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407 results on '"Archibald, Alan L."'

1. Stem cell-derived porcine macrophages as a new platform for studying host-pathogen interactions

Author

Meek, Stephen, Watson, Tom, Eory, Lel, McFarlane, Gus, Wynne, Felicity J, McCleary, Stephen, Dunn, Laura EM, Charlton, Emily M, Craig, Chloe, Shih, Barbara, Regan, Tim, Taylor, Ryan, Sutherland, Linda, Gossner, Anton, Chintoan-Uta, Cosmin, Fletcher, Sarah, Beard, Philippa M, Hassan, Musa A, Grey, Finn, Hope, Jayne C, Stevens, Mark P, Nowak-Imialek, Monika, Niemann, Heiner, Ross, Pablo J, Tait-Burkard, Christine, Brown, Sarah M, Lefevre, Lucas, Thomson, Gerard, McColl, Barry W, Lawrence, Alistair B, Archibald, Alan L, Steinbach, Falko, Crooke, Helen R, Gao, Xuefei, Liu, Pentao, and Burdon, Tom

Subjects
Genetics, Biodefense, Stem Cell Research, Biotechnology, Emerging Infectious Diseases, Vaccine Related, Prevention, Regenerative Medicine, Infectious Diseases, 2.1 Biological and endogenous factors, 2.2 Factors relating to the physical environment, Aetiology, Infection, Good Health and Well Being, African Swine Fever Virus, Animals, Communicable Diseases, Host-Pathogen Interactions, Macrophages, Stem Cells, Swine, Pig, Pluripotent stem cell, Macrophage, PRRSV, ASFV, CRISPR, gene editing, Developmental Biology
Abstract

Infectious diseases of farmed and wild animals pose a recurrent threat to food security and human health. The macrophage, a key component of the innate immune system, is the first line of defence against many infectious agents and plays a major role in shaping the adaptive immune response. However, this phagocyte is a target and host for many pathogens. Understanding the molecular basis of interactions between macrophages and pathogens is therefore crucial for the development of effective strategies to combat important infectious diseases. We explored how porcine pluripotent stem cells (PSCs) can provide a limitless in vitro supply of genetically and experimentally tractable macrophages. Porcine PSC-derived macrophages (PSCdMs) exhibited molecular and functional characteristics of ex vivo primary macrophages and were productively infected by pig pathogens, including porcine reproductive and respiratory syndrome virus (PRRSV) and African swine fever virus (ASFV), two of the most economically important and devastating viruses in pig farming. Moreover, porcine PSCdMs were readily amenable to genetic modification by CRISPR/Cas9 gene editing applied either in parental stem cells or directly in the macrophages by lentiviral vector transduction. We show that porcine PSCdMs exhibit key macrophage characteristics, including infection by a range of commercially relevant pig pathogens. In addition, genetic engineering of PSCs and PSCdMs affords new opportunities for functional analysis of macrophage biology in an important livestock species. PSCs and differentiated derivatives should therefore represent a useful and ethical experimental platform to investigate the genetic and molecular basis of host-pathogen interactions in pigs, and also have wider applications in livestock.

Published
2022

3. Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping

Author

Kyratzi, Panagiota, primary, Matika, Oswald, additional, Brassington, Amey H, additional, Connie, Clare E, additional, Xu, Juan, additional, Barrett, David A, additional, Emes, Richard D, additional, Archibald, Alan L., additional, Paldi, Andras, additional, Sinclair, Kevin D, additional, Wattis, Jonathan, additional, and Rauch, Cyril, additional

Published
2024
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5. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

Author

The FAANG Consortium, Andersson, Leif, Archibald, Alan L, Bottema, Cynthia D, Brauning, Rudiger, Burgess, Shane C, Burt, Dave W, Casas, Eduardo, Cheng, Hans H, Clarke, Laura, Couldrey, Christine, Dalrymple, Brian P, Elsik, Christine G, Foissac, Sylvain, Giuffra, Elisabetta, Groenen, Martien A, Hayes, Ben J, Huang, LuSheng S, Khatib, Hassan, Kijas, James W, Kim, Heebal, Lunney, Joan K, McCarthy, Fiona M, McEwan, John C, Moore, Stephen, Nanduri, Bindu, Notredame, Cedric, Palti, Yniv, Plastow, Graham S, Reecy, James M, Rohrer, Gary A, Sarropoulou, Elena, Schmidt, Carl J, Silverstein, Jeffrey, Tellam, Ross L, Tixier-Boichard, Michele, Tosser-Klopp, Gwenola, Tuggle, Christopher K, Vilkki, Johanna, White, Stephen N, Zhao, Shuhong, and Zhou, Huaijun

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Human Genome, Genetics, Animals, Animals, Domestic, Databases, Genetic, Genome, Genomics, Molecular Sequence Annotation, Software, FAANG Consortium, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

Published
2015

6. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.

Author

Andersson, Leif, Archibald, Alan L, Bottema, Cynthia D, Brauning, Rudiger, Burgess, Shane C, Burt, Dave W, Casas, Eduardo, Cheng, Hans H, Clarke, Laura, Couldrey, Christine, Dalrymple, Brian P, Elsik, Christine G, Foissac, Sylvain, Giuffra, Elisabetta, Groenen, Martien A, Hayes, Ben J, Huang, LuSheng S, Khatib, Hassan, Kijas, James W, Kim, Heebal, Lunney, Joan K, McCarthy, Fiona M, McEwan, John C, Moore, Stephen, Nanduri, Bindu, Notredame, Cedric, Palti, Yniv, Plastow, Graham S, Reecy, James M, Rohrer, Gary A, Sarropoulou, Elena, Schmidt, Carl J, Silverstein, Jeffrey, Tellam, Ross L, Tixier-Boichard, Michele, Tosser-Klopp, Gwenola, Tuggle, Christopher K, Vilkki, Johanna, White, Stephen N, Zhao, Shuhong, Zhou, Huaijun, and FAANG Consortium

Subjects
FAANG Consortium, Animals, Animals, Domestic, Genomics, Genome, Software, Databases, Genetic, Molecular Sequence Annotation, Domestic, Databases, Genetic, Genetics, Human Genome, Bioinformatics, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

Published
2015

7. Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Author

Frantz, Laurent AF, Schraiber, Joshua G, Madsen, Ole, Megens, Hendrik-Jan, Bosse, Mirte, Paudel, Yogesh, Semiadi, Gono, Meijaard, Erik, Li, Ning, Crooijmans, Richard PMA, Archibald, Alan L, Slatkin, Montgomery, Schook, Lawrence B, Larson, Greger, and Groenen, Martien AM

Abstract

Abstract Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.

Published
2013

10. Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

Author

Dutta, Prasun, Talenti, Andrea, Young, Rachel, Jayaraman, Siddharth, Callaby, Rebecca, Jadhav, Santosh Kumar, Dhanikachalam, Velu, Manikandan, Mayakannan, Biswa, Bhim B., Low, Wai Y., Williams, John L., Cook, Elizabeth, Toye, Phil, Wall, Eileen, Djikeng, Appolinaire, Marshall, Karen, Archibald, Alan L., Gokhale, Suresh, Kumar, Satish, Hume, David A., and Prendergast, James G. D.

Published
2020
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16. Strong signatures of selection in the domestic pig genome

Author

Rubin, Carl-Johan, Megens, Hendrik-Jan, Barrio, Alvaro Martinez, Maqbool, Khurram, Sayyab, Shumaila, Schwochow, Doreen, Wang, Chao, Carlborg, Örjan, Jern, Patric, Jørgensen, Claus B., Archibald, Alan L., Fredholm, Merete, Groenen, Martien A. M., and Andersson, Leif

Published
2012

18. Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection

Author

Noyes, Harry, Brass, Andy, Obara, Isaiah, Anderson, Susan, Archibald, Alan L., Bradley, Dan G., Fisher, Paul, Freeman, Abigail, Gibson, John, Gicheru, Michael, Hall, Laurence, Hanotte, Olivier, Hulme, Helen, McKeever, Declan, Murray, Caitriona, Oh, Sung Jung, Tate, Catriona, Smith, Ken, Tapio, Miika, Wambugu, John, Williams, Diana J., Agaba, Morris, and Kemp, Stephen J.

Published
2011

20. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

Author

Salavati, Mazdak, Woolley, Shernae A., Cortés Araya, Yennifer, Halstead, Michelle M., Stenhouse, Claire, Johnsson, Martin, Ashworth, Cheryl J., Archibald, Alan L., Donadeu, Francesc X., Hassan, Musa A., and Clark, Emily L.

Subjects
Genetics and Breeding
Abstract

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.

Published
2022

23. Stem cell-derived macrophages as a new platform for studying host-pathogen interactions in livestock

Author

Meek, Stephen, primary, Watson, Tom, additional, Eory, Lel, additional, McFarlane, Gus, additional, Wynne, Felicity J., additional, McCleary, Stephen, additional, Dunn, Laura E.M., additional, Charlton, Emily M., additional, Criag, Chloe, additional, Shih, Barbara, additional, Regan, Tim, additional, Taylor, Ryan, additional, Sutherland, Linda, additional, Gossner, Anton, additional, Chintoan-Uta, Cosmin, additional, Fletcher, Sarah, additional, Beard, Philippa M., additional, Hassan, Musa A., additional, Grey, Finn, additional, Hope, Jayne C., additional, Stevens, Mark P., additional, Nowak-Imialek, Monika, additional, Niemann, Heiner, additional, Ross, Pablo J., additional, Tait-Burkard, Christine, additional, Brown, Sarah M., additional, Lefevre, Lucas, additional, Thomson, Gerard, additional, McColl, Barry W., additional, Lawrence, Alistair B., additional, Archibald, Alan L., additional, Steinbach, Falko, additional, Crooke, Helen R., additional, Gao, Xuefei, additional, Liu, Pentao, additional, and Burdon, Tom, additional

Published
2021
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25. Analyses of pig genomes provide insight into porcine demography and evolution

Author

Groenen, Martien A. M., Archibald, Alan L., Uenishi, Hirohide, Tuggle, Christopher K., Takeuchi, Yasuhiro, Rothschild, Max F., Rogel-Gaillard, Claire, Park, Chankyu, Milan, Denis, Megens, Hendrik-Jan, Li, Shengting, Larkin, Denis M., Kim, Heebal, Frantz, Laurent A. F., Caccamo, Mario, Ahn, Hyeonju, Aken, Bronwen L., Anselmo, Anna, Anthon, Christian, Auvil, Loretta, Badaoui, Bouabid, Beattie, Craig W., Bendixen, Christian, Berman, Daniel, Blecha, Frank, Blomberg, Jonas, Bolund, Lars, Bosse, Mirte, Botti, Sara, Bujie, Zhan, Bystrom, Megan, Capitanu, Boris, Carvalho-Silva, Denise, Chardon, Patrick, Chen, Celine, Cheng, Ryan, Choi, Sang-Haeng, Chow, William, Clark, Richard C., Clee, Christopher, Crooijmans, Richard P. M. A., Dawson, Harry D., Dehais, Patrice, De Sapio, Fioravante, Dibbits, Bert, Drou, Nizar, Du, Zhi-Qiang, Eversole, Kellye, Fadista, João, Fairley, Susan, Faraut, Thomas, Faulkner, Geoffrey J., Fowler, Katie E., Fredholm, Merete, Fritz, Eric, Gilbert, James G. R., Giuffra, Elisabetta, Gorodkin, Jan, Griffin, Darren K., Harrow, Jennifer L., Hayward, Alexander, Howe, Kerstin, Hu, Zhi-Liang, Humphray, Sean J., Hunt, Toby, Hornshøj, Henrik, Jeon, Jin-Tae, Jern, Patric, Jones, Matthew, Jurka, Jerzy, Kanamori, Hiroyuki, Kapetanovic, Ronan, Kim, Jaebum, Kim, Jae-Hwan, Kim, Kyu-Won, Kim, Tae-Hun, Larson, Greger, Lee, Kyooyeol, Lee, Kyung-Tai, Leggett, Richard, Lewin, Harris A., Li, Yingrui, Liu, Wansheng, Loveland, Jane E., Lu, Yao, Lunney, Joan K., Ma, Jian, Madsen, Ole, Mann, Katherine, Matthews, Lucy, McLaren, Stuart, Morozumi, Takeya, Murtaugh, Michael P., Narayan, Jitendra, Truong Nguyen, Dinh, Ni, Peixiang, Oh, Song-Jung, Onteru, Suneel, Panitz, Frank, Park, Eung-Woo, Park, Hong-Seog, Pascal, Geraldine, Paudel, Yogesh, Perez-Enciso, Miguel, Ramirez-Gonzalez, Ricardo, Reecy, James M., Rodriguez-Zas, Sandra, Rohrer, Gary A., Rund, Lauretta, Sang, Yongming, Schachtschneider, Kyle, Schraiber, Joshua G., Schwartz, John, Scobie, Linda, Scott, Carol, Searle, Stephen, Servin, Bertrand, Southey, Bruce R., Sperber, Goran, Stadler, Peter, Sweedler, Jonathan V., Tafer, Hakim, Thomsen, Bo, Wali, Rashmi, Wang, Jian, Wang, Jun, White, Simon, Xu, Xun, Yerle, Martine, Zhang, Guojie, Zhang, Jianguo, Zhang, Jie, Zhao, Shuhong, Rogers, Jane, Churcher, Carol, and Schook, Lawrence B.

Published
2012
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28. The sheep genome illuminates biology of the rumen and lipid metabolism

Author

Jiang, Yu, Xie, Min, Chen, Wenbin, Talbot, Richard, Maddox, Jillian F., Faraut, Thomas, Wu, Chunhua, Muzny, Donna M., Li, Yuxiang, Zhang, Wenguang, Stanton, Jo-Ann, Brauning, Rudiger, Barris, Wesley C., Hourlier, Thibaut, Aken, Bronwen L., Searle, Stephen M. J., Adelson, David L., Bian, Chao, Cam, Graham R., Chen, Yulin, Cheng, Shifeng, DeSilva, Udaya, Dixen, Karen, Dong, Yang, Fan, Guangyi, Franklin, Ian R., Fu, Shaoyin, Fuentes-Utrilla, Pablo, Guan, Rui, Highland, Margaret A., Holder, Michael E., Huang, Guodong, Ingham, Aaron B., Jhangiani, Shalini N., Kalra, Divya, Kovar, Christie L., Lee, Sandra L., Liu, Weiqing, Liu, Xin, Lu, Changxin, Lv, Tian, Mathew, Tittu, McWilliam, Sean, Menzies, Moira, Pan, Shengkai, Robelin, David, Servin, Bertrand, Townley, David, Wang, Wenliang, Wei, Bin, White, Stephen N., Yang, Xinhua, Ye, Chen, Yue, Yaojing, Zeng, Peng, Zhou, Qing, Hansen, Jacob B., Kristiansen, Karsten, Gibbs, Richard A., Flicek, Paul, Warkup, Christopher C., Jones, Huw E., Oddy, Hutton V., Nicholas, Frank W., McEwan, John C., Kijas, James W., Wang, Jun, Worley, Kim C., Archibald, Alan L., Cockett, Noelle, Xu, Xun, Wang, Wen, and Dalrymple, Brian P.

Published
2014
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31. Additional file 2 of Illuminating the dark side of the human transcriptome with long read transcript sequencing

Author

Kuo, Richard I., Yuanyuan Cheng, Runxuan Zhang, Brown, John W. S., Smith, Jacqueline, Archibald, Alan L., and Burt, David W.

Subjects
ComputingMethodologies_PATTERNRECOGNITION
Abstract

Additional file 2: Table S1. Table of long read datasets information on number of mapped reads, reference annotation, and genome assembly scaffold numbers.

Published
2020
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33. An assessment of European pig diversity using molecular markers: Partitioning of diversity among breeds

Author

Ollivier, Louis, Alderson, Lawrence, Gandini, Gustavo C., Foulley, Jean-Louis, Haley, Chris S., Joosten, Ruth, Rattink, Annemieke P., Harlizius, Barbara, Groenen, Martien A. M., Amigues, Yves, Boscher, Marie-Yvonne, Russell, Geraldine, Law, Andy, Davoli, Roberta, Russo, Vincenzo, Matassino, Donato, Désautés, Céline, Fimland, Erling, Bagga, Meena, Delgado, Juan-Vicente, Vega-Pla, Jose L., Martinez, AmparoM., Ramos, Antonio M., Glodek, Peter, Meyer, Johann-Nikolaus, Plastow, Graham S., Siggens, Kenneth W., Archibald, Alan L., Milan, Denis, San Cristobal, Magali, Laval, Guillaume, Hammond, Keith, Cardellino, Ricardo, and Chevalet, Claude

Published
2005
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36. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig

Author

Van Laere, Anne-Sophie, Nguyen, Minh, Braunschweig, Martin, Nezer, Carine, Collette, Catherine, Moreau, Laurence, Archibald, Alan L., Haley, Chris S., Buys, Nadine, Tally, Michael, Andersson, Goran, Georges, Michel, and Andersson, Leif

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Anne-Sophie Van Laere [1, 7]; Minh Nguyen [3, 7]; Martin Braunschweig [1]; Carine Nezer [3]; Catherine Collette [3]; Laurence Moreau [3]; Alan L. Archibald [4]; Chris S. Haley [4]; [...]

Published
2003
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39. From FAANG to Fork: Application of Highly Annotated Genomes to Improve Farmed Animal Production

Author

Clark, Emily L, primary, Archibald, Alan L, additional, Daetwyler, Hans D, additional, Groenen, Martien AM, additional, Harrison, Peter W, additional, Houston, Ross D, additional, Kuehn, Christa, additional, Lien, Sigbjorn, additional, Macqueen, Daniel J, additional, Reecy, James M, additional, Robledo, Diego, additional, Watson, Mick, additional, Tuggle, Christopher K, additional, and Giuffra, Elisabetta, additional

Published
2020
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43. An improved pig reference genome sequence to enable pig genetics and genomics research

Author

Warr, Amanda, primary, Affara, Nabeel, primary, Aken, Bronwen, primary, Beiki, Hamid, primary, Bickhart, Derek M, primary, Billis, Konstantinos, primary, Chow, William, primary, Eory, Lel, primary, Finlayson, Heather A, primary, Flicek, Paul, primary, Girón, Carlos G, primary, Griffin, Darren K, primary, Hall, Richard, primary, Hannum, Greg, primary, Hourlier, Thibaut, primary, Howe, Kerstin, primary, Hume, David A, primary, Izuogu, Osagie, primary, Kim, Kristi, primary, Koren, Sergey, primary, Liu, Haibou, primary, Manchanda, Nancy, primary, Martin, Fergal J, primary, Nonneman, Dan J, primary, O'Connor, Rebecca E, primary, Phillippy, Adam M, primary, Rohrer, Gary A, primary, Rosen, Benjamin D, primary, Rund, Laurie A, primary, Sargent, Carole A, primary, Schook, Lawrence B, primary, Schroeder, Steven G, primary, Schwartz, Ariel S, primary, Skinner, Ben M, primary, Talbot, Richard, primary, Tseng, Elizabeth, primary, Tuggle, Christopher K, primary, Watson, Mick, primary, Smith, Timothy P L, primary, and Archibald, Alan L, primary

Published
2020
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44. Metagenomic sequencing of clinical samples reveals a single widespread clone of Lawsonia intracellularis responsible for porcine proliferative enteropathy

Author

Bengtsson, Rebecca J., primary, Wee, Bryan A., additional, Yebra, Gonzalo, additional, Bacigalupe, Rodrigo, additional, Watson, Eleanor, additional, Guedes, Roberto M. C., additional, Jacobson, Magdalena, additional, Stadejek, Tomasz, additional, Archibald, Alan L., additional, Fitzgerald, J. Ross, additional, and Ait-Ali, Tahar, additional

Published
2020
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45. Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

Author

Summers, Kim M., primary, Bush, Stephen J., additional, Wu, Chunlei, additional, Su, Andrew I., additional, Muriuki, Charity, additional, Clark, Emily L., additional, Finlayson, Heather A., additional, Eory, Lel, additional, Waddell, Lindsey A., additional, Talbot, Richard, additional, Archibald, Alan L., additional, and Hume, David A., additional

Published
2020
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46. Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human

Author

Kuo, Richard I, Tseng, Elizabeth, Eory, Lel, Paton, Ian R, Archibald, Alan L, and Burt, David W

Subjects
PacBio, Avian, lcsh:QH426-470, lcsh:Biotechnology, Iso-Seq, Gallus gallus, Single molecule long read sequencing, Coding RNA, RNAseq, Chicken, lcsh:Genetics, lcsh:TP248.13-248.65, Transcriptome sequencing, Non-coding RNA, Genome annotation
Abstract

BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences.RESULTS: We sequenced normalised chicken brain and embryo RNA libraries with Pacific Bioscience Iso-Seq. 5' cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncRNA transcripts with ~3 k classified as sense exonic overlapping lncRNA, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences.CONCLUSIONS: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics.

Published
2017

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