Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 187, P. 107869 - 107869

Published: July 8, 2023

Language: Английский

---

Use of Genomic Resources to Assess Adaptive Divergence and Introgression in Oaks

Forests, Journal Year: 2021, Volume and Issue: 12(6), P. 690 - 690

Published: May 27, 2021

Adaptive divergence is widely accepted as a contributor to speciation and the maintenance of species integrity. However, mechanisms leading reproductive isolation, genes involved in adaptive divergence, traits that shape adaptation wild changes climate are still largely unknown. In studying role ecological interactions environment-driven selection, trees have emerged potential model organisms because their longevity large genetic diversity, especially natural habitats. Due recurrent gene flow among with different preferences, oaks arose early 1970s for understanding how can occur face interspecific flow, what we mean by “species” when geographically genomically heterogeneous introgression seems undermine species’ coherence. this review, provide an overview recent research into genomic underpinnings integrity flow. We review analytical tools instrumental better isolation oaks. evidence oak coherent entities, focusing on sympatric populations ongoing discuss hypotheses regarding linking isolation. As evolution drought- freezing-tolerance been key parallel diversification oaks, investigate question whether same or similar set drought stress tolerance across taxa sections. Finally, propose future directions hybridization change.

Language: Английский

---

5S‐IGS rDNA in wind‐pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

The Plant Journal, Journal Year: 2021, Volume and Issue: 109(4), P. 909 - 926

Published: Nov. 22, 2021

Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality wind-pollinated trees with long evolutionary histories more complex: species evolve from other through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new (hybrid taxa such as nothospecies and allopolyploids). multi-copy, potentially multi-locus 5S rDNA one few regions conserving signal reticulate processes down level intra-genomic recombination. Therefore, it provide unique insights into dynamic lineages that diversified tens millions years ago. Here, we first high-throughput sequencing (HTS) intergenic spacers (5S-IGS) for subtropical temperate trees, Fagus crenata - F. sylvatica s.l. lineage, its distant relative japonica. observed 4963 5S-IGS variants reflect complex history hybrid origins, sorting, via secondary flow, competition between or paralogous-homoeologous lineages. We show modern are mosaics represent striking case ongoing evolution during past 55 million years.

Language: Английский

---

Tree population genomics

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 325 - 356

Published: Jan. 1, 2025

Language: Английский

---

Dairy Cattle Reproduction, Production, and Disease Resistance in the Omics Era: Genome-Wide Selection Signatures Identify Candidate Genes in Sahiwal Cattle

OMICS A Journal of Integrative Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 21, 2025

Climate emergency and ecological sustainability call for new ways of thinking livestock health, including the dairy cattle. This study unpacks genetic diversity selection sweeps Sahiwal cattle in relation to adaptability, production, disease resistance. Using nucleotide (π) calculated from 10 kb windows across genome with VCFtools, 716 regions were identified 29 chromosomes, importantly, chromosome 15 showing highest density. A total 92 quantitative trait loci (QTL) linked genes analyzed, 1 harboring number. Trait association analysis using Cattle QTL database showed that 14 production traits, reproduction 8 susceptibility. Notable included CSMD2 EFNA1, which influence milk traits such as fat percentage yield, PCBP3 SGCD, affect reproductive traits. Additionally, TBXAS1 ASTN2 associated bovine respiratory sole ulcers. Selection sweeps, Tajima's D, revealed 728 genome, chromosomes 6 frequencies. These indicate under strong selective pressure, likely due breed's adaptation arid environments specific selection. The present highlights how contribute cattle's efficiency, insights reported here provide a foundation health targeted breeding strategies case diverse conditions tropical climate.

Language: Английский

---

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(17), P. 9980 - 9980

Published: Sept. 1, 2022

The holm oak (Quercus ilex L.) is the dominant tree species of Mediterranean forest and Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since prehistoric period, an important part Iberian population from a social, cultural, religious point view, providing ample variety goods services, forming basis economy in rural areas. Currently, there renewed interest its use for dietary diversification sustainable food production. cultural richness, both economically (tangible) environmentally (intangible), must be preserved future generations. However, worrisome degradation associated ecosystems occurring, observed increase decline mortality, which requires urgent action. Breeding programs based on selection elite genotypes by molecular markers only plausible biotechnological approach. To this end, authors’ group started, 2004, research line aimed at characterizing biology Q. ilex. been challenging task due to biological characteristics (long life cycle, allogamous, high phenotypic variability) recalcitrant nature. characterized following central dogma using omics cascade. Molecular responses biotic abiotic stresses, as well seed maturation germination, are two main objectives our research. contributions knowledge level DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, metabolomics discussed here. Moreover, data compared with those reported Quercus spp. All generated, genome available, will integrated morphological physiological systems direction. Thus, we propose possible related resilient productive used reforestation programs. In addition, nutritional value acorn derivate products, bioactive compounds (peptides phenolics) allergens, suggested. Subsequently, selected validated genome-wide association functional genomic analyses.

Language: Английский

---

High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species

Authorea (Authorea), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 30, 2024

Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality more complex: plant species can evolve from other via isolation when genetic drift exceeds gene flow; lineage mixing give rise to new (hybrid taxa such as nothospecies and allopolyploids). multi-copy, potentially multi-locus 5S rDNA one few regions conserving signal reticulate evolutionary processes down level intra-genomic recombination. Here, we provide first high-throughput sequencing (HTS) intergenic spacer (5S-IGS) data for wind-pollinated subtropical temperate trees, Fagus crenata – F. sylvatica s.l. lineage, its distant relative japonica. observed 4,963 unique 5S-IGS variants reflect long history repeated incomplete sorting since early Cenozoic or paralogous-homoeologous lineages. Extant are mosaics and, at least some part, hybrid origin.

Language: Английский

---

ddRAD-seq generated genomic SNP dataset of Central and Southeast European Turkey oak (Quercus cerris L.) populations

Genetic Resources and Crop Evolution, Journal Year: 2024, Volume and Issue: 71(7), P. 3193 - 3203

Published: Jan. 31, 2024

Abstract Turkey oak ( Quercus cerris L.) is one of the most ecologically and economically significant deciduous tree species in Central Southeast European regions. The has long been known to exhibit high levels genetic phenotypic variation. Recent climate response predictions for suggest a distribution extension Europe under change. Since relative drought-tolerant behaviour, it regarded as potential alternative other forest during forestry adaptation efforts, not only its native regions but also Western Europe. For this reason, survey existing variability, resources, adaptability great significance. Next-generation sequencing approaches, such ddRAD-seq (Double digest restriction-site associated DNA sequencing), allow attainment high-resolution genome-wide single nucleotide polymorphisms (SNPs). This study provides first highly variable SNP data generated by ddRAD-seq. dataset comprises 17 607 de novo 26 059 reference mapped SNPs 88 individuals from eight populations, two Bulgaria, Kosovo, five Hungary. Reference mapping was carried out using cork oak’s suber genome. obtained markers are suitable investigating selection local inferring diversity, differentiation, population structure. accessible at: https://doi.org/10.5281/zenodo.8091252

Language: Английский

---

Missing genotype imputation in non‐model species using self‐organizing maps

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown

Published: July 6, 2024

Abstract Current methodologies of genome‐wide single‐nucleotide polymorphism (SNP) genotyping produce large amounts missing data that may affect statistical inference and bias the outcome experiments. Genotype imputation is routinely used in well‐studied species to buffer impact downstream analysis, several algorithms are available fill genotypes. The lack reference haplotype panels precludes use these methods genomic studies on non‐model organisms. As an alternative, machine learning employed explore genotype estimate Here, we propose method based self‐organizing maps (SOM), a widely neural networks formed by spatially distributed neurons cluster similar inputs into close neurons. explores datasets select SNP loci build binary vectors from genotypes, initializes trains for each query genotype. SOM‐derived clustering then impute best To automate process, have implemented gtImputation , open‐source application programmed Python3 with user‐friendly GUI facilitate whole process. performance was validated comparing its accuracy, precision sensitivity benchmark other algorithms. Our approach produced highly accurate precise imputations even SNPs alleles at low frequency outperformed algorithms, especially mixed populations unrelated individuals.

Language: Английский

---

Population structure in Quercus suber L. revealed by nuclear microsatellite markers

PeerJ, Journal Year: 2022, Volume and Issue: 10, P. e13565 - e13565

Published: June 16, 2022

Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, region that considered highly vulnerable increased temperatures and severe dry conditions due environmental changes. Understanding population structure demographics of Q. essential in order anticipate whether populations at greater risk as whole have genetic background reproductive dynamics enable rapid adaptation. The diversity has been subject different studies using both chloroplast nuclear data, but patterns remain unclear. Here, we perform analyses on 13 microsatellite markers, analysed 17 distinct locations across entire range species. Structure revealed may contain three major clusters likely result from isolation refugia combined with posterior admixture putative introgression other Our results show more complex scenario than previously inferred for markers suggest southern high levels variation contribute resilience context change adaptive pressure.

Language: Английский

---