De novo Phased Genome Assembly, Annotation and Population Genotyping of Alectoris Chukar.

The Alectoris Chukar (chukar) is the most geographically widespread partridge species in the world, demonstrating exceptional adaptability to diverse ecological environments. However, the scarcity of genetic resources for chukar has hindered research into its adaptive evolution and molecular breeding. In this study, we have sequenced and assembled a high-quality, phased chukar genome that consists of 31 pairs of relatively complete diploid chromosomes. Our BUSCO analysis reported a high completeness score of 96.8% and 96.5%, with respect to universal single-copy orthologs and a low duplication rate (0.3% and 0.5%) for two assemblies. Through resequencing and population genomic analyses of six subspecies, we have curated invaluable genotype data that underscores the adaptive evolution of chukar in response to both arid and high-altitude environments. These data will significantly contribute to research on how chukars adaptively evolve to cope with desertification and alpine climates.

Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens.

The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985-4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467-2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.

MicroRNAs Involved in Oxidative Stress Processes Regulating Physiological and Pathological Responses.

Oxidative stress influences several physiological and pathological cellular events, including cell differentiation, excessive growth, proliferation, apoptosis, and inflammatory response. Therefore, oxidative stress is involved in the pathogenesis of various diseases, including pulmonary fibrosis, epilepsy, hypertension, atherosclerosis, Parkinson's disease, cardiovascular disease, and Alzheimer's disease. Recent studies have shown that several microRNAs (miRNAs) are involved in the development of various diseases caused by oxidative stress and that miRNAs may be useful to determine the inflammatory characteristics of immune responses during infection and disease. In this review, we describe the known effects of miRNAs on reactive oxygen species to induce oxidative stress and miRNA regulatory mechanisms involved in the uncoupling of Keap1-Nrf2 complexes. Finally, we summarized the functions of miRNAs in several antioxidant genes. Understanding the crosstalk between miRNAs and oxidative stress-inducing factors during physiological and pathological cellular events may have implications for the design of more effective treatments for immune diseases.

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China.

Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.

Genomic variations and signatures of selection in Wuhua yellow chicken.

Wuhua yellow chicken (WHYC) is an important traditional yellow-feathered chicken from China, which is characterized by its white tail feathers, white flight feathers, and strong disease resistance. However, the genomic basis of these unique traits associated with WHYC is poorly understood. In this study, whole-genome resequencing was performed with an average coverage of 20.77-fold to investigate heritable variation and identify selection signals in WHYC. Reads were mapped onto the chicken reference genome (Galgal5) with a coverage of 85.95%. After quality control, 11,953,471 single nucleotide polymorphisms and 1,069,574 insertion/deletions were obtained. In addition, 41,408 structural variants and 33,278 copy number variants were found. Comparative genomic analysis of WHYC and other yellow-feathered chicken breeds showed that selected regions were enriched in genes involved in transport and catabolism, immune system, infectious diseases, signal transduction, and signaling molecules and interactions. Several genes associated with disease resistance were also identified, including IFNA, IFNB, CD86, IL18, IL11RA, VEGFC, and ATG10. Furthermore, our results suggest that PMEL and TYRP1 may contribute to the white feather coloring in WHYC. These findings can improve our understanding of the genetic characteristics of WHYC and may contribute to future breed improvement.

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds.

BACKGROUND: Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration. RESULTS: The whole-genomes of 100 YFCs from 10 major traditional breeds and 10 Huaibei partridge chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed three geographically based clusters among the YFCs. Compared to other Chinese indigenous chicken genomes incorporated from previous studies, a closer genetic proximity within YFC breeds than between YFC breeds and other chicken populations is evident. Through genome-wide scans for selective sweeps, we identified RALY heterogeneous nuclear ribonucleoprotein (RALY), leucine rich repeat containing G protein-coupled receptor 4 (LGR4), solute carrier family 23 member 2 (SLC23A2), and solute carrier family 2 member 14 (SLC2A14), besides the classical beta-carotene dioxygenase 2 (BCDO2), as major candidates pigment determining genes in the YFCs. CONCLUSION: We provide the first comprehensive genomic data of the YFCs. Our analyses show phylogeographical patterns among the YFCs and potential candidate genes giving rise to the yellow color trait of the YFCs. This study lays the foundation for further research on the genome-phenotype cross-talks that define important poultry traits and for formulating genetic breeding and conservation strategies for the YFCs.

Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus).

In this study, we sequenced the complete mitochondrial DNA genome (mitogenome) of the Zhengyang Yellow chicken (Gallus gallus domesticus) by next-generation sequencing technology. Samples were taken from Zhumadian city, Henan Province, China. The complete mitogenome was 16 785 bp in size, and had a nucleotide composition of 30.3% (A), 23.7% (T), 32.5% (C), and 13.5% (G), with a high AT content of 54.0%. The assembled mitogenome exhibited typical mitochondrial DNA (mtDNA) structure, including a non-coding control region, two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. Phylogenetic analysis indicated that this mitogenome defined a novel sub-haplogroup B3 within haplogroup B. These results should provide essential information for chicken domestication and insight into the evolution of genomes.

Complete mitochondrial genome of the Wuhua three-yellow chicken (Gallus gallus domesticus).

Wuhua three-yellow chicken is a native breed of Guangdong Province in China. The complete mitochondrial DNA (mtDNA) genome presented here was the first assemble of Wuhua three-yellow chicken, which was determined through the polymerase chain reaction-based method. The complete mitogenome was 16,784 bp in length, with the nucleotide composition of 30.29% for A, 23.75% for T, 32.48% for C and 13.48% for G, and exhibited the typical mitochondrial structure, including 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes and a non-coding control region.