Project description:To investigate the cellular basis of parental species bias at birdsong, we performed single nuclei RNA-seq for six zebra finch and owl finch F1 hybrid juvenile birds.
Project description:To investigate the cellular basis of parental species bias at birdsong, we performed single nuclei RNA-seq for six zebra finch and owl finch F1 hybrid juvenile birds.
Project description:The unraveling of heterogenous cell populations, — previously masked in bulk transcriptome measurements — are made possible through analysis of single-cell transcriptomics. The goals of this study are to examine single-cell NGS-derived gonadal cell transcriptome profiling and to evaluate heterogeneity of gonadal germ cells in avian species. We performed single-cell RNA sequencing using embryonic gonadal cells of HH stage 28 from male and female zebra finches. We identified 12,489 male transcripts and 10,046 female transcripts. We annotated 9 different cell types from a total of 20 clustered single cells and identified that primordial germ cells, which have been considered as single population, can be distinguishable into three subtypes. The three PGC subtypes were specifically enriched for genes with expression patterns related to germness or pluripotency, suggesting functional differences in PGCs according to the three subtypes. Our study represents the first single-cell RNA seq analysis of gonadal transcriptomes in zebra finch. Our results revealed the first heterogeneity and intrinsic changes of gonadal primordial germ cells, which have hitherto been considered as a single population in avian species. We conclude that single-cell RNA seq based transcriptome analysis would offers new perspectives on avian primordial germ cells.
Project description:We have performed a comparison of global patterns of gene expression between two bird species, the chicken and zebra finch, especially with regard to sex bias of autosomal vs. Z chromosome genes, dosage compensation and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the non-coding RNA MHM (male hypermethylated), and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male to female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. The current study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows dosage compensation for a different set of Z genes than the chicken. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms.
Project description:Primordial germ cells (PGCs), major cell resource used in the production of germline chimeras in birds, have been used in conservation of avian genetic resources and production of transgenic animals. Numerous bird species have been put on the brink of extinction due to habitat loss and degradation caused by environmental destruction and climate change, but research on PGCs is limited to specific poultry, such as chickens. Although it has recently been expanding to various bird species, it is still difficult to utilize PGCs due to biological differences and difficulties in in vitro long-term culture. Here, we constructed a single-cell landscape of chicken gonadal PGCs with established long-term culture systems of PGCs and compared them with those of the vocal learning wild bird, the zebra finches. Our results identified the interspecific differences in signaling pathways in gonadal PGCs and somatic cells, respectively. In particular, the NODAL and insulin signaling pathways were more active in zebra finch than in chickens, whereas the FGF downstream signaling pathway known to be important for the proliferation of chicken PGCs, was more active in chickens. These differences may contribute to optimizing the in vitro culture conditions of zebra finch PGCs. This study is the first cross-species single-cell transcriptomic analysis targeting birds, and laid an essential groundwork to contribute to the restoration of endangered birds and the production of transgenic birds by securing sufficient PGCs from various bird species in the future.
