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5 results on '"Alison P. Lee"'

1. The seahorse genome and the evolution of its specialized morphology

Author

Dai Shan, Qiang Lin, Geng Qin, Gang Li, Zhi Wei Lim, Ralf F. Schneider, Ying Sun, Xinhui Zhang, Hongyue Qu, Meng Xu, Chi Zhang, Ying Qiu, Qiang Gao, Jiumeng Min, Yulan Yang, Shaohua Fan, Xin Wang, Kai Wang, Qiong Shi, Yanhong Zhang, Joost M. Woltering, Liangmin Huang, Vydianathan Ravi, Wei Luo, Zexia Gao, Helen M. Gunter, Huixian Zhang, Chao Bian, Peiwen Xiong, Alison P. Lee, Axel Meyer, Weiming He, Byrappa Venkatesh, and Jie Bai

Subjects
0106 biological sciences, 0301 basic medicine, Fish Proteins, Male, Time Factors, Genome, Evolutionary developmental biology, Molecular Sequence Data, Zoology, Genomics, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Article, 03 medical and health sciences, stomatognathic system, Mutation Rate, ddc:570, Animals, Amino Acid Sequence, Horses, Gene, Zebrafish, Conserved Sequence, Phylogeny, Multidisciplinary, Base Sequence, Reproduction, Molecular Sequence Annotation, Zebrafish Proteins, biology.organism_classification, Biological Evolution, Smegmamorpha, Hindlimb, 030104 developmental biology, Phenotype, Evolutionary biology, Seahorse, Multigene Family, Hippocampus comes, Animal Fins, Evolutionary developmental biology, Brood pouch, T-Box Domain Proteins, Lined seahorse, Gene Deletion
Abstract

Seahorses have a specialized morphology that includes a toothless tubular mouth, a body covered with bony plates, a male brood pouch, and the absence of caudal and pelvic fins. Here we report the sequencing and de novo assembly of the genome of the tiger tail seahorse, Hippocampus comes. Comparative genomic analysis identifies higher protein and nucleotide evolutionary rates in H. comes compared with other teleost fish genomes. We identified an astacin metalloprotease gene family that has undergone expansion and is highly expressed in the male brood pouch. We also find that the H. comes genome lacks enamel matrix protein-coding proline/glutamine-rich secretory calcium-binding phosphoprotein genes, which might have led to the loss of mineralized teeth. tbx4, a regulator of hindlimb development, is also not found in H. comes genome. Knockout of tbx4 in zebrafish showed a ‘pelvic fin-loss’ phenotype similar to that of seahorses. Supplementary information The online version of this article (doi:10.1038/nature20595) contains supplementary material, which is available to authorized users., Here, the genome sequence of the tiger tail seahorse is reported and comparative genomic analyses with other ray-finned fishes are used to explore the genetic basis of the unique morphology and reproductive system of the seahorse. Supplementary information The online version of this article (doi:10.1038/nature20595) contains supplementary material, which is available to authorized users., Evolution at a gallop Seahorses are prime examples of the exuberance of evolution and are unique among bony fish on several counts, including their equine body shape and male brood pouch. An international collaboration reporting in this issue of Nature has determined the genome sequence of a seahorse (Hippocampus comes, the tiger tail seahorse). They find it to be the most rapidly evolving fish genome studied so far. H. comes is among the most commonly traded seahorse species—dried for traditional medicines and live for the aquarium trade—and is on the IUCN Red List as a 'vulnerable' species. Analysis of the genomic sequence provides insights into the evolution of its unique morphology. Of note is the absence of a master control gene, tbx4, which functions in the development of hindlimbs and pelvic fins. Pelvic fins are missing in seahorses, and tbx4-knockout mutant zebrafish also lack pelvic fins. Supplementary information The online version of this article (doi:10.1038/nature20595) contains supplementary material, which is available to authorized users.

Published
2016

2. Author Correction: Elephant shark genome provides unique insights into gnathostome evolution

Author

Manuel Irimia, Byrappa Venkatesh, Sydney Brenner, Masanori Kasahara, Jeremy B. Swann, Yoichi Sutoh, Yuko Ohta, Wesley C. Warren, Brian J. Raney, Shawn Hoon, Richard K. Wilson, Vydianathan Ravi, Shufen Ho, Patrick Minx, LaDeana W. Hillier, Sumanty Tohari, Vamshidhar Gangu, Belen Lorente-Galdos, Alice Tay, Michelle M. Lian, Ashish K. Maurya, Scott William Roy, Igor Kondrychyn, Philip W. Ingham, Alison P. Lee, Zhi Wei Lim, Martin F. Flajnik, Vladimir Korzh, Kiat Whye Kong, Javier Quilez, Thomas Boehm, Boon-Hui Tay, and Tomas Marques-Bonet

Subjects
Fish Proteins, Time Factors, T-Lymphocytes, Molecular Sequence Data, MEDLINE, Computational biology, Biology, Genome, Evolution, Molecular, Osteogenesis, Animals, Cell Lineage, Author Correction, Phylogeny, Zebrafish, Immunity, Cellular, Multidisciplinary, Published Erratum, Molecular Sequence Annotation, Genomics, Phosphoproteins, Protein Structure, Tertiary, Vertebrates, Sharks, Calcium, Gene Deletion
Abstract

The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the 'living fossil' coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity.

Published
2020

3. The African coelacanth genome provides insights into tetrapod evolution

Author

Mariko Forconi, Tereza Manousaki, Peter F. Stadler, Anna Maria Fausto, Simon D. M. White, Shigehiro Kuraku, Sumir Panji, Marcia Lara, Andreas Gnirke, Hervé Philippe, Shaohua Fan, Axel Meyer, Jean Nicolas Volff, Tsutomu Miyake, Sante Gnerre, Thorsten Burmester, Anne Nitsche, Igor Schneider, John J. Stegeman, Alison P. Lee, Kerstin Lindblad-Toh, Peter van Heusden, Chris T. Amemiya, Michael S. Campbell, Ettore Olmo, Vydianathan Ravi, Jason Turner-Maier, Denis Baurain, Gary W. Litman, Federica Di Palma, Nicolas Rohner, Manfred Schartl, Giuseppe Scapigliati, Oleg Simakov, Aaron M. Berlin, Barbara Picone, Ingo Braasch, Byrappa Venkatesh, David R. Nelson, Wilfried Haerty, Diana Tabbaa, M. Gail Mueller, Francesco Buonocore, Eric S. Lander, Gianluca De Moro, Uljana Hesse, Chris P. Ponting, Nathalie Feiner, Junaid Gamieldien, Clifford J. Tabin, Gregory L. Blatch, Tatsuya Ota, Steve Hoffmann, Maria Assunta Biscotti, John H. Postlethwait, Chris L. Organ, Jessica Alföldi, Lin Fan, Mark Robinson, Stephen M. J. Searle, Louise Williams, Mark E. Hahn, Sonja J. Prohaska, Jared V. Goldstone, Dariusz Przybylski, Iain MacCallum, Rosemary A. Dorrington, Joshua Z. Levin, Tatjana Sauka-Spengler, Kenta Sumiyama, Nil Ratan Saha, Henner Brinkmann, Jeremy Johnson, John P. Cannon, Filipe J. Ribeiro, Marco Gerdol, David B. Jaffe, Adriana Canapa, Hakim Tafer, Marco Barucca, Mark Yandell, Evan Mauceli, Alan Christoffels, Sibel I. Karchner, Adrienne L. Edkins, J. Joshua Smith, Bronwen Aken, Neil H. Shubin, Ted Sharpe, Domitille Chalopin, Alberto Pallavicini, Molecular Genetics Program, Benaroya Research Institute, Department of Biology, Northern Arizona University [Flagstaff], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Partenaires INRAE, Université de Montréal (UdeM), Institute of Neuroscience, University of Oregon [Eugene], University of Konstanz, Instituto de Ciências Biológicas, Federal University of Para - Universidade Federal do Para [Belem - Brésil], Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Utah State University (USU), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Rhodes University, Grahamstown, Department of Life Sciences, Università degli studi di Trieste, Wellcome Trust Sanger Institute, Università Politecnica delle Marche [Ancona] (UNIVPM), Université de Liège, Victoria University [Melbourne], Department for Innovation in Biological, Agro-Food and Forest Systems, Tuscia University, University of Hamburg, Eccles Institute of Human Genetics, University of Utah, University of South Florida [Tampa] (USF), South African National Bioinformatics Institute (SANBI), University of the Western Cape, International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft-University of Konstanz, Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), University of Oxford [Oxford], Leipzig University, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, Keio University, All Children’s Hospital, University of Tennessee, Bioinformatics Group, Department of Computer Science, Universität Leipzig [Leipzig], Graduate University for Advanced Studies, Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore, European Molecular Biology Laboratory (EMBL), National Institute of Genetics (NIG), University of Chicago, Department Physiological Chemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), South African National Department of Science and Technology, National Human Genome Research Institute (NHGRI), European Science Foundation, Amemiya, Chris T., Alföldi, Jessica, Meyer, Axel, Lindblad-Toh, Kerstin, Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Trieste = University of Trieste, Università degli studi della Tuscia [Viterbo], University of the Western Cape (UWC), University of Oxford, Universität Leipzig, Julius-Maximilians-Universität Würzburg (JMU), Chris T., Amemiya, Jessica, Alföldi, Alison P., Lee, Shaohua, Fan, Hervé, Philippe, Iain, Maccallum, Ingo, Braasch, Tereza, Manousaki, Igor, Schneider, Nicolas, Rohner, Chris, Organ, Domitille, Chalopin, Jeramiah J., Smith, Mark, Robinson, Rosemary A., Dorrington, Gerdol, Marco, Bronwen, Aken, Maria Assunta, Biscotti, Marco, Barucca, Denis, Baurain, Aaron M., Berlin, Gregory L., Blatch, Francesco, Buonocore, Thorsten, Burmester, Michael S., Campbell, Adriana, Canapa, John P., Cannon, Alan, Christoffel, DE MORO, Gianluca, Adrienne L., Edkin, Lin, Fan, Anna Maria, Fausto, Nathalie, Feiner, Mariko, Forconi, Junaid, Gamieldien, Sante, Gnerre, Andreas, Gnirke, Jared V., Goldstone, Wilfried, Haerty, Mark E., Hahn, Uljana, Hesse, Steve, Hoffmann, Jeremy, Johnson, Sibel I., Karchner, Shigehiro, Kuraku, Marcia, Lara, Joshua Z., Levin, Gary W., Litman, Evan, Mauceli, Tsutomu, Miyake, M., Gail Mueller, David R., Nelson, Anne, Nitsche, Ettore, Olmo, Tatsuya, Ota, Pallavicini, Alberto, Sumir, Panji, Barbara, Picone, Chris P., Ponting, Sonja J., Prohaska, Dariusz, Przybylski, Nil Ratan, Saha, Vydianathan, Ravi, Filipe J., Ribeiro, Tatjana Sauka, Spengler, Giuseppe, Scapigliati, Stephen M. J., Searle, Ted, Sharpe, Oleg, Simakov, Peter F., Stadler, John J., Stegeman, Kenta, Sumiyama, Diana, Tabbaa, Hakim, Tafer, Jason Turner, Maier, Peter van, Heusden, Simon, White, Louise, William, Mark, Yandell, Henner, Brinkmann, Jean Nicolas, Volff, Clifford J., Tabin, Neil, Shubin, Manfred, Schartl, David B., Jaffe, John H., Postlethwait, Byrappa, Venkatesh, Federica Di, Palma, Eric S., Lander, Axel, Meyer, and Kerstin Lindblad, Toh

Subjects
0106 biological sciences, terrestrial environment, adaptation, ancestry, brain, excretion, finfish, gene expression, genome, immunity, olfaction, phylogenetics, protein, terrestrial environment, tetrapod, [SDV]Life Sciences [q-bio], LATIMERIA-MENADOENSIS, adaptation, Chick Embryo, MITOCHONDRIAL GENOME, LIVING FOSSIL, SEQUENCE, GENES, MODEL, TRANSCRIPTION, CHROMOSOMES, RETENTION, CHALUMNAE, 01 natural sciences, Genome, Animals, Genetically Modified, Mice, poisson, Coelacanth, Conserved Sequence, Phylogeny, Lungfish, 0303 health sciences, Multidisciplinary, biology, Latimeria, Fishes, Genes, Homeobox, Vertebrate, Genomics, Biological Evolution, phylogenetics, Enhancer Elements, Genetic, évolution du génome, Vertebrates, excretion, Comperative genomics, Living fossil, olfaction, Genome evolution, finfish, brain, Molecular Sequence Data, tetrapod, 010603 evolutionary biology, Article, Evolution, Molecular, 03 medical and health sciences, ddc:570, biology.animal, Animals, [INFO]Computer Science [cs], 14. Life underwater, 030304 developmental biology, Comparative genomics, ancestry, génome, Extremities, Molecular Sequence Annotation, Sequence Analysis, DNA, biology.organism_classification, immunity, body regions, Immunoglobulin M, Evolutionary biology, gene expression, protein, Sequence Alignment
Abstract

Acquisition and storage of Latimeria chalumnae samples was supported by grants from the African Coelacanth Ecosystem Programme of the South African National Department of Science and Technology. Generation of the Latimeria chalumnae and Protopterus annectens sequences by the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University was supported by grants from the National Human Genome Research Institute (NHGRI). K.L.T. is the recipient of a EURYI award from the European Science Foundation. We would also like to thank the Genomics Sequencing Platform of the Broad Institute for sequencing the L. chalumnae genome and L. chalumnae and P. annectens transcriptomes, S. Ahamada, R. Stobbs and the Association pour le Protection de Gombesa (APG) for their help in obtaining coelacanth samples, Y. Zhao for the use of data from Rana chensinensis, and L. Gaffney, C. Hamilton and J. Westlund for assistance with figure preparation. 10; International audience; The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

Published
2013

4. Venkatesh et al. reply

Author

Byrappa Venkatesh, Thomas Boehm, Alison P. Lee, Martin F. Flajnik, Wesley C. Warren, Jeremy B. Swann, Masanori Kasahara, and Yuko Ohta

Subjects
Genetics, Candidate gene, Genome, Multidisciplinary, biology, Sequence assembly, biology.organism_classification, Evolution, Molecular, Transcriptome, Sharks, Animals, Cytokine genes, Nurse shark, Gene, Synteny
Abstract

Replying to J. M. Dijkstra Nature511,http://dx.doi.org/10.1038/nature13446(2014) In the accompanying Comment1, Dijkstra has identified gene models potentially encoding cytokines in regions of the Callorhinchus milii genome, whose syntenic counterparts in teleost and tetrapod genomes harbour interleukin genes. These genes were not predicted by our assembly and annotation pipeline2. TBLASTN searches of the genome assembly and RNA-sequencing (RNA-seq) transcriptomes from 10 tissues (including thymus and spleen) of the elephant shark, and RNA-seq transcriptomes from the thymus and spleen of nurse shark using human and teleost fish interleukins as query sequences, were also unable to pick up these genes; although we readily detected other cytokine genes in the same family (for example, interleukin-7 (IL-7) and IL-15). Below are our comments on the candidate genes identified by Dijkstra.

Published
2014

5. Erratum: Corrigendum: Elephant shark genome provides unique insights into gnathostome evolution

Author

Vamshidhar Gangu, Belen Lorente-Galdos, Philip W. Ingham, Ashish K. Maurya, Alison P. Lee, Michelle M. Lian, Thomas Boehm, Yoichi Sutoh, Sydney Brenner, Byrappa Venkatesh, Igor Kondrychyn, Masanori Kasahara, Shufen Ho, Boon-Hui Tay, Shawn Hoon, Alice Tay, Rick K. Wilson, Vladimir Korzh, Jeremy B. Swann, Yuko Ohta, Brian J. Raney, LaDeana W. Hillier, Martin F. Flajnik, Sumanty Tohari, Manuel Irimia, Vydianathan Ravi, Javier Quilez, Scott William Roy, Wesley C. Warren, Kiat Whye Kong, Patrick Minx, Zhi Wei Lim, and Tomas Marques-Bonet

Subjects
0301 basic medicine, Comparative genomics, 03 medical and health sciences, Cellular immunity, 030104 developmental biology, Multidisciplinary, Evolutionary biology, Molecular evolution, GenBank, 14. Life underwater, Biology, Genome
Abstract

Nature 505, 174–179 (2014); doi:10.1038/nature12826 The ranges of accession numbers JW861113–JW881738 and KA353634–KA353668 (20,661 in total) cited in this Article include 3,630 sequences that were unrelated and hence removed from the NCBI GenBank database before the analysis of the data and submission of the manuscript to Nature.

Published
2014

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