Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 17, 2025

The innovations of the "Omics Era" have ushered in significant advancements genetic improvement agriculturally important animal species through transforming genetics, genomics and breeding strategies. These were often coordinated, part, by support provided over 30 years 1993-2023 National Research Support Project 8 (NRSP8, Animal Genome Program, NAGRP) affiliate projects focused on enabling genomic discoveries livestock, poultry, aquaculture species. parallel advances demand strategic planning future research priorities. This paper, as an output from May 2023 Aquaculture Genomics, Genetics, Breeding Workshop, provides updated status resources for United States species, highlighting major achievements emerging Finfish shellfish genome omics enhance our understanding architecture heritability performance production traits. Workshop identified present aims genomics/omics to build this progress: (1) advancing reference assembly quality; (2) integrating multi-omics data analysis traits; (3) developing collection integration phenomics data; (4) creating pathways applying information across industries; (5) providing training, extension, outreach application phenome. focuses should emphasize collection, artificial intelligence, identifying causative relationships between genotypes phenotypes, establishing apply tools industries, expansion training programs next-generation workforce facilitate sciences into operations productivity, competitiveness, sustainability. collective vision with focus highlighted priorities is intended continued advancement genomics, genetics community industries. Critical challenges ahead include practical analytical frameworks beyond academic communities that require collaborative partnerships academia, government, industry. scope review encompasses use applications study aquatic animals cultivated human consumption settings throughout their life-cycle.

Language: Английский

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Impaired reproduction, energy reserves and dysbiosis: The overlooked consequences of heatwaves in a bivalve mollusc

Marine Pollution Bulletin, Journal Year: 2023, Volume and Issue: 193, P. 115192 - 115192

Published: June 24, 2023

Extreme events like Marine Heatwaves (MHWs) are becoming more intense, severe, and frequent, threatening benthic communities, specifically bivalves. However, the consequences of non-lethal MHWs on animals still poorly understood. Here, we exposed Manila clam Ruditapes philippinarum to MHW for 30 days provided an integrative view its effects. Our result indicated that albeit non-lethal, reduced clam's energy reserves (by reducing their hepato-somatic index), triggered antioxidant defenses (particularly in males), impaired reproduction (via production smaller oocytes females), dysbiosis digestive gland microbiota altered animals' behaviour impacting burying capacity) filtration rate. Such effects were seen also at RNA-seq (i.e. many down-regulated genes belonged reproduction) metabolome level. Interestingly, negative pronounced males than females. results show influence animal physiology multiple levels, likely fitness ecosystem services.

Language: Английский

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Exploring the evolution of sex determination related genes through a cross-species genomics analysis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

Abstract The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood many animal groups. Bivalves, a diverse class molluscs with variety reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution sexual systems. However, absence comprehensive framework has limited progress this field, particularly regarding study sex-determination related genes (SRGs). In study, we performed genome-wide sequence evolutionary analysis Dmrt, Sox, Fox gene families more than 40 bivalve species. For first time, provide extensive phylogenetic-aware dataset these SRGs, find support to hypothesis that Dmrt-1L Sox-H may act as primary sex-determining genes, by showing their high levels diversity within genomic context. To validate our findings, same two well-characterized systems, mammals Drosophila . former, found male Sry exhibits pattern amino acid similar bivalves, consistent its role master regulator. contrast, no such was observed among fruit fly cascade, which is controlled chromosomic mechanism. Overall, findings highlight similarities some mammal possibly driven comparable architecture cascades. This work underscores once again importance employing comparative approach when understudied non-model

Language: Английский

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The underrated immune role of bivalve ‘serous cells’: new insight from inflammatory responses of the Manila clam Ruditapes philippinarum

Fish & Shellfish Immunology, Journal Year: 2025, Volume and Issue: unknown, P. 110188 - 110188

Published: Feb. 1, 2025

This study investigated the immune role of serous cells from bivalve Ruditapes philippinarum. Histochemical and immunohistochemical assays revealed that contained large cytoplasmic vacuoles rich in heparinoid molecules. Heparin histamine were detected within vacuoles, with distinct spatial distributions, histoenzymatic for serine proteases both tryptase chymase activity. These findings, together membrane immunolabelling c-kit, suggest similarities vertebrate mast cells. After vivo bacterial inoculation, first accumulated at injury site 12 h, 15 h after vitro treatment, a significant increase percentage was observed bacteria-treated samples, supporting targeted responses proliferation differentiation following challenge. Serous also underwent marked degranulation stimulation, aggregates granulocytes, hyalinocytes appeared 1 treatment. Extracellular trap formation (ETosis), which is degranulated trapped dying bacteria, h. showed nuclear envelope loss chromatin fragmentation. The extracellular nets primarily composed fragmented amyloid fibrils forming scaffold woven fibres, to adhesion heparin, histamine, occurred their release into environment. To our knowledge, this highlights important response bivalves provides new perspectives future investigations modulation inflammatory process.

Language: Английский

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Genome Assembly of Arctica islandica, the Longest-Lived Non-Colonial Animal Species

Animals, Journal Year: 2025, Volume and Issue: 15(5), P. 690 - 690

Published: Feb. 27, 2025

We report the first high-quality genome-wide assembly for Arctica islandica, longest-lived non-colonial species, with a reported maximum life span of 507 years. The genome was assembled using short- and long-read DNA sequencing RNA four tissues. All assessment approaches indicated that is complete, contiguous, accurate. size estimated at 1781.15 million base pairs (Mbps) coverage 247.8×. heterozygous rate 1.15% repeat content 67.66%. Genome completeness evaluated by complete BUSCOs 92.7%. non-redundant gene set consisted 39,509 genes an average transcript length 15,429 bp. More than 98% could be annotated across databases. Predicted non-coding RNAs included 801 miRNAs, 11,114 tRNAs, 909 rRNAs, 349 snRNAs. islandica genome, along genomes from other clam sets stage elucidating molecular basis convergence extreme longevity these bivalve species.

Language: Английский

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Genome-wide identification and expression analysis of Dmrt gene family and their role in gonad development of Pacific oyster (Crassostrea gigas)

Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology, Journal Year: 2023, Volume and Issue: 269, P. 110904 - 110904

Published: Sept. 24, 2023

Language: Английский

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Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(10)

Published: Oct. 1, 2023

Bivalves are a diverse group of molluscs that have recently attained central role in plenty biological research fields, thanks to their peculiar life history traits. Here, we propose bivalves should be considered as emerging model systems also sex-determination (SD) studies, since they would allow investigate: 1) the transition between environmental and genetic SD, with respect different reproductive backgrounds sexual (from species strict gonochorism various forms hermaphroditism); 2) genomic evolution sex chromosomes (SCs), considering no heteromorphic SCs currently known homomorphic been identified only few scallops; 3) putative mitochondria at some level SD signaling pathway, mechanism may resemble cytoplasmatic male sterility plants; 4) evolutionary SD-related gene (SRG) families other animal groups. In particular, think this last topic lay foundations for expanding our understanding bivalve current knowledge is quite fragmented limited species. As matter fact, tracing phylogenetic diversity SRG (such Dmrt, Sox, Fox genes) not perform more targeted functional experiments analyses, but foster possibility establishing solid comparative framework.

Language: Английский

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Advances in biotechnology and breeding innovations in China’s marine aquaculture

Advanced Biotechnology, Journal Year: 2024, Volume and Issue: 2(4)

Published: Oct. 18, 2024

Biotechnology is the key driving force behind sustainable development of aquaculture, as biological innovation would significantly improve capabilities aquatic breeding and achieve independent controllable seeding sources to ensure food safety. In this article, we have analyzed current status existing problems marine aquaculture in China. Based on these data, summarized recent (especially last 10 years) biotechnological progress China, including whole genome sequencing, sex-related marker screening, genomic selection, editing, well improved fish varieties Finally, perspectives field been discussed, three future countermeasures proposed.

Language: Английский

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Sex‐specific gene expression in eastern oyster, Crassostrea virginica, gonad and mantle tissues

Invertebrate Biology, Journal Year: 2024, Volume and Issue: 143(1)

Published: Feb. 7, 2024

Abstract The eastern oyster ( Crassostrea virginica ) is a protandrous hermaphrodite of commercial importance. As with many marine invertebrates, little known about sex determination and differentiation systems in this species. Such knowledge has important implications not only for understanding the evolution but also applied questions aquaculture. In order to examine mechanistic differences reproductive development between sexes, we compared transcriptomes gonad mantle tissues from six male female oysters. A total 7675 transcripts were differentially expressed gonads (3936 3739 upregulated males females, respectively). Transcripts identified include those associated other invertebrate vertebrate species such as Dmrt1 , Sox‐30 Bindin Dpy‐30 Histone H4 Foxl2 Vitellogenin Bystin females. GO terms protein modification, process, cell projection organization, whereas RNA metabolic process amino acid Far fewer tissues, 87 females 16 males. However, 41% including . This study represents first characterization transcriptomes. We further identify differing expression profiles which provides evidence sex‐specific functions suggests that tissue could harbor biomarkers identifying non‐destructively.

Language: Английский

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Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance

Evolution, Journal Year: 2024, Volume and Issue: 78(11), P. 1790 - 1803

Published: July 11, 2024

Abstract Mitonuclear coevolution is common in eukaryotes, but bivalve lineages that have doubly uniparental inheritance (DUI) of mitochondria may be an interesting example. In this system, females transmit mtDNA (F mtDNA) to all offspring, while males a different (M solely their sons. Molecular evolution and functional data suggest oxidative phosphorylation (OXPHOS) genes encoded M evolve under relaxed selection due function being limited sperm only (vs. other tissues for F mtDNA). This has led the hypothesis mitonuclear less important mtDNA. Here, we use comparative phylogenetics, transcriptomics, proteomics understand interactions DUI bivalves. We found nuclear OXPHOS proteins coevolve maintain compatibility similarly with both proteins. Mitochondrial recombination did not influence nuclear-encoded were upregulated offset dysfunction. Our results support maintains despite on Strict transmission, lower effective population size, higher mutation rates explain study highlights broad features eukaryotes.

Language: Английский

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