How genomics can help biodiversity conservation

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(7), P. 545 - 559

Published: Feb. 16, 2023

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches applications in conservation genomics, considering practical factors, such as cost, time, prerequisite skills, current shortcomings applications. Most perform best combination with reference genomes from target species or closely related species. We review case studies to illustrate how facilitate research across tree life. conclude that time is ripe view fundamental integrate their use a practice genomics.

Language: Английский

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The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(11), P. 5066 - 5081

Published: July 29, 2021

Domestication and breeding have reshaped the genomic architecture of chicken, but retention loss elements during these evolutionary processes remain unclear. We present first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from reference genome (GRCg6a). The encoded 20,491 predicated protein-coding genes, higher expression levels observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated gene PAV was shaped by selection, genetic drift, hybridization. PAV-based genome-wide association studies numerous candidate mutations related growth, carcass composition, meat quality, or physiological traits. Among them, a deletion promoter region IGF2BP1 affecting body size is reported, supported functional extra samples. This time report causal variant quantitative trait locus located at chromosome 27 repeatedly reported. Therefore, useful resource for biological discovery breeding. It improves our understanding diversity provides materials unveil evolution history domestication.

Language: Английский

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A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 5, 2023

Abstract As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to complex routes of origin and migration, suggesting possible omission some population-specific sequences in current genome. Conversely, pangenome is collection all DNA contains shared by individuals (core genome) also able display sequence information unique each individual (variable genome). The progress research humans, plants proved missing components identification large structural variants (SVs) can be explored through pangenomic studies. Many specific shown related biological adaptability, phenotype important economic traits. maturity technologies methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic reference-free assembly will further promote development pangenome. In future, combined with long-read data multi-omics help resolve SVs their relationship main traits interest domesticated animals, providing better insights into animal domestication, evolution breeding. this review, we mainly discuss how analysis reveals variations (sheep, cattle, pigs, chickens) impacts on phenotypes contribute understanding diversity. Additionally, go potential issues future perspectives livestock poultry.

Language: Английский

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Pangenome graphs and their applications in biodiversity genomics

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

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A genome-based phylogeny for Mollusca is concordant with fossils and morphology

Science, Journal Year: 2025, Volume and Issue: 387(6737), P. 1001 - 1007

Published: Feb. 27, 2025

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—each represent diverse radiation with myriad morphological, ecological, behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed living on basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members all eight classes two high-quality genome assemblies monoplacophorans. Our analyses confirm proposed morphology show widespread genomic variation. flexibility likely explains both historic challenges their genomes evolutionary success.

Language: Английский

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Fungal evolution: cellular, genomic and metabolic complexity

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2020, Volume and Issue: 95(5), P. 1198 - 1232

Published: April 17, 2020

The question of how phenotypic and genomic complexity are inter-related they shaped through evolution is a central in biology that historically has been approached from the perspective animals plants. In recent years, however, fungi have emerged as promising alternative system to address such questions. Key their ecological success, present broad diverse range traits. Fungal cells can adopt many different shapes, often within single species, providing them with great adaptive potential. cellular organizations span unicellular forms complex, macroscopic multicellularity, multiple transitions higher or lower levels occurring throughout evolutionary history fungi. Similarly, fungal genomes very architecture. Deep changes genome organization occur quickly, these phenomena known mediate rapid adaptations environmental changes. Finally, biochemical huge, particularly regard secondary metabolites, chemical products aspects biology, including interactions. Herein, we explore interplay cellular, metabolic traits mediates emergence complex phenotypes, this Fungi.

Language: Английский

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The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(3), P. 641 - 652

Published: Dec. 17, 2020

Abstract The quality of genome assemblies has improved rapidly in recent years due to continual advances sequencing technology, assembly approaches, and control. In the field molecular ecology, this led development exceptional that will be important long‐term resources for broader studies into ecological, conservation, evolutionary, population genomics naturally occurring species. Moreover, extent which a single reference represents diversity within species varies: pan‐genomes become increasingly ecological resources, particularly systems found have considerable presence‐absence variation their functional content. Here, we highlight technology raised bar provide guidance on standards achieve genomes. Key recommendations include following: (a) Genome should long‐read except rare cases where it is effectively impossible acquire adequately preserved samples needed high weight DNA standards. (b) At least one scaffolding approach included with such as Hi‐C or optical mapping. (c) carefully evaluated, may involve utilising short read data polishing, error correction, k‐mer analyses, estimating percent reads map back an assembly. Finally, most valuable if all methods are made publicly available utility further verified through examples. While these based current anticipate future push ecology community continue adopt new approaches attain highest assemblies.

Language: Английский

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Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia

GigaScience, Journal Year: 2021, Volume and Issue: 10(4)

Published: April 1, 2021

Abstract Background The hard-shelled mussel (Mytilus coruscus) is widely distributed in the temperate seas of East Asia and an important commercial bivalve China. Chromosome-level genome information this species will contribute not only to development genetic breeding but also studies on larval ecology, climate change biology, marine aquaculture, biofouling, antifouling. Findings We applied a combination Illumina sequencing, Oxford Nanopore Technologies high-throughput chromosome conformation capture technologies construct chromosome-level mussel, with total length 1.57 Gb median contig 1.49 Mb. Approximately 90.9% assemblies were anchored 14 linkage groups. assayed completeness using BUSCO. In metazoan dataset, present have 89.4% complete, 1.9% incomplete, 8.7% missing BUSCOs. Gene modeling enabled annotation 37,478 protein-coding genes 26,917 non-coding RNA loci. Phylogenetic analysis showed that M. coruscus sister taxon clade including Modiolus philippinarum Bathymodiolus platifrons. Conserved synteny was observed between king scallop, suggesting shared ancestrally. Transcriptomic profiling indicated pathways catecholamine biosynthesis adrenergic signaling cardiomyocytes might be involved metamorphosis. Conclusions assembly provide novel insights into evolution serve as fundamental platform for regarding planktonic-sessile transition, diversity, genomic bivalve.

Language: Английский

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Recent advances in crustacean genomics and their potential application in aquaculture

Reviews in Aquaculture, Journal Year: 2023, Volume and Issue: 15(4), P. 1501 - 1521

Published: Jan. 23, 2023

Abstract Genomic resources are increasingly being used to improve the production efficiency and profitability of aquaculture. Crustaceans a large group invertebrates that encompasses some most important farmed species in aquaculture industry. However, very few crustacean genomes have been published although an genome project was proposed as early 1997. Breakthroughs next‐generation third‐generation sequencing technologies development high‐complexity sequence assembly strategies promoted publication increasing number genomes, thus paving broad way for biological genetic studies applications In this review, we summarize recent advances genomic research June 2022, including assembly, characteristics, mechanisms underlying various phenotypes, such environmental adaptation, lifestyle, development, sex determination. This review also discusses application aquaculture, dissection economic traits genome‐based selective breeding via genome‐wide association selection. High‐quality not only understanding basis biologically economically but improvement species. utilization genomics still lags far behind those other animals. Therefore, additional multi‐omics technological needed accelerate

Language: Английский

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Integrated evidence of transcriptional, metabolic, and intestinal microbiota changes in Ruditapes philippinarum due to perfluorooctanoic acid-induced immunotoxicity

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 916, P. 170341 - 170341

Published: Jan. 23, 2024

Language: Английский

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