Cephalopod genomics: A plan of strategies and organization

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Abstract

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this white paper.

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Computational methods for transcriptome annotation and quantification using RNA-seq.

Manuel Garber, Manfred Grabherr, Mitchell Guttman … (2011)

High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications.

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Initial impact of the sequencing of the human genome.

Eric S. Lander (2011)

The sequence of the human genome has dramatically accelerated biomedical research. Here I explore its impact, in the decade since its publication, on our understanding of the biological functions encoded in the genome, on the biological basis of inherited diseases and cancer, and on the evolution and history of the human species. I also discuss the road ahead in fulfilling the promise of genomics for medicine.

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The Schistosoma japonicum genome reveals features of host-parasite interplay.

(2009)

Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. Here we present a draft genomic sequence for the worm. The genome provides a global insight into the molecular architecture and host interaction of this complex metazoan pathogen, revealing that it can exploit host nutrients, neuroendocrine hormones and signalling pathways for growth, development and maturation. Having a complex nervous system and a well-developed sensory system, S. japonicum can accept stimulation of the corresponding ligands as a physiological response to different environments, such as fresh water or the tissues of its intermediate and mammalian hosts. Numerous proteases, including cercarial elastase, are implicated in mammalian skin penetration and haemoglobin degradation. The genomic information will serve as a valuable platform to facilitate development of new interventions for schistosomiasis control.

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Author and article information

Journal

Journal ID (nlm-ta): Stand Genomic Sci

Journal ID (iso-abbrev): Stand Genomic Sci

Journal ID (publisher-id): SIGS

Title: Standards in Genomic Sciences

Publisher: Michigan State University

ISSN (Electronic): 1944-3277

Publication date (Electronic): 26 September 2012

Publication date Collection: 10 October 2012

Volume: 7

Issue: 1

Pages: 175-188

Affiliations

[1 ]Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA

[2 ]Muséum National d'Histoire Naturelle, Université Paris Diderot, Sorbonne Paris Cité, Paris, France

[3 ]Departments of Computer Science and Engineering, and Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA

[4 ]Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH, USA

[5 ]Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

[6 ]Department of Biological, Geological and Environmental Sciences, University of Sannio, Benevento, Italy

[7 ]Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA

[8 ]Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA

[9 ]Department of Systems Biology, Harvard Medical School, Boston, MA, USA

[10 ]Marine Biological Laboratory, Woods Hole, MA, USA

[11 ]Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA

[12 ]Department of Biology, Portland State University, Portland, OR, USA

[13 ]Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI, USA

[14 ]The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA

[15 ]Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA

[16 ]Department of Theoretical Biology, University of Vienna, Vienna, Austria

[17 ]Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA

[18 ]Institute for Genome Research, University of Tokushima, Tokushima, Japan

[19 ]Hopkins Marine Station of Stanford University, Pacific Grove, CA, USA

[20 ]Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA

[21 ]Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA

[22 ]Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan

[23 ]Department of Genetics, La Trobe University, Bundoora, Victoria, Australia

[24 ]Department of Integrative Zoology, University of Vienna, Vienna, Austria

[25 ]BGI-Shenzhen, Shenzhen, China

[26 ]Department of Neurobiology, University of Chicago, Chicago, IL, USA

Author notes

[* ]Corresponding author: Clifton W. Ragsdale ( cragsdale@ 123456uchicago.edu )

Article

Publisher ID: sigs.3136559

DOI: 10.4056/sigs.3136559

PMC ID: 3570802

PubMed ID: 23451296

SO-VID: 7fe49023-c183-430d-b75d-666efbab7d65

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Funding

Funded by: National Science Foundation through the National Evolutionary Synthesis Center

Cephalopod genomics: A plan of strategies and organization

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Most cited references 70

Computational methods for transcriptome annotation and quantification using RNA-seq.

Initial impact of the sequencing of the human genome.

The Schistosoma japonicum genome reveals features of host-parasite interplay.

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