Feather Evolution from Precocial to Altricial Birds.

Birds are the most abundant terrestrial vertebrates and their diversity is greatly shaped by the feathers. How avian evolution is linked to feather evolution has long been a fascinating question. Numerous excellent studies have shed light on this complex relationship by investigating feather diversity and its underlying molecular mechanisms. However, most have focused on adult domestic birds, and the contribution of feather diversity to environmental adaptation has not been well-studied. In this review, we described bird diversity using the traditional concept of the altricial-precocial spectrum in bird hatchlings. We combined the spectrum with a recently published avian phylogeny to profile the spectrum evolution. We then focused on the discrete diagnostic character of the spectrum, the natal down, and propose a hypothesis for the precocial-to-altricial evolution. For the underlying molecular mechanisms in feather diversity and bird evolution, we reviewed the literature and constructed the known mechanisms for feather tract definition and natal down development. Finally, we suggested some future directions for research on altricial-precocial divergence, which may expand our understanding of the relationship between natal down diversity and bird evolution.

Identification and evolutionary analysis of long non-coding RNAs in zebra finch.

BACKGROUND: Long non-coding RNAs (lncRNAs) are important in various biological processes, but very few studies on lncRNA have been conducted in birds. To identify IncRNAs expressed during feather development, we analyzed single-stranded RNA-seq (ssRNA-seq) data from the anterior and posterior dorsal regions during zebra finch (Taeniopygia guttata) embryonic development. Using published transcriptomic data, we further analyzed the evolutionary conservation of IncRNAs in birds and amniotes. RESULTS: A total of 1,081 lncRNAs, including 965 intergenic lncRNAs (lincRNAs), 59 intronic lncRNAs, and 57 antisense lncRNAs (lncNATs), were identified using our newly developed pipeline. These avian IncRNAs share similar characteristics with lncRNAs in mammals, such as shorter transcript length, lower exon number, lower average expression level and less sequence conservation than mRNAs. However, the proportion of lncRNAs overlapping with transposable elements in birds is much lower than that in mammals. We predicted the functions of IncRNAs based on the enriched functions of co-expressed protein-coding genes. Clusters of lncRNAs associated with natal down development were identified. The sequences and expression levels of candidate lncRNAs that shared conserved sequences among birds were validated by qPCR in both zebra finch and chicken. Finally, we identified three highly conserved lncRNAs that may be associated with natal down development. CONCLUSIONS: Our study provides the first systematical identification of avian lncRNAs using ssRNA-seq analysis and offers a resource of embryonically expressed lncRNAs in zebra finch. We also predicted the biological function of identified lncRNAs.

Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken.

Birds can be classified into altricial and precocial. The hatchlings of altricial birds are almost naked, whereas those of precocial birds are covered with natal down. This regulatory divergence is thought to reflect environmental adaptation, but the molecular basis of the divergence is unclear. To address this issue, we chose the altricial zebra finch and the precocial chicken as the model animals. We noted that zebra finch hatchlings show natal down growth suppressed anterior dorsal (AD) skin but partially down-covered posterior dorsal (PD) skin. Comparing the transcriptomes of AD and PD skins, we found that the feather growth promoter SHH (sonic hedgehog) was expressed higher in PD skin than in AD skin. Moreover, the data suggested that the FGF (fibroblast growth factor)/Mitogen-activated protein kinase (MAPK) signaling pathway is involved in natal down growth suppression and that FGF16 is a candidate upstream signaling suppressor. Ectopic expression of FGF16 on chicken leg skin showed downregulation of SHH, upregulation of the feather growth suppressor FGF10, and suppression of feather bud elongation, similar to the phenotype found in zebra finch embryonic AD skin. Therefore, we propose that FGF16-related signals suppress natal down elongation and cause the naked AD skin in zebra finch. Our study provides insights into the regulatory divergence in natal down formation between precocial and altricial birds.

Topographical mapping of α- and ß-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives.

Avian integumentary organs include feathers, scales, claws, and beaks. They cover the body surface and play various functions to help adapt birds to diverse environments. These keratinized structures are mainly composed of corneous materials made of α-keratins, which exist in all vertebrates, and ß-keratins, which only exist in birds and reptiles. Here, members of the keratin gene families were used to study how gene family evolution contributes to novelty and adaptation, focusing on tissue morphogenesis. Using chicken as a model, we applied RNA-seq and in situ hybridization to map α- and ß-keratin genes in various skin appendages at embryonic developmental stages. The data demonstrate that temporal and spatial α- and ß-keratin expression is involved in establishing the diversity of skin appendage phenotypes. Embryonic feathers express a higher proportion of ß-keratin genes than other skin regions. In feather filament morphogenesis, ß-keratins show intricate complexity in diverse substructures of feather branches. To explore functional interactions, we used a retrovirus transgenic system to ectopically express mutant α- or antisense ß-keratin forms. α- and ß-keratins show mutual dependence and mutations in either keratin type results in disrupted keratin networks and failure to form proper feather branches. Our data suggest that combinations of α- and ß-keratin genes contribute to the morphological and structural diversity of different avian skin appendages, with feather-ß-keratins conferring more possible composites in building intrafeather architecture complexity, setting up a platform of morphological evolution of functional forms in feathers.

Transcriptomic analyses of regenerating adult feathers in chicken.

BACKGROUND: Feathers have diverse forms with hierarchical branching patterns and are an excellent model for studying the development and evolution of morphological traits. The complex structure of feathers allows for various types of morphological changes to occur. The genetic basis of the structural differences between different parts of a feather and between different types of feather is a fundamental question in the study of feather diversity, yet there is only limited relevant information for gene expression during feather development. RESULTS: We conducted transcriptomic analysis of five zones of feather morphologies from two feather types at different times during their regeneration after plucking. The expression profiles of genes associated with the development of feather structure were examined. We compared the gene expression patterns in different types of feathers and different portions of a feather and identified morphotype-specific gene expression patterns. Many candidate genes were identified for growth control, morphogenesis, or the differentiation of specific structures of different feather types. CONCLUSION: This study laid the ground work for studying the evolutionary origin and diversification of feathers as abundant data were produced for the study of feather morphogenesis. It significantly increased our understanding of the complex molecular and cellular events in feather development processes and provided a foundation for future studies on the development of other skin appendages.

Genomic organization, transcriptomic analysis, and functional characterization of avian α- and ß-keratins in diverse feather forms.

Feathers are hallmark avian integument appendages, although they were also present on theropods. They are composed of flexible corneous materials made of α- and ß-keratins, but their genomic organization and their functional roles in feathers have not been well studied. First, we made an exhaustive search of α- and ß-keratin genes in the new chicken genome assembly (Galgal4). Then, using transcriptomic analysis, we studied α- and ß-keratin gene expression patterns in five types of feather epidermis. The expression patterns of ß-keratin genes were different in different feather types, whereas those of α-keratin genes were less variable. In addition, we obtained extensive α- and ß-keratin mRNA in situ hybridization data, showing that α-keratins and ß-keratins are preferentially expressed in different parts of the feather components. Together, our data suggest that feather morphological and structural diversity can largely be attributed to differential combinations of α- and ß-keratin genes in different intrafeather regions and/or feather types from different body parts. The expression profiles provide new insights into the evolutionary origin and diversification of feathers. Finally, functional analysis using mutant chicken keratin forms based on those found in the human α-keratin mutation database led to abnormal phenotypes. This demonstrates that the chicken can be a convenient model for studying the molecular biology of human keratin-based diseases.

Genome-wide patterns of genetic variation in two domestic chickens.

Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.