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Article
Open AccessThe black honey bee genome: insights on specific structural elements and a first step towards pangenomes
The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred...
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Article
Open AccessMulti-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along wi...
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Article
Open AccessSoluble CD14 produced by bovine mammary epithelial cells modulates their response to full length LPS
Bovine mastitis remains a major disease in cattle world-wide. In the mammary gland, mammary epithelial cells (MEC) are sentinels equipped with receptors allowing them to detect and respond to the invasion by b...
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Article
Open AccessA candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes
Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowle...
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Article
Open AccessEnriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues
Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA ...
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Article
Open AccessThe genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles
Venoms have evolved independently over a hundred times in the animal kingdom to deter predators and/or subdue prey. Venoms are cocktails of various secreted toxins, whose origin and diversification provide an ...
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Article
Open AccessA pangenome graph reference of 30 chicken genomes allows genoty** of large and complex structural variants
The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of c...
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Article
Open AccessWhole genome sequencing reveals signals of adaptive admixture in Creole cattle
The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of sele...
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Article
Open AccessA Bos taurus sequencing methods benchmark for assembly, haploty**, and variant calling
Inspired by the production of reference data sets in the Genome in a Bottle project, we sequenced one Charolais heifer with different technologies: Illumina paired-end, Oxford Nanopore, Pacific Biosciences (Hi...
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Open AccessCorrection to: Development of a polymerase chain reaction (PCR)-based genetic sex identification method in the chub mackerel Scomber japonicus and blue mackerel S. australasicus
The original article has been corrected.
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Article
Open AccessA duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)
Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating ...
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Article
Open AccessDevelopment of a polymerase chain reaction (PCR)-based genetic sex identification method in the chub mackerel Scomber japonicus and blue mackerel S. australasicus
Chub mackerel Scomber japonicus and blue mackerel S. australasicus have become important aquaculture target species in Japan. For an efficient and stable aquaculture production of mackerels, it is desirable to wo...
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Open AccessAuthor Correction: An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
Open AccessGenetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in deve...
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Article
Open AccessAn integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken gene...
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Article
Open AccessSex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758)
Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a mal...
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Article
Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning
Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher h...
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Article
Open AccessBiological rhythms in the deep-sea hydrothermal mussel Bathymodiolus azoricus
Biological rhythms are a fundamental property of life. The deep ocean covers 66% of our planet surface and is one of the largest biomes. The deep sea has long been considered as an arrhythmic environment becau...
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Article
Open AccessThe sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons...
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Article
Open AccessMulti-species annotation of transcriptome and chromatin structure in domesticated animals
Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-t...
