A computational approach for positive genetic identification and relatedness detection from low-coverage shotgun sequencing data DOI Creative Commons
Remy Nguyen, Joshua D. Kapp, Samuel Sacco

et al.

Journal of Heredity, Journal Year: 2023, Volume and Issue: 114(5), P. 504 - 512

Published: June 29, 2023

Abstract Several methods exist for detecting genetic relatedness or identity by comparing DNA information. These generally require genotype calls, either single-nucleotide polymorphisms short tandem repeats, at the sites used comparison. For some samples, like those obtained from bone fragments single rootless hairs, there is often not enough present to generate calls that are accurate and complete these comparisons. Here, we describe IBDGem, a fast robust computational procedure genomic regions of identity-by-descent low-coverage shotgun sequence data against known query individual. At less than 1× genome coverage, IBDGem reliably detects segments can make high-confidence detections with as little 0.01× coverage.

Language: Английский

The UCSC Genome Browser database: 2024 update DOI Creative Commons
Brian J. Raney,

Galt P Barber,

Anna Benet‐Pagès

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D1082 - D1088

Published: Nov. 11, 2023

The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation on thousands of genome assemblies, ranging from human SARS-CoV2. This year, we have introduced new the Human Pangenome Reference Consortium viral genomes including We added 1,200 our GenArk system, increasing overall diversity representation. support for nine user-contributed track hubs public hub system. Additionally, released 29 tracks 11 mouse genome. Collectively, these features expand both breadth depth knowledge share publicly with

Language: Английский

Citations

263
Plant pangenomes for crop improvement, biodiversity and evolution DOI
Mona Schreiber, Murukarthick Jayakodi, Nils Stein

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(8), P. 563 - 577

Published: Feb. 20, 2024

Language: Английский

Citations

28
The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics DOI Creative Commons
Montserrat Corominas, Tomás Marquès‐Bonet, Miquel A. Arnedo

et al.

NAR Genomics and Bioinformatics, Journal Year: 2024, Volume and Issue: 6(3)

Published: July 2, 2024

Abstract The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing genome of >40 000 eukaryotic species estimated to live in Catalan-speaking territories (Catalan Linguistic Area, CLA). These represent a biodiversity hotspot. While covering less than 1% Europe, they are home about one fourth all known European species. include high proportion endemisms, many which threatened. This trend likely get worse as effects global change expected be particularly severe across Mediterranean Basin, freshwater ecosystems and mountain areas. Following EBP model, CBP networked organization that has been able engage scientific non-scientific partners. In pilot phase, genomes 52 being sequenced. As case study conservation, we highlight Balearic shearwater Puffinus mauretanicus, sequenced under umbrella.

Language: Английский

Citations

11
Research on Genome Data Recognition and Analysis based on Louvain Algorithm DOI Open Access
Danyi Huang, Lidong Xu,

Weilun Tao

et al.

Published: July 16, 2024

In genomics analysis, with the development of sequencing technology and rapid growth data volume, how to effectively identify analyze important information in genomic from massive has become an challenge. Identify key patterns features through advanced community testing methods. First, often contains a lot noise redundant that needs be processed steps such as normalization, filtering, dimensionality reduction. Normalization makes at different scales comparable, filtering out points low quality or missing values, reduction reduces dimensions principal component analysis (PCA) retains main information. The gene co-expression network establishes connection relationship between genes by calculating expression similarity matrix genes, applies Louvain algorithm maximize modularity network, aggregate nodes layer layer, form structure, complex potential structure genes. Finally, we utilize cancer dataset evaluate proposed model. From our extensive experimental results, can observe Louvain's indicates outperformances accuracy recognition data.

Language: Английский

Citations

10
The Idiot's Guide to Effective Population Size DOI Open Access
Robin S. Waples

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 10, 2025

This is a reference manual for the elegant, yet hideously complex concept of effective population size (Ne), inspired by classic, self-published automotive repair 'for compleat idiot'. The Guide timely, given recent Kunming-Montreal Global Biodiversity Framework, where 196 Parties committed to tracking genetic diversity-and estimating Ne-for all species. Ne human construct, but useful one that allows us capture diverse aspects an organism's biology in single number. collates location factual information about size, with focus on topics practical relevance scientists and managers studying real populations; it covers definition, computation estimation both demographically genetically. As appropriate, reader directed other primary sources more details. A 'Don't Do These Things' section lists several ill-advised approaches dealing Ne, Appendix provides tools suggestions interested users. special considers possibilities challenges presented genomics revolution. Availability vast numbers markers increases precision, less than some might think, simultaneously introduces new involving filtering bioinformatics processing. annotated genomes become common non-model species, opportunities are opened address qualitatively different questions, including reconstructing historical changes through time.

Language: Английский

Citations

1
Translating genomic advances into biodiversity conservation DOI
Carolyn J. Hogg

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 25(5), P. 362 - 373

Published: Nov. 27, 2023

Language: Английский

Citations

20
Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles DOI Creative Commons
Daren C. Card, W. Bryan Jennings, Scott V. Edwards

et al.

Animals, Journal Year: 2023, Volume and Issue: 13(3), P. 471 - 471

Published: Jan. 29, 2023

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles—lizards and snakes—recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity phenotypic genomic traits, resources in non-avian have accumulated more slowly than they mammals birds, remaining amniotes. Here we review remarkable natural history reptiles, focus on physical characteristics, sequence compositional patterns that key axes variation across We argue high evolutionary can fuel new generation whole-genome phylogenomic analyses. A survey phylogenetic investigations shows capture-based approaches are commonly used, studies markers known ultraconserved elements (UCEs) especially well represented. However, many other types exist increasingly being mined from genome assemblies silico, including some greater information potential UCEs for certain investigations. discuss importance high-quality methods bioinformatically extracting range marker sets assemblies. Finally, encourage herpetologists working genomics, genetics, biology, fields to work collectively towards building squamates, rival those already place birds. Overall, development this cross-amniote tree life will contribute illuminate interesting dimensions biodiversity broader

Language: Английский

Citations

17
Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii) DOI Creative Commons
Tyler Wooldridge, Chloé Orland, Erik D. Enbody

et al.

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

Published: April 29, 2024

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by bacterial disease known as withering syndrome (WS) wiped out >90% individuals, leading to closure all U.S. abalone fisheries since 1993. Current conservation strategies include restoring diminished translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, current prevalence WS remains unknown. To address these uncertainties, we sequenced analysed genomes 133 individuals from across their present range. We observed no spatial structure among with exception single chromosomal inversion increases in frequency latitude. Outside inversion, differentiation between sites minimal does not either distance or environmental dissimilarity. Genetic appears uniformly high Demographic inference indicate severe bottleneck beginning just 15 generations past, but decline short lived, present-day size far exceeding pre-bottleneck status quo. Finally, find agent equally sampled range, only 10% lack structure, uniform bacteria indicates translocation could be valid low-risk means restoration for species' recovery.

Language: Английский

Citations

7
Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery DOI Creative Commons
Phred M. Benham, Carla Cicero, Merly Escalona

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(4)

Published: April 1, 2024

Abstract Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact these on host genomes. The increased capacity long-read sequencing technologies span highly regions promises provide new insights into patterns activity across diverse taxa. Here we report generation contiguous reference genomes using PacBio and Omni-C for three species Passerellidae sparrow. We compared assemblies chromosome-level sparrow nine other generated variety short- technologies. All based were longer (range: 1.12 1.41 Gb) than short-read (0.91 1.08 length was strongly correlated with amount repeat content. Repeat content Bell's (31.2% genome) highest level ever reported within order Passeriformes, which comprises over half avian diversity. levels (79.2% 93.7%) found W chromosome relative genome. Finally, show that proliferation different classes varied even among similar These support dynamic model expansion contraction clade where TEs once thought be fairly depauperate static. Our work highlights how resolution difficult-to-assemble transform our understanding

Language: Английский

Citations

6
Landscape transcriptomics as a tool for addressing global change effects across diverse species DOI Creative Commons
Jason Keagy, Chloe P. Drummond, Kadeem Gilbert

et al.

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: unknown

Published: April 1, 2023

Abstract Landscape transcriptomics is an emerging field studying how genome‐wide expression patterns reflect dynamic landscape‐scale environmental drivers, including habitat, weather, climate, and contaminants, the subsequent effects on organismal function. This benefitting from advancing increasingly accessible molecular technologies, which in turn are allowing necessary characterization of transcriptomes wild individuals distributed across natural landscapes. research especially important given rapid pace anthropogenic change potential impacts that span levels biological organization. We discuss three major themes landscape transcriptomic research: connecting transcriptome variation landscapes to variation, generating testing hypotheses about mechanisms evolution responses environment, applying this knowledge species conservation management. challenges associated with approach suggest solutions. conclude has great promise for addressing fundamental questions biology, ecology, evolution, while providing tools needed management species.

Language: Английский

Citations

14