Population genomics, Journal Year: 2021, Volume and Issue: unknown
Published: Jan. 1, 2021
Language: Английский
International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(2), P. 966 - 966
Published: Jan. 16, 2022
Due to the economic and ecological importance of forest trees, modern breeding genetic manipulation trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, widely accepted tool for analyzing gene function precise modification in virtually any species but remains largely unexplored species. Rapidly accumulating genomic resources enabled identification numerous genes biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating selection suitable editing targets. Here, we introduce discuss latest progress, opportunities, challenges genome sequencing improving sustainability.
Language: Английский
Citations
33
Cladistics, Journal Year: 2024, Volume and Issue: 40(4), P. 357 - 373
Published: Jan. 10, 2024
Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex in and observe variations across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution southwest China probably constitute syngameon. In this study, we mapped resequencing from different group Quercus aquifolioides reference genome obtain high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. reconstructed phylogenetic relationships, explored level pattern introgression these investigated tree variation using sliding windows. same or plastomes were found be shared extensively within specific geographical area. Phylogenomic analyses genome-wide SNP that most clade showed genetic coherence, but several connected by introgression. trees obtained windows are highly heterogeneous therefore obscured. Our study all form obscured observed empirically best explained conjunction incomplete lineage sorting.
Language: Английский
Citations
7
G3 Genes Genomes Genetics, Journal Year: 2023, Volume and Issue: 13(11)
Published: Sept. 14, 2023
Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. generated by the combination PacBio sequences chromatin conformation capture (Hi-C) scaffolding. This first reference from clade (section Lobatae). The assembly spans 739 Mb with 95.27% in 12 chromosomes 33,333 protein-coding genes. Comparisons genomes Quercus lobata mongolica revealed high collinearity, intrachromosomal structural variants present. Orthologous gene family analysis other species that families associated defense response were expanding contracting simultaneously across genome. had most CC-NBS-LRR TIR-NBS-LRR resistance genes out 9 analyzed. Terpene synthase comparisons further reveal tandem duplications TPS-b subfamily, similar robur. Phylogenetic also identified 4 subfamilies IGT/LAZY for plant structure. Single major QTL regions vegetative bud break marcescence, which contain candidate research, including putative ortholog circadian clock constituent cryptochrome (CRY2) 8 tandemly duplicated serine protease inhibitors, respectively. Genome-environment associations natural populations abiotic stress tolerance predicted performance common garden. high-quality represents essential resource genomic community, will expedite comparative genomics biological studies species.
Language: Английский
Citations
11
Annals of Forest Science, Journal Year: 2024, Volume and Issue: 81(1)
Published: May 21, 2024
Abstract Key message Mining genome-wide DNA sequences enabled the discovery of near-diagnostic markers for species assignment in four European white oaks ( Quercus petraea (Matt.) Liebl., pubescens Willd., pyrenaica and robur L.) despite their low interspecific differentiation. Near-diagnostic are almost fully fixed one absent three others. As a result, only handful needed identification, making this genetic assay very promising operational taxonomic procedure research forestry. Context Identifying oak complex has been long-standing concern taxonomy, evolution, forest research, management. Q. L., Willd. part western temperate Europe hybridize mixed stands, challenging identification. Aims Our aim was to identify single-nucleotide polymorphisms (SNPs) each that suitable routine use rapid diagnosis applied Methods We first scanned existing whole-genome target-capture data sets reduced number samples (training set) candidate diagnostic SNPs, i.e., genomic positions being characterized by reference allele alternative all other species. Allele frequencies candidates SNPs were then explored larger, range-wide sample populations (validation step). Results found subset 38 (10 , 7 9 12 ) showed features across distribution ranges with exhibiting highest (0.876) lowest (0.747) diagnosticity, respectively. Conclusions provide new, efficient, reliable molecular tool identification which can be used as This study highlights resolution offered sequencing design marker assignment, even complexes relatively
Language: Английский
Citations
4
Plants, Journal Year: 2025, Volume and Issue: 14(1), P. 109 - 109
Published: Jan. 2, 2025
Pedunculate oak (Quercus robur L.) is widely distributed across Europe and serves critical ecological, economic, recreational functions. Investigating its responses to stressors such as drought, extreme temperatures, pests, pathogens provides valuable insights into capacity adapt climate change. Genetic dendrochronological studies offer complementary perspectives on this adaptability. Tree-ring analysis (dendrochronology) reveals how Q. has historically responded environmental stressors, linking growth patterns specific conditions drought or temperature extremes. By examining tree-ring width, density, dynamics, researchers can identify periods of suppression enhancement predict forest future climatic events. further complement by uncovering adaptive genetic diversity inheritance patterns. Identifying markers associated with stress tolerance enables managers prioritize the conservation populations higher potential. These guide reforestation efforts support development climate-resilient populations. integrating data, gain a holistic understanding robur’s mechanisms resilience. This knowledge vital for management sustainable planning in face challenges, ultimately helping ensure long-term viability their ecosystems. The topics covered review are very broad. We tried include most relevant, important, significant studies, but focused mainly relatively recent Eastern European because they species’ area. However, although more than 270 published works have been cited review, we have, course, missed some studies. apologize advance authors those relevant that not cited.
Language: Английский
Citations
0
Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(2)
Published: Feb. 1, 2025
Although many tree species frequently hybridize and backcross, management decisions in forestry nature conservation are usually concentrated on pure species. Therefore, understanding which environmental factors drive the distribution admixture of a local stand scale is great interest to support decision-making establishment resilient forests. Here, we extensively sampled mixed hybridizing white oaks (Quercus petraea Q. pubescens) near Lake Neuchâtel (Switzerland), where limestone glacier moraine geologies coexist proximity, test whether micro-environmental conditions can predict taxonomic genetic admixture. We collected DNA from bud tissue, individual soil samples, extracted high-resolution topographic data for 385 oak trees. used 50 species-discriminatory single nucleotide polymorphism (SNP) markers determine composition levels trees tested their association with conditions. show that trees' be explained mainly by geographic position, pH, potential rooting depth, proxy water availability. found admixed individuals tend grow habitats characteristic more drought-tolerant pubescens rather than intermediate habitats. Using situ measurements, first fine-scale variation properties related pH availability potentially drives stand. Microenvironmental therefore promotes diversity, facilitates adaptive introgression, contributes resilience forests under change. Consequently, such as should managed protected complex
Language: Английский
Citations
0
New Phytologist, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 11, 2025
Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that ecologically, culturally, and economically important. We report the first haplotype‐resolved chromosome‐scale genome assembly of Q. conduct comparative analyses structure gene content against other published Fagaceae genomes. investigate genetic diversity this widespread phylogenetic relationships among oaks using whole data. Despite strongly conserved chromosome synteny size , certain families have undergone rapid changes in size, including defense genes. Unbiased annotation resistance (R) genes revealed overall number R similar – as are chromosomal locations clusters but, within more labile. found has high diversity, much which predates its divergence from likely impacts time estimations. Our results highlight discordance genus. The white represents a major new resource for studying evolution . Additionally, we show unbiased key to accurately assessing
Language: Английский
Citations
0
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
Citations
16
Forests, Journal Year: 2023, Volume and Issue: 14(4), P. 777 - 777
Published: April 10, 2023
Quercus spp. have formed broad-leaved evergreen forests in the Hindu Kush and Himalayan regions of Pakistan. Seven species genus (Q. baloot Griff., Q. dilatata Royle., glauca Thunb., incana Roxb., robur Linn., semecarpifolia Smith., leucotrichophora A. Camus.) been identified. These received little attention compared with other economically valuable plant Pakistan, which has mainly linked to traditional medicine identification phytonutrients evaluate their bioactivities toxicological effects. are promising for commercial applications, so government policy should encourage management conservation. However, they currently threatened by severe human activities climate change. The goal this review is highlight relevance these forgotten species, describing overall aspects related distribution, morphology, uses, phytochemical constituents, threats. To date, no proper comprehensive molecular studies on populations found Pakistan conducted, a critical gap as essential conservation strategies. Finally, we discuss future directions approaches that follow strategies being used not
Language: Английский
Citations
5
Forests, Journal Year: 2023, Volume and Issue: 14(12), P. 2279 - 2279
Published: Nov. 21, 2023
The genetic composition of 5797 white oaks assigned in forest inventories as Quercus robur (3342), petraea (2090), pubescens (170), or unspecified Quercus. spp. (195) sampled all over Europe were genotyped at 355 nuclear SNPs and 28 maternally inherited the chloroplast mitochondria. sampling had a focus on Central Eastern Europe, well Black Sea Caucasus region. Using sparse nonnegative matrix factorization (snmf) algorithm, information was best represented by K = 4 different clusters, whereas principal component analysis visualized three groups. snmf run with 3 corresponded, for most individuals assignment inventories, to species. majority samples (88%) an admixture coefficient q > 0.8 one species underlining integrity minor level admixture. In contrast Q. petraea, showed clear geographic substructure. These large-scale within-species structures correlated regionally variable levels introgression between For from less focused particular regions, this widespread inter-specific gene flow reduced differentiation. variation led 12 haplotypes cross-species pattern, further supporting observation significant hybridization among
Language: Английский
Citations
5