Frequently Asked Questions

Questions

Sequencing

Misc

Answers

Sequencing

  • How big is the Batrachochytrium dendrobatidis genome?
    Our current total unique contig length is 23,403,618 bp (base pairs). The estimated genome size of B. dendrobatidis is 23.7 Mb.
  • What strain was sequenced?
    Batrachochytrium dendrobatidis diploid strain JEL423.
  • What is the current state of the assembly?

    The current assembly contains 348 contigs in 69 scaffolds (supercontigs). There are no current plans for additional sequencing or finishing. See Assembly for detail.

  • How has the sequence been generated for the Batrachochytrium dendrobatidis project?

    Our data consist of over 280,000 individual sequencing reads obtained by sequencing each end of plasmids and Fosmids from libraries containing randomly sheared fragments of 4 kb, 10 kb, and 40 kb average size respectively. See Assembly for details.

  • Will the genome be finished?

    There are no plans to finish this genome at this time.

  • How will we know the assembly is correct?

    The quality of the assembly will be assessed in several ways. In addition to requiring that the paired plasmid and Fosmid ends occur in a logical manner, our assembly of the Batrachochytrium dendrobatidis genome will be verified through comparison with available genomic sequences.

  • What data are available?

    In this version of our data release, all sequence contigs and supercontigs are available. Sequence data can be accessed in several ways: either through a search with BLASTN or TBLASTN, retrieving of a specific region of the assembly, or by downloading the entire genome. Supercontig and contig sequences are subject to change throughout this project, so each data release version number will be appended to the contig number as a prefix (e.g. 1.1 denotes assembly version 1, supercontig #1).

    Fosmid clones have been integrated into the current assembly, and you can search and view the locations of these clones within the sequence supercontigs.

    A fasta file of raw reads excluded from the assembly is also available for BLAST and download. Also available for download are an AGP file describing the supercontigs and contigs in this assembly and a file listing coordinates of paired endreads.

  • This sequence release looks different from previous releases, like Neurospora crassa. What's different?

    Important information about this release can be found here.

Misc

  • How do I cite the sequence for publication?

    Publications should include the following citation:
    Batrachochytrium dendrobatidis Sequencing Project. Broad Institute of Harvard and MIT (http://www.broad.mit.edu)

  • Who do I contact with questions about the sequencing?

    Our email address is annotation-webmaster@broad.mit.edu.

  • Where can I get the Fosmids from this sequencing project?

    They are available from the FGSC (Fungal Genetics Stock Center).

  • What are the descriptions of the photos in this website?

    All photos are courtesy of Joyce Longcore, from The University of Maine.

    Captions for the photos in the Home page (from left to right):

    1. Phylomedusa lemur in native habitat (Panama). This individual was sick, as evidenced by its lack of righting response; it was the source of the sequenced strain JEL423.
    2. B. dendrobatidis begins its life cycle as a zoospore (shown), which grows into a thallus producing a single zoosporangium, which releases new zoospores.
    3. A zoosporangium with zoospores exiting through discharge papilla.
    4. Frog skin (smooth-sided toad: Bufo guttatus) infected with Batrachochytrium dendrobatidis; this frog died at the National Zoological Park.
    5. Swabbing a Phylomedusa lemur for later molecular detection of B. dendrobatidis DNA by a PCR-based assay.

    Captions for the photos in the Project Information page (from left to right):

    1. Zoospores.
    2. A thallus bearing thread-like rhizoids develops from an individual zoospore.
    3. After zoospores discharge, no nuclei remain and the thallus ceases growth. This zoosporangium is nearly empty but still contains a few motile zoospores.
    4. Newly released zoospores, which are frequently amoeboid when first released, but when they swim free in liquid they are spherical. The colors on the spherical shapes here indicate that they are in motion.
    5. B. dendrobatidis infected skin of a Northern Leopard Frog. This is a localized infection, note uninfected skin cells around the infected area.