Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice

Phenogenomic resources immortalized in a panel of wild-derived strains of five species of house mice

The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. This study quantifies genetic and phenotypic data of 101 WDS representing 5 species, 3 subspecies, and 8 natural Y consomic strains and compares them with CLS. Genetic variability was estimated using whole mtDNA sequences, the Prdm9 gene, and copy number variation at two sex chromosome-linked genes. WDS exhibit a large natural variation with up to 2173 polymorphic sites in mitogenomes, whereas CLS display 92 sites. Moreover, while CLS have two Prdm9 alleles, WDS harbour 46 different alleles. Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 10 and 14 out of 16 phenotypic traits, respectively. The results suggest that WDS can be a useful tool in evolutionary and biomedical studies with great potential for medical applications.

Genomically Selected Genes Associated with a High Rate of Egg Production in Puan Panjiang Black-Bone Chickens

Puan Panjiang black-bone chickens are renowned for their distinctive traits, deep black coloration, and high-quality protein content, making them a focus of genetic research due to their unique egg-laying abilities. In this study, 110 Puan Panjiang black-bone chickens were used to investigate the effects of natural and artificial selection influencing egg production. Whole-genome resequencing data from red junglefowl (RJF) and high-egg-production (HEP) and low-egg-production (LEP) groups of Puan Panjiang black-bone chickens revealed significant genetic variants associated with egg production traits. Additionally, transcriptome analysis of 47 samples from ovary stroma, small white follicles (SWFs), small yellow follicles (SYFs), and liver tissues from 6 HEP and 6 LEP groups identified differentially expressed genes. Notably, differences in egg production were linked to small yellow follicles rather than ovary stroma or SWFs. Key candidate genes, including TRIM7, CASR, SPTBN5, GAL1, ZP1, IL4I1, and CCL19, were identified as potential contributors to egg-laying performance. This study underscores the genetic diversity within this breed and provides valuable insights for future breeding programs to enhance egg production, supporting the sustainable development of this local resource.

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

Introduction

The Wuzhishan ant (MY) chicken exhibits significant differences from other chicken breeds. However, the molecular genetic relationship between the MY breed and other chicken breeds has not been assessed.

Methods

Whole-genome resequencing was used to compare genetic diversity, nucleotide diversity, the fixation index, the linkage disequilibrium coefficient, and phylogenetic tree relationships between the MY breed and the Wenchang (WC), Danzhou (DZ), Bawangling (BW), and Longsheng Feng (LF) breeds.

Results

A total of 21,586,378 singlenucleotide polymorphisms and 4,253,341 insertions/deletions were screened out among the five breeds. The MY breed had the second highest genomic genetic diversity and nucleotide diversity and the lowest LD coefficient among the five breeds. Moreover, the phylogenetic tree analysis showed that individual birds of each breed clustered together with those of their respective breeds.

Discussion

Our data indicated that the MY breed is distinct from the other breeds and can be considered a new genetic resource.

Fraxin (7-hydroxy-6-methoxycoumarin 8-glucoside) confers protection against ionizing radiation-induced intestinal epithelial injury in vitro and in vivo

The small intestine exhibits remarkable sensitivity to ionizing radiation (IR), which significantly hampers the effectiveness of radiotherapy in the treatment of abdominal and pelvic tumors. Unfortunately, no effective medications are available to treat radiation-induced intestinal damage (RIID). Fraxin (7-hydroxy-6-methoxycoumarin 8-glucoside), is a coumarin derivative extracted from the Chinese herb Cortex Fraxini. Several studies have underscored the anti-inflammatory, antibacterial, antioxidant, and immunomodulatory properties of fraxin. However, the efficacy of fraxin at preventing or mitigating RIID remains unclear. Thus, the present study aimed to investigate the protective effects of fraxin against RIID in vitro and in vivo and to elucidate the underlying mechanisms. The study findings revealed that fraxin markedly ameliorated intestinal injuries induced by 13 Gy whole abdominal irradiation (WAI), which was accompanied by a significant increase in the population of Lgr5+ intestinal stem cells (ISCs) and Ki67+ progeny. Furthermore, fraxin mitigated WAI-induced intestinal barrier damage, and reduced oxidative stress and intestinal inflammation in mice. Transcriptome sequencing of fraxin-treated mice revealed upregulation of IL-22, a pleiotropic cytokine involved in regulating the function of intestinal epithelial cells. Moreover, in both human intestinal epithelial cells and ex vivo cultured mouse intestinal organoids, fraxin effectively ameliorated IR-induced damage by promoting the expression of IL-22. The radioprotective effects of fraxin were partially negated in the presence of an IL-22-neutralizing antibody. In summary, fraxin is demonstrated to possess the ability to alleviate RIID and maintain intestinal homeostasis, suggesting that fraxin might serve as a strategy for mitigating accidental radiation exposure- or radiotherapy-induced RIID.

What made us "hunter-gatherers of words"

This paper makes three interconnected claims: (i) the "human condition" cannot be captured by evolutionary narratives that reduce it to a recent 'cognitive modernity', nor by narratives that eliminates all cognitive differences between us and out closest extinct relatives, (ii) signals from paleogenomics, especially coming from deserts of introgression but also from signatures of positive selection, point to the importance of mutations that impact neurodevelopment, plausibly leading to temperamental differences, which may impact cultural evolutionary trajectories in specific ways, and (iii) these trajectories are expected to affect the language phenotypes, modifying what is being learned and how it is put to use. In particular, I hypothesize that these different trajectories influence the development of symbolic systems, the flexible ways in which symbols combine, and the size and configurations of the communities in which these systems are put to use.