The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Huang Yinhua,Li Yingrui,Burt David W,Chen Hualan,Zhang Yong,Qian Wubin,Kim Heebal,Gan Shangquan,Zhao Yiqiang,Li Jianwen,Yi Kang,Feng Huapeng,Zhu Pengyang,Li Bo,Liu Qiuyue,Fairley Suan,Magor Katharine E,Du Zhenlin,Hu Xiaoxiang,Goodman Laurie,Tafer Hakim,Vignal Alain,Lee Taeheon,Kim Kyu-Won,Sheng Zheya,An Yang,Searle Steve,Herrero Javier,Groenen Martien A M,Crooijmans Richard P M A,Faraut Thomas,Cai Qingle,Webster Robert G,Aldridge Jerry R,Warren Wesley C,Bartschat Sebastian,Kehr Stephanie,Marz Manja,Stadler Peter F,Smith Jacqueline,Kraus Robert H S,Zhao Yaofeng,Ren Liming,Fei Jing,Morisson Mireille,Kaiser Pete,Griffin Darren K,Rao Man,Pitel Frederique,Wang Jun,Li Ning Nature genetics The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 virus. Further, we show how the duck's defense mechanisms against influenza infection have been optimized through the diversification of its β-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses. 10.1038/ng.2657

The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver. Lu Lizhi,Chen Yan,Wang Zhuo,Li Xiaofeng,Chen Weihu,Tao Zhengrong,Shen Junda,Tian Yong,Wang Deqian,Li Guoqin,Chen Li,Chen Fang,Fang Dongming,Yu Lili,Sun Yudong,Ma Yong,Li Jinjun,Wang Jun Genome biology BACKGROUND:Geese were domesticated over 6,000 years ago, making them one of the first domesticated poultry. Geese are capable of rapid growth, disease resistance, and high liver lipid storage capacity, and can be easily fed coarse fodder. Here, we sequence and analyze the whole-genome sequence of an economically important goose breed in China and compare it with that of terrestrial bird species. RESULTS:A draft sequence of the whole-goose genome was obtained by shotgun sequencing, and 16,150 protein-coding genes were predicted. Comparative genomics indicate that significant differences occur between the goose genome and that of other terrestrial bird species, particularly regarding major histocompatibility complex, Myxovirus resistance, Retinoic acid-inducible gene I, and other genes related to disease resistance in geese. In addition, analysis of transcriptome data further reveals a potential molecular mechanism involved in the susceptibility of geese to fatty liver disease and its associated symptoms, including high levels of unsaturated fatty acids and low levels of cholesterol. The results of this study show that deletion of the goose lep gene might be the result of positive selection, thus allowing the liver to adopt energy storage mechanisms for long-distance migration. CONCLUSIONS:This is the first report describing the complete goose genome sequence and contributes to genomic resources available for studying aquatic birds. The findings in this study are useful not only for genetic breeding programs, but also for studying lipid metabolism disorders. 10.1186/s13059-015-0652-y

Regulatory cocktail for dopaminergic neurons in a protovertebrate identified by whole-embryo single-cell transcriptomics. Genes & development The CNS of the protovertebrate contains a single cluster of dopaminergic (DA) neurons, the coronet cells, which have been likened to the hypothalamus of vertebrates. Whole-embryo single-cell RNA sequencing (RNA-seq) assays identified as the most strongly expressed cell-specific transcription factor (TF) in DA/coronet cells. Knockdown of activity results in their loss, while misexpression results in the appearance of supernumerary DA/coronet cells. Photoreceptor cells and ependymal cells are the most susceptible to transformation, and both cell types express high levels of Coexpression of both and caused the wholesale transformation of the entire CNS into DA/coronet cells. We therefore suggest that the reiterative use of functional manipulations and single-cell RNA-seq assays is an effective means for the identification of regulatory cocktails underlying the specification of specific cell identities. 10.1101/gad.317669.118

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord. Development (Cambridge, England) The coordinated spatial and temporal regulation of gene expression in the vertebrate neural tube determines the identity of neural progenitors and the function and physiology of the neurons they generate. Progress has been made deciphering the gene regulatory programmes that are responsible for this process; however, the complexity of the tissue has hampered the systematic analysis of the network and the underlying mechanisms. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions of the developing mouse neural tube between embryonic days 9.5-13.5. We confirmed that the data accurately recapitulates neural tube development, allowing us to identify new markers for specific progenitor and neuronal populations. In addition, the analysis highlighted a previously underappreciated temporal component to the mechanisms that generate neuronal diversity, and revealed common features in the sequence of transcriptional events that lead to the differentiation of specific neuronal subtypes. Together, the data offer insight into the mechanisms that are responsible for neuronal specification and provide a compendium of gene expression for classifying spinal cord cell types that will support future studies of neural tube development, function and disease. 10.1242/dev.173807

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis. Cell reports Iterative liver injury results in progressive fibrosis disrupting hepatic architecture, regeneration potential, and liver function. Hepatic stellate cells (HSCs) are a major source of pathological matrix during fibrosis and are thought to be a functionally homogeneous population. Here, we use single-cell RNA sequencing to deconvolve the hepatic mesenchyme in healthy and fibrotic mouse liver, revealing spatial zonation of HSCs across the hepatic lobule. Furthermore, we show that HSCs partition into topographically diametric lobule regions, designated portal vein-associated HSCs (PaHSCs) and central vein-associated HSCs (CaHSCs). Importantly we uncover functional zonation, identifying CaHSCs as the dominant pathogenic collagen-producing cells in a mouse model of centrilobular fibrosis. Finally, we identify LPAR1 as a therapeutic target on collagen-producing CaHSCs, demonstrating that blockade of LPAR1 inhibits liver fibrosis in a rodent NASH model. Taken together, our work illustrates the power of single-cell transcriptomics to resolve the key collagen-producing cells driving liver fibrosis with high precision. 10.1016/j.celrep.2019.10.024