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; Li, Jianwen; Yi, Kang; Feng, Huapeng; Zhu, Ping; Li, Bo; Liu, Qiuyue; Fairley, Susan; 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, R.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; Jing, Fei; Morisson, Mireille; Kaiser, Pete; Griffin, Darren K.; Rao, Man; Pitel, Frédérique; Wang, Jun; Li, Ning

doi:10.1038/ng.2657

Cited by 315 publications

(307 citation statements)

References 45 publications

(56 reference statements)

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“…Since the caspase-like activity is strongly downregulated upon the r e p l a c e m e n t o f c o n s t i t u t i v e p r o t e a s o m e s b y immunoproteasomes in the mouse and human (Groettrup et al 1996), the absence of such a change when comparing proteasome from the chicken brain and spleen already strongly suggests that no immunoproteasome is present in the chicken spleen, bursa of Fabricius, or thymus. After the duck genome was reported last year, we blasted the available sequences for the immunosubunits β1i, β2i, and β5i as well as the thymus-specific subunit β5t, but these subunits were not detectable as already reported for Galliformes and zebra finch (Huang et al 2013).…”

Section: Discussionmentioning

confidence: 99%

No evidence for immunoproteasomes in chicken lymphoid organs and activated lymphocytes

Erath

Groettrup

2014

Immunogenetics

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The proteasome is the main protein-degrading machine within the cell, producing ligands for MHC class I molecules. It is a cylindrical multicatalytic protease complex, and the catalytic activity is mediated by the three subunits β1, β2, and β5 which possess caspase-, trypsin-, and chymotrypsin-like activities, respectively. By stimulation with interferon (IFN)-γ the replacement of these subunits by β1i, β2i, and β5i is induced leading to formation of immunoproteasomes with altered proteolytic and antigen processing properties. The genes coding for these immunosubunits are restricted to jawed vertebrates but have so far not been found in the genomes of birds, e.g., chicken, turkey, quail, black grouse and zebra finch. However, the chicken genome sequences are not completely assigned; therefore, we investigated the presence of immunoproteasome on protein level. 20S proteasome was purified from the chicken brain, blood, spleen, and bursa of Fabricius, followed by separation via two-dimensional (2D) gel electrophoresis. We analyzed the protein spots derived from the spleen and brain by mass spectrometry and could identify all 14 proteasomal subunits, but there were no differences detectable in the spot patterns. Moreover, we stimulated the chicken spleen cells with phorbol 12-myristate 13-acetate (PMA) and ionomycin aiming at the induction of immunoproteasome, but in spite of the induction of proliferation and IFN-γ, no evidence for immunoproteasome formation in chicken could be obtained. This result was substantiated by the finding that 20S proteasomes isolated from immune and non-immune tissues showed very similar peptidolytic activities. Taken together, our results indicate that chicken lack immunoproteasomes also on protein level.

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Section: Discussionmentioning

confidence: 99%

No evidence for immunoproteasomes in chicken lymphoid organs and activated lymphocytes

Erath

Groettrup

2014

Immunogenetics

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“…About 30% of the sequence reads could be aligned to the bovine genome, a closely-related species. The study of Jonker et al (2012) used the same technique to identify SNPs in the Barnacle Goose (Branta leucopsis) by aligning 1.77 million reads to the Mallard (Anas platyrhynchos) genome (divergence time 30 million years) (Huang et al, 2013). In that study, 16.1% of the reads successfully aligned, subsequently allowing the identification of 2188 high confidence SNPs.…”

Section: Model Species Reference Genome and Snp Validationmentioning

confidence: 99%

Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

et al. 2016

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a b s t r a c tThis study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed.

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“…Paired end reads {lOObp) were mapped to the Mallard (Anas platyrhynchos) genome, version 73 (Huang et al, 2013, supplemen tary material) using SMALT (http://www.sanger.ac.uk/re sourcesfsoftwarefsmalt/). Previous research indicated that SMALT is appropriate for mapping paired end reads when the reference genome is distantly related to the sampled species (Frantz et al, 2013 ).…”

Section: Processing Sequencesmentioning

confidence: 99%

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs

Megens

Kraus

et al. 2016

Molecular Phylogenetics and Evolution

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a b s t r a c tPhylogenetic incongruence can be caused by analytical shortcomings or can be the result of biological processes, such as hybridization, incomplete lineage sorting and gene duplication. Differentiation between these causes of incongruence is essential to unravel complex speciation and diversification events. The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) was, until now, con tentious, i.e., the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. We sequenced nineteen goose genomes (representing seventeen spe cies of which three subspecies of the Brent Goose, Branta bernicla) and used an exon based phylogenomic approach (41,736 exons, representing 5887 genes) to unravel the evolutionary history of this bird group. We thereby provide general guidance on the combination of whole genome evolutionary analyses and analytical tools for such cases where previous attempts to resolve the phylogenetic history of several taxa could not be unravelled. Identical topologies were obtained using either a concatenation (based upon an alignment of 6,630,626 base pairs) or a coalescent based consensus method. Two major lineages, corre sponding to the genera Anser and Branta, were strongly supported. Within the Branta lineage, the White cheeked Geese form a well supported sub lineage that is sister to the Red breasted Goose (Branta ruficol lis). In addition, two main clades of Anser species could be identified, the White Geese and the Grey Geese. The results from the consensus method suggest that the diversification of the genus Anser is heavily influ enced by rapid speciation and by hybridization, which may explain the failure of previous studies to resolve the phylogenetic relationships within this genus. The majority of speciation events took place in the late Pliocene and early Pleistocene (between 4 and 2 million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of tem perate grasslands. Our approach will be a fruitful strategy for resolving many other complex evolutionary histories at the level of genera, species, and subspecies.

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The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

Cited by 315 publications

References 45 publications

No evidence for immunoproteasomes in chicken lymphoid organs and activated lymphocytes

No evidence for immunoproteasomes in chicken lymphoid organs and activated lymphocytes

Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

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