Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species

Piégu, Benoît; Arensburger, Peter; Chabault, Marie; Raynaud, Emilie; Coustham, Vincent; Brard, Sophie; Guizard, Sébastien; Burlot, Thierry; Bihan-Duval, Élisabeth Le; Bigot, Yves

doi:10.1016/j.ygeno.2019.10.004

Cited by 20 publications

(20 citation statements)

References 74 publications

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“…For chicken, Illumina genome re-sequencing libraries were collected for two females and three males of Gallus gallus gallus (red junglefowl) from [ 77 ] (originally uploaded on NCBI as of undetermined sex) and a female library of Gallus gallus bankiva (red junglefowl from Java) from [ 78 ]. The sexes of the individuals from [ 77 ] were determined using the SEXCMD with default sex markers [ 79 ].…”

Section: Methodsmentioning

confidence: 99%

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

Peona

Palacios-Gimenez

Blommaert

et al. 2021

Phil. Trans. R. Soc. B

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It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

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Section: Methodsmentioning

confidence: 99%

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

Peona

Palacios-Gimenez

Blommaert

et al. 2021

Phil. Trans. R. Soc. B

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“…The tandem and segmental duplicated genes play an important role in evolution, domestication, functional regulation, and biotic and abiotic stresses (Ahmad et al, 2020a; Li et al, 2020; Liu et al, 2020; Piégu et al, 2020; Song et al, 2020). We determined segmental duplication of nine genes that form four groups as: tcGASA 2- tcGASA 3- tcGASA 13, tcGASA 8- tcGASA 9, tcGASA 14- tcGASA 15, and tcGASA10 - tcGASA17 .…”

Section: Discussionmentioning

confidence: 99%

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

Abdullah

Faraji

Mehmood

et al. 2021

Preprint

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The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20–25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.

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“…Not surprisingly, relatively little is known about the aging transcriptome in birds, with the exception of studies of brain [160] and thymus [161] transcriptomes in populations of domestic chicken. Dramatic differences in the basic genomics of wild vs. domesticated species may be problematic when trying to extrapolate findings from these studies to birds in general [162].…”

Section: Avian Transcriptomicsmentioning

confidence: 99%

New Perspectives on Avian Models for Studies of Basic Aging Processes

Harper

Holmes

2021

Biomedicines

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Avian models have the potential to elucidate basic cellular and molecular mechanisms underlying the slow aging rates and exceptional longevity typical of this group of vertebrates. To date, most studies of avian aging have focused on relatively few of the phenomena now thought to be intrinsic to the aging process, but primarily on responses to oxidative stress and telomere dynamics. But a variety of whole-animal and cell-based approaches to avian aging and stress resistance have been developed—especially the use of primary cell lines and isolated erythrocytes—which permit other processes to be investigated. In this review, we highlight newer studies using these approaches. We also discuss recent research on age-related changes in neural function in birds in the context of sensory changes relevant to homing and navigation, as well as the maintenance of song. More recently, with the advent of “-omic” methodologies, including whole-genome studies, new approaches have gained momentum for investigating the mechanistic basis of aging in birds. Overall, current research suggests that birds exhibit an enhanced resistance to the detrimental effects of oxidative damage and maintain higher than expected levels of cellular function as they age. There is also evidence that genetic signatures associated with cellular defenses, as well as metabolic and immune function, are enhanced in birds but data are still lacking relative to that available from more conventional model organisms. We are optimistic that continued development of avian models in geroscience, especially under controlled laboratory conditions, will provide novel insights into the exceptional longevity of this animal taxon.

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Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species

Cited by 20 publications

References 74 publications

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

New Perspectives on Avian Models for Studies of Basic Aging Processes

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