From QTL to gene: C. elegans facilitates discoveries of the genetic mechanisms underlying natural variation

Trends in Genetics, Journal Year: 2021, Volume and Issue: 37(10), P. 933 - 947

Published: July 3, 2021

Language: Английский

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Nematode chromosomes

Genetics, Journal Year: 2022, Volume and Issue: 221(1)

Published: March 22, 2022

Abstract The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell and genomics. A major factor in the success C. as a model organism been availability, since late 1990s, an essentially gap-free well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss structure, function, biology chromosomes then provide general perspective chromosome other diverse species. We highlight malleable features centromeres, telomeres, repetitive elements, well remarkable process programmed DNA elimination (historically described chromatin diminution) that induces loss portions somatic cells handful An exciting future prospect is species may enable experimental approaches to study test models evolution. long term, fundamental insights regarding how speciation integrated with be revealed.

Language: Английский

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Inferring Balancing Selection From Genome-Scale Data

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(3)

Published: Feb. 23, 2023

Abstract The identification of genomic regions and genes that have evolved under natural selection is a fundamental objective in the field evolutionary genetics. While various approaches been established for detection targets positive selection, methods identifying balancing form preserves genetic phenotypic diversity within populations, yet to be fully developed. Despite this, increasingly acknowledged as significant driver its signatures genomes essential understanding role evolution. In recent years, plethora sophisticated has developed patterns linked variation produced by such high levels polymorphism, altered allele-frequency distributions, polymorphism sharing across divergent populations. this review, we provide comprehensive overview classical contemporary methods, offer guidance on choice appropriate discuss importance avoiding artifacts considering alternative processes. increasing availability genome-scale datasets holds potential assist new quantification prevalence thus enhancing our

Language: Английский

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CaeNDR, the Caenorhabditis Natural Diversity Resource

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D850 - D858

Published: Oct. 19, 2023

Abstract Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability genomes and expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used identify measure effects variants on traits quantitative genetics. Since 2016, C. Natural Diversity Resource (CeNDR) has facilitated many studies providing an archive wild strains, genome-wide sequence variant data for each strain, a association (GWA) mapping portal community. Here, we present updated platform, (CaeNDR), that enables genetics genomics across three species: elegans, briggsae tropicalis. The CaeNDR platform hosts several databases continually addition new whole-genome annotated variants. Additionally, provides interactive tools explore variation enable GWA mappings. All accessible through freely available web located at caendr.org.

Language: Английский

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Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 27, 2023

Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These can lead to negative frequency-dependent selection, a form balancing that is hypothesised explain high levels polymorphism seen in many immune parasite antigen loci. Here, we sequence several individuals Heligmosomoides bakeri, model house mice, polygyrus, closely related wood mice. Although H. bakeri commonly referred as polygyrus literature, their show divergence are consistent with at least million years independent evolution. The species contain hyper-divergent haplotypes enriched for proteins interact response. Many these originated prior between suggesting they have been maintained by long-term selection. Together, our results suggest exerted response played key role shaping patterns genetic diversity parasitic nematodes.

Language: Английский

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The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 19, 2024

Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration genetic approaches interrupt Schistosoma mansoni transmission, the causative agent for human intestinal in sub-Saharan Africa South America, has led genomic research snail vector hosts genus Biomphalaria. Few complete resources exist, African Biomphalaria species being particularly underrepresented despite this where majority S. infections occur. Here we generate annotate first genome assembly sudanica sensu lato, a responsible transmission lake marsh habitats Rift Valley. Supported by whole-genome diversity data among five inbred lines, describe orthologs immune-relevant gene regions American B. glabrata present bioinformatic pipeline identify candidate novel pathogen recognition receptors (PRRs).

Language: Английский

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The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: June 16, 2022

Abstract Phenotypic variation in organism-level traits has been studied Caenorhabditis elegans wild strains, but the impacts of differences gene expression and underlying regulatory mechanisms are largely unknown. Here, we use natural to connect genetic variants organismal-level traits, including drug toxicant responses. We perform transcriptomic analyses on 207 genetically distinct C. strains study expression. Using this massive dataset, genome-wide association mappings investigate basis reveal complex architectures. find a large collection hotspots enriched for quantitative trait loci across genome. further mediation analysis understand how could underlie phenotypic variety traits. These results diversity possible keystone model organism, highlighting promise using is generated.

Language: Английский

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Natural genetic variation as a tool for discovery in Caenorhabditis nematodes

Genetics, Journal Year: 2022, Volume and Issue: 220(1)

Published: Jan. 1, 2022

Abstract Over the last 20 years, studies of Caenorhabditis elegans natural diversity have demonstrated power quantitative genetic approaches to reveal evolutionary, ecological, and factors that shape traits. These complement use laboratory-adapted strain N2 enable additional discoveries not possible using only one background. In this chapter, we describe how perform in Caenorhabditis, with an emphasis on C. elegans. correlations between genotype phenotype across populations genetically diverse individuals discover causes phenotypic variation. We present methods linkage, near-isogenic lines, association, bulk-segregant mapping, advantages disadvantages each approach. The mapping is best shown ability connect differences specific genes variants. will narrow genomic regions candidate then tests identify gene or variant involved a trait. same features make preeminent experimental model animal contribute its exceptional value as tool understand

Language: Английский

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Defining characteristics and conservation of poorly annotated genes in Caenorhabditis elegans using WormCat 2.0

Genetics, Journal Year: 2022, Volume and Issue: 221(4)

Published: May 19, 2022

Omics tools provide broad datasets for biological discovery. However, the computational identifying important genes or pathways in RNA-seq, proteomics, GWAS (Genome-Wide Association Study) data depend on Gene Ontogeny annotations and are biased toward well-described pathways. This limits their utility as poorly annotated genes, which could have novel functions, often passed over. Recently, we developed an annotation category enrichment tool Caenorhabditis elegans genomic data, WormCat, provides intuitive visualization output. Unlike Ontogeny-based tools, exclude with no information, WormCat 2.0 retains these a special UNASSIGNED category. Here, show that gene exhibits tissue-specific expression patterns can include functions identified published datasets. Poorly considered to be potentially species-specific thus, of reduced interest biomedical community. Instead, find around 3% human orthologs, including some linked diseases. These orthologs themselves little information. A recently method incorporates lineage relationships (abSENSE) indicates failure BLAST detect homology explains apparent specificity many genes. suggests larger subset related strategy allows association specific phenotypes known Building associations C. elegans, its robust genetic path further functional study insight into understudied

Language: Английский

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Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(4)

Published: March 22, 2022

The publication of the Caenorhabditis briggsae reference genome in 2003 enabled first comparative genomics studies between C. elegans and briggsae, shedding light on evolution content structure genus. However, despite being widely used, currently available is substantially less complete structurally accurate than genome. Here, we used high-coverage Oxford Nanopore long-read chromosome-conformation capture data to generate chromosome-level genomes for two strains: QX1410, a new strain closely related laboratory AF16 strain, VX34, highly divergent isolated China. We also sequenced 99 recombinant inbred lines generated from reciprocal crosses QX1410 VX34 create recombination map identify chromosomal domains. Additionally, both short- RNA sequencing high-quality gene annotations. By comparing these current reference, reveal that hyper-divergent haplotypes cover large portions genome, similar recent reports tropicalis. show selfing species have undergone more rearrangement their outcrossing relatives, which has biased previous estimates rate Caenorhabditis. These provide improved platform narrow gap quality genomic resources briggsae.

Language: Английский

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