Biomphalaria Genome Initiative

Introduction

  • The international consortium has characterized the genome of the freshwater gastropod Biomphalaria glabrata.
  • An important motivation for this project is that Biomphalaria glabrata is a major snail host for transmission of human schistosomiasis
  • This site provides a time line of the efforts that have yielded a first genome assembly.
  • The sequence data have been deposited in public databases (GenBank NCBI; Vectorbase)
  • Investigators are encouraged to access the Biomphalaria glabrata genome for study of snail biology and comparative genomics.

Report

  • 2017 May:
    • "Whole genome analysis of a schistosomiasis-transmitting freshwater snail," Nature Communications, 8, Article number: 15451 (2017), doi:10.1038/ncomms15451.
  • Companion papers:
    • "Proteomic analysis of Biomphalaria glabrata plasma proteins with binding affinity to those expressed by early developing larval Schistosoma mansoni, PLOS Pathogens, doi.org/10.1371/journal.ppat.1006081.
    • "The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni," PLOS Neglected Tropical Diseases , doi.org/10.1371/journal.pntd.0005246.

    Timeline

    • 2015 Oct -- Publication process
    • 2015 Oct Community-contributed analyses completed, manuscript submission
    • 2013 WebApollo implemented by Vectorbase for Community annotation
    • 2013 Vectorbase hosts, curates annotations and assembly
    • 2013- MGI-supported conference calls support annotation effort
    • 2012 Aug Formation steering committee, organization of internatinal annotation effort for Biomphalaria glabrata genome.
    • 2012 Jun Biomphalaria glabrata genome assembly v4.3 (MGI)
    • 2011 Jul MGI initiates Illumina sequencing of PE gDNA
    • 2011 Jul MGI completes Illumina cDNA sequencing for 12 tissue types of Biomphalaria glabrata
    • 2011 Jun MGI completes ~51x Illumina coverage short gDNA fragments.
    • 2011 May MGI to obtain additional Illumina coverage to improve assembly
    • 2011 Apr PRELIMINARY Biomphalaria glabrata genome assembly v4.0.1 (MGI)
    • 2011 Mar MGI Illumina sequencing of 5 Gb gDNA
    • 2010 Dec MGI to sequence Illumina paired ends (PE; 3kb; 8kb) for improved assembly
    • 2010 Dec Illumina cDNA sequencing for 12 tissue types of Biomphalaria glabrata in progress.
    • 2010 Jun PRELIMINARY Biomphalaria glabrata genome assembly v2.1 (MGI)
    • 2009 Sep MGI LS454 paired end gDNA data (6Gbases), > 23x coverage in NCBI SRA
    • 2009 Jul MGI LS454 gDNA data (17.1Gbases) in NCBI SRA
    • 2009 Feb MGI releases full-length sequence data from several BACs to NCBI
    • 2008 Jan MGI releases 100,304 BAC clone end sequences (BES) from the BG-BBa library to NCBI
    • 2007 November: Biomphalaria glabrata genome project progress meeting at ASTMH 2007
    • 2007 January: RNA, DNA template from selfed BB02 provided to initiate sequencing at MGI
    • 2006 January: Over 46,000 nucleotide database entries for Biomphalaria glabrata
    • 2005 October: Planning meeting for sequencing strategy at McDonnell Genome Institute MGI, St. Louis MO
    • 2005 Planning meeting at NIH, Bethesda MD
    • 2004 August: Biomphalaria glabrata prioritized as genomic sequencing target by NHGRI
    • White paper proposal for genome sequencing Biomphalaria glabrata
    • 2004 August: High quality BAC library (BG-BBa)
    • 2004 January: Mitochondrial genome sequence of Biomphalaria glabrata completed
    • 2003 September: Genome size for Biomphalaria glabrata published (check link below)
    • 2002 October: Prioritization for BAC library publicly posted by NHGRI
    • White paper proposal for BAC library Biomphalaria glabrata
  • Follow

    Submissions from 2006

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    rDNA gene region (18S-ITS1-5.8S-ITS2-28S) of Biomphalaria glabrata, Coen Adema

    Submissions from 2004

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    Construction of the BAC library for Biomphalaria glabrata, Coen Adema

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    Full-length mitochondrial genome sequence of Biomphalaria glabrata, Coen Adema

    Submissions from 2003

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    Genome size of Biomphalaria glabrata, Coen Adema

    Submissions from 2002

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    Biomphalaria glabrata field isolate (BB02) collected for construction of BAC library, Coen Adema

    Submissions from 2001

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    Rationale for a focus on Biomphalaria glabrata, Coen M. Adema, Eric S. Loker, Fred Lewis, and Matty Knight