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Genomic Signatures of Domestication Selection in the Australasian Snapper (Chrysophrys auratus).

ABSTRACT: Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of F_ST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations F_ST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.

SUBMITTER: Baesjou JP

PROVIDER: S-EPMC8623400 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:In Australia and New Zealand (NZ), snapper Chrysophrys auratus is known for delicate mild flavoured flesh and is a favoured species to serve raw as sashimi or in sushi. The diet of snapper includes a variety of intermediate hosts of larval nematodes, and as a result, snapper has potential to become highly infected with zoonotic/non-zoonotic nematodes. The aims of this study were to survey nematodes in snapper from Australia and New Zealand waters and to identify nematode species using combined morphological and molecular methods. The zoonotic potential of nematodes identified in this study are discussed. A total of 112 snapper were purchased from the Sydney fish market, New South Wales, Australia. Fish were dissected and only the visceral content and digestive tract were examined for nematode infection. Parasites were initially identified by the microscopic method as four different types belonging to the families Anisakidae (Anisakis types I & III, and Terranova type II) and Cucullanidae (Dichelyne spp.). All Anisakidae nematodes were at infective stages. Species-level identification was actualised through sequencing of the internal transcribed spacer (ITS-1, 5.8S, ITS-2) regions. The Anisakis types I & III were confirmed as Anisakis pegreffii and A. brevispiculata, respectively of which A. pegreffii is considered globally as a zoonotic nematode. The specific identification of Terranova type II and Dichelyne spp. was not possible as no comparable sequence data were available in GenBank. The phylogenetic tree clustered Anisakis types I & III with A. pegreffii and A. brevispiculata, respectively; Terranova type II sequences as a separate clade with previously identified larval and adult Terranova and Pseudoterranova species. Based on phylogenetic analyses the present Cucullanid specimens were assigned herein as Dichelyne cf. pleuronectidis, and an unknown species Dichelyne sp. 1. This study represents the first host record globally for zoonotic Anisakid nematodes in this popularly consumed table fish and a new region record for D. cf. pleuronectidis and Dichelyne sp. 1. Further investigation is required, using more comprehensive parasite detection and recovery methods, to assess the health risk these nematodes may pose to human and fish health in Australia/NZ.

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Genomic Signatures of Domestication Selection in the Australasian Snapper (Chrysophrys auratus).

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