Comparing the methods in sample collection and storage for genomic research DOI
Sod-erdene Byambadash, Delgerzul Baatar,

Dechingavaa Tsend-Ayush

и другие.

Proceedings of the Institute of Biology, Год журнала: 2023, Номер 39(2), С. 9 - 26

Опубликована: Дек. 31, 2023

The quality of DNA is a crucial factor in molecular genetics and conservation genomics research. Degradation can be caused due to many factors. To prevent degradation, it’s essential keep samples free from contamination, dry them quickly after collection, store places. Therefore careful attention storage conditions post-collection important minimize degradation. In this study, we compared three different sample collection methods by running agarose gel electrophoresis determine their suitability for long-term without compromising quality. We found that whole organ or large-sized degraded, while thinly sliced, chopped, dehydrated, dried stored silica ethanol remained intact with high yield. Геномын судалгааны дээж цуглуулалт, түүний хадгалах аргуудын харьцуулалт Хураангуй. Молекул генетик болон хамгааллын генетикийн чанарт нөлөөлдөг хамгийн чухал хүчин зүйл нь ДНХ-ийн чанар байдаг. ДНХ маш олон зүйлээс болж задардаг тул ДНХ-ийг задрахаас сэргийлэхийн тулд дээжийг авахдаа бохирдуулахгүйгээр, хурдан хатааж хуурай нөхцөлд юм. Тиймээс аливаа анх цуглуулахад задралыг бага байлгах үүднээс хадгалалтын сайтар анхаарах хэрэгтэй Иймд бид энэхүү судалгаагаар цуглуулах, 3 өөр арга зүйг туршсан ба аль чанарыг алдагдуулахгүй, удаан хадгалахад тохиромжтой байгааг агарозын гель элеткрофорезод гүйлгэн харьцуулав. Ингэхэд эрхтэнээр буюу том хэмжээтэй авсан дээжийн задарсан, харин нимгэн, жижиглэж усгүйжүүлж хатаасан силика гельд хадгалсан сайн задраагүй, гарц ихтэй байв. Түлхүүр үгс: задрал, Генетикийн дээж, Силика гель, RADseq, Дээж хадгалалт

Язык: Английский

Next-generation data filtering in the genomics era DOI
William Hemstrom, Jared A. Grummer, Gordon Luikart

и другие.

Nature Reviews Genetics, Год журнала: 2024, Номер unknown

Опубликована: Июнь 14, 2024

Язык: Английский

Процитировано

20

Genome‐wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe DOI Creative Commons
Juan Carranza, Javier Pérez‐González, Gabriel Anaya

и другие.

Molecular Ecology, Год журнала: 2024, Номер 33(18)

Опубликована: Авг. 19, 2024

Abstract Genome‐wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci mitochondrial sequences. Here, we used 736 individual red deer ( Cervus elaphus ) samples genotyped at 35,701 single nucleotide polymorphism (SNPs) assess the population species throughout Europe. The results identified 28 populations, higher degrees distinction in peripheral compared mainland populations. Iberian show high differentiation, lineages Western Central Iberia maintaining their distinctiveness, which supports separate refugial ranges within along little recent connection between remaining European Norwegian exhibited lowest variability largest allele frequency differences from compatible a bottlenecks drift during post‐glacial colonization southern refugia. Scottish populations showed distance but levels diversity. Hybrid zones were found Eastern Europe as well Pyrenees, where France are close contact deer. Anthropogenic restocking has promoted Pyrenean zone, admixture events Isle Rum Netherlands, least partly two main central‐eastern Our analysis enabled detailed resolution large mammal widely distributed contributes resolving evolutionary history, can also inform conservation management policies.

Язык: Английский

Процитировано

5

Lasiodiplodia species associated with mango (Mangifera indica L.) decline in Burkina Faso and influence of climatic factors on the disease distribution DOI Creative Commons
Oumarou Zoéyandé Dianda, Issa Wonni, L. Ouedraogo

и другие.

Physiological and Molecular Plant Pathology, Год журнала: 2023, Номер 126, С. 102041 - 102041

Опубликована: Май 9, 2023

Язык: Английский

Процитировано

9

Genomic exploration of Thuja plicata indicates no loss of diversity from adults to offspring in UK Woodlands DOI Creative Commons
Laura Guillardín-Calvo,

Ella Glover,

Gary Kerr

и другие.

Tree Genetics & Genomes, Год журнала: 2025, Номер 21(1)

Опубликована: Фев. 1, 2025

Abstract Thuja plicata is a conifer tree that valued for its cultural, ecological and wood quality features in natural range western North America used Europe as an exotic timber species. It increasingly mixed species forests the UK are managed using regeneration, raising questions about genetic diversity of both adult trees offspring these stands. We studied population structure four woodlands adults naturally regenerated T. . discovered 194,154 Single Nucleotide Polymorphisms (SNPs) Genotyping-by-Sequencing (GBS) retained 655 SNPs across 598 genome sequence scaffolds analysis. The majority included only one SNP, suggesting that; selected were widely distributed within genome. found many monomorphic sites, most which restricted to single woodland, indicative differentiation among woodlands. three ancestral populations (K = 3) low levels admixture indicating starting materials largely from populations. Estimates heterozygosity (H o ) nucleotide (π) (overall H 0.174, π 0.00226) all sites but slightly higher juveniles at two sites. Our genotyping methods results on standing this important provide insight into ability planted face environmental shifts disease threats.

Язык: Английский

Процитировано

0

Phylogeography of the kelp-dwelling isopod Amphoroidea typa H. Milne Edwards (1840) along the coast of continental Chile DOI
Lapo Ragionieri,

Ariel O. Fierro,

Miguel Angel Penna-Díaz

и другие.

Estuarine Coastal and Shelf Science, Год журнала: 2025, Номер 317, С. 109168 - 109168

Опубликована: Фев. 6, 2025

Язык: Английский

Процитировано

0

Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis DOI Creative Commons
Emeline Charbonnel, Laure Benoit, Sabine Nidelet

и другие.

Molecular Ecology Resources, Год журнала: 2025, Номер unknown

Опубликована: Апрель 11, 2025

ABSTRACT The bestRAD technique is a reduced genome representation approach with high‐capacity sample multiplexing and physical isolation of biotin‐labelled target DNA fragments using streptavidin beads, which should reduce total cost genotyping errors. While we here formalise the relevance this within HTS landscape, our foremost aim was to improve its replicability, validity, transparency. We first optimised molecular laboratory protocol shared associated protocols (e.g., final detailed methodologies, quality control, best practices) under FAIR principles. Using 84 worldwide individual samples Oriental fruit fly, Bactrocera dorsalis , major invasive pest, revealed low rate PCR duplicates, robustness quantity, high genotype call rate, insignificant error nuclear mitochondrial representativeness, level genetic information. This in‐depth data assessment, along handling time by an estimated one‐third relative parent RAD‐Seq version, demonstrates that excellent compromise between quality. generated high‐quality genomic resources for B. also share details recommendations can be readily used in any applied all organisms, even without published sequence.

Язык: Английский

Процитировано

0

How transdisciplinarity can help biotech-driven biodiversity research DOI Creative Commons
Jean‐Baptiste Jouffray, Jessica M. da Silva, Robert Blasiak

и другие.

Trends in biotechnology, Год журнала: 2025, Номер unknown

Опубликована: Май 1, 2025

Язык: Английский

Процитировано

0

Solving a century-old conundrum: genetic integrity of a rare and local endemic shrub facing introgression with a widespread congener DOI Creative Commons

Alice Atikessé,

Luc Sirois, Guillaume de Lafontaine

и другие.

Botanical Journal of the Linnean Society, Год журнала: 2025, Номер unknown

Опубликована: Апрель 14, 2025

Abstract Hybridization is a key driver of evolutionary processes and speciation. Advances in sequencing technology provide unprecedented opportunity to study discriminating phenotypic characters at the molecular level identify candidate loci associated with speciation process. Salix chlorolepis rare threatened endemic shrub species restricted upper slopes Mount Albert (Canada) proposed hybridize S. brachycarpa, locally abundant geographically widespread congener. We aimed characterize rangewide genetic variation chlorolepis, establish whether it actually hybridizes assess leaf pilosity an indicative variable trait related introgressive hybridization. Using single nucleotide polymorphism data, we inferred patterns structure diversity. tested for associations environmental distance, taxonomic identity, or variability hair density using populations genomics approaches multilocus (partial Mantel tests generalized dissimilarity models) single-locus (latent factor mixed model, pRDA, PCAdapt, OutFLANK) levels. Although common ancestry persists within fine-scale spatial reflects its fragmented distribution. Interspecific admixture sympatry zones corroborates existence Leaf important explaining genotype between two taxa. flagged nine that are both strongly phenotype divergent selection The such ‘impermeable’ introgression ensures maintenance interspecific barrier clear differentiation species. Such genomic heterogeneity alleviates assimilation risk by more congener despite ongoing introgression.

Язык: Английский

Процитировано

0

ddRAD-seq generated genomic SNP dataset of Central and Southeast European Turkey oak (Quercus cerris L.) populations DOI Creative Commons
Botond Boldizsár Lados, Klára Cseke, Attila Benke

и другие.

Genetic Resources and Crop Evolution, Год журнала: 2024, Номер 71(7), С. 3193 - 3203

Опубликована: Янв. 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

Язык: Английский

Процитировано

2

The future is here: an easy‐to‐use toolkit for integrating genetics into conservation management DOI Creative Commons
Carolyn J. Hogg, Katherine A. Farquharson, Parice Brandies

и другие.

Animal Conservation, Год журнала: 2024, Номер unknown

Опубликована: Июль 20, 2024

Abstract Over the past decade, development of genetic and genomic tools for conservation management has come forward in leaps bounds. Once considered a ‘nice to have’, data are fast becoming an essential tool informing managing translocations. However, due complexity field, easily using decision‐making monitoring remains beyond reach most managers biologists. In May 2020, we launched Threatened Species Initiative (TSI), programme designed generate resources Australia's threatened species. Critical project is not only generation reference genomes population but online toolkit managers. The ‘one stop shop’ from collecting samples, generating analysing data, interpretable report. A series workflows pipelines have been developed, including TSI Biodiversity Portal, that uses point click web interfaces transfer raw sequence assemble genomes, transcriptomes soon genetics decisions. Here present how current works provide case study examples it being used inform translocations

Язык: Английский

Процитировано

2