key candidate genes involved gibberellin biosynthesis anthocyanin regulation, hypothesize underlie phenotypic effects inversion. Although little evidence found suggest breakpoint mutations drive effects, our findings dynamic continuous process.

Язык: Английский

Процитировано

10
Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone DOI Creative Commons
David L. Field, Sean Stankowski, Taylor Reiter

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 20, 2025

Abstract Identification of the genomic regions that contribute to reproductive isolation and how they interact is a major goal evolutionary genetics. Much effort has focused on locating candidate genes potential barrier loci by scanning genomes for excess differentiation ( F ST ). An alternative, perhaps more robust approach, would be scan exhibiting steep clines in allele frequency across hybrid zone. Here we develop this approach apply it data from zone between varieties Antirrhinum majus subspecies with different flower colour patterns A. m. m var. pseudomajus striatum Most are clustered seven regions, only four which were present scans all pair-wise comparisons. Six these carry previously identified influence The seventh region harbours novel locus , RUBIA modifying magenta intensity. Clines at approached towards fixation side zone, whilst remaining polymorphic yellow side. This polymorphism may reflect smaller phenotypic effect compared genetic backgrounds. Our findings illustrate whole-genome cline zones can robustly detect contributing differences highlight genome.

Язык: Английский

Процитировано

0
The Evolution of Locally Adaptive Chromosome Inversions in Mimulus guttatus DOI Creative Commons
Leslie M. Kollar, Lauren E. Stanley, Sunil K. Kenchanmane Raju

и другие.

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Март 5, 2025

Chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a significant role in evolution adaptations those species. Inversions thought to operate as supergenes by trapping adaptive alleles at multiple linked loci through suppression recombination. While there is now considerable support for supergene mechanism evolution, extent which inversions trap pre-existing genetic variation versus accumulate new variants over time remains unclear. In this study, we report insights into locally chromosomal polymorphism (inv_chr8A), contributes divergence between coastal perennial inland annual ecotypes yellow monkeyflower, Mimulus guttatus. This research was enabled sequencing, assembly annotation genomes M. guttatus using Oxford Nanopore long-read sequencing technology. addition inv_chr8A inversion, identified three other large polymorphisms, including previously unknown (inv_chr8B) nested within inv_chr8A. Through population genomic analyses, determined that inv_chr8B significantly older than larger it resides. We also evaluated potential key candidate genes underlying phenotypic effects These involved gibberellin biosynthesis anthocyanin regulation. Although little evidence found suggest breakpoint mutations drive effects, our findings do adaptation may sometimes involve evolve different times.

Язык: Английский

Процитировано

0
Whole-genomic comparison reveals complex population dynamics and parasitic adaptation of Echinococcus granulosus sensu stricto DOI Creative Commons
Yao‐Dong Wu, Z. Y. Ren, Ao Li

и другие.

mBio, Год журнала: 2025, Номер unknown

Опубликована: Апрель 10, 2025

ABSTRACT Cystic echinococcosis (CE), caused by Echinococcus granulosus sensu stricto ( s.s. ), poses a substantial risk to both humans and domestic animals globally. Here, we compared the whole genomes of 111 E. samples from China. Genomic variation data revealed frequent cross-fertilization in hermaphroditic . The G1 G3 genotypes represent distinct mitochondrial lineages, while showing no differentiation nuclear genome, suggesting mito-nuclear discordance historical geographic separation subsequent fusion. Population structure, demographic history, gene flow among populations reflected transmission route Middle East Qinghai-Xizang Plateau through migration nomadic people, followed introgression during secondary contact. variations highlighted selection signatures within genome prone balancing selection, particularly impacting genes encoding membrane-related proteins, representing potential evolutionary strategy for adaptation parasitic life. Balancing pressure on gene-coding sodium/bile acid cotransporter led its high level genetic stability, which may play crucial role survival development stage, making it drug target treatment CE. Meanwhile, other genomic regions under strong provide targets protective immunity. These findings offer valuable insights into complex dynamics adaptive evolution IMPORTANCE ) is primary cause cystic disease affecting livestock with significant health economic impacts. Previous studies this parasite relied DNA classify understand diversity. However, these cannot capture full complexity strategies. Our research employs comprehensive genome-wide sequencing, offering more nuanced view landscape. We discovered that appears be prevalent reproductive , underpinning observed deep divergence between G3, as well populations. history China widespread mixing were likely facilitated migrations peoples. Furthermore, identified including involved uptake host bile acids, parasite’s development, potentially new intervention. advances understanding diversity strategies laying foundation improved control measures

Язык: Английский

Процитировано

0
A GBS-based interspecific and high-density genetic map of Hemerocallis reveals QTLs for horticulturally important traits in daylily and night lily DOI Creative Commons

Yang Gao,

Juan Liu,

Jiang Nan

и другие.

Horticultural Plant Journal, Год журнала: 2025, Номер unknown

Опубликована: Май 1, 2025

Язык: Английский

Процитировано

0
A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta) DOI Creative Commons
Hui Zhen Tan,

Phoebe Scherer,

Katarina C. Stuart

и другие.

Heredity, Год журнала: 2024, Номер 133(4), С. 262 - 275

Опубликована: Авг. 2, 2024

Abstract Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation recombination rate is widespread despite often being essential for progression meiosis. One such variation heterochiasmy, where rates differ sexes. Heterochiasmy has been observed across broad taxonomic groups, yet it remains an enigma. We used Lep-MAP3, pedigree-based software that efficient handling large datasets, to generate linkage maps hihi or stitchbird ( Notiomystis cincta) , utilising information from >36 K SNPs 36 families. constructed 29 maps, including previously unscaffolded Z chromosome. The endangered passerine endemic Aotearoa New Zealand sexually dimorphic exhibits high levels sexual conflict, sperm competition. Patterns are consistent with those other birds, higher micro-chromosomes. male-biased, line predictions Haldane-Huxley rule, male map 15% longer. Micro-chromosomes exhibit heterochiasmy greater extent, contrary reported birds. At intra-chromosomal level, nearer chromosome ends gene-rich regions. Regions extreme enriched genes implicated cell structure. This study adds important contribution assessing theories provides framework future studies investigating fine-scale heterochiasmy.

Язык: Английский

Процитировано

2
Contribution of GC content to differentiated region formation along a speciation continuum DOI
Fushi Ke, Liette Vasseur

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

Опубликована: Сен. 4, 2024

Abstract Genome features can interact with external evolutionary processes and are involved in the formation of highly differentiated regions (i.e., genomic islands) potentially containing adaptation speciation loci. However, GC content that elevate both regional recombination mutation has not been investigated evolving lineages to test its effects on heterozygous differentiation landscape. Here, we employed genomes 499 Asian honey bee ( Apis cerana ), a widely-distributed central lineage diverged admixed peripheral at population genetic phylogenetic levels, investigate accumulation divergence along continuum. We find islands generally low lower-than-average), lower-than-average d xy ) initially higher-than-average ones deeper divergence, corresponding suggested evolution models transforming from linked selection divergent selection. When comparing high-GC however, higher load indicating inefficient natural low-GC regions, which thus support important role instead process (e.g., selection) island formation. Finally, possess proportion lineage-specific polymorphisms than due limited admixture under gene-flow scenario, reconciliate discordance between mitochondrial nuclear phylogenies A. . Our results shed light contribution region continuum their application reconstruction intraspecific phylogeny, especially gene flow.

Язык: Английский

Процитировано

0