JGI B. floridae v1.0 Info

Project Status

The genome of Branchiostoma floridae is estimated to be approximately 575 Mb contained in 19 pairs of chromosomes, and is being sequenced to approximately 8.1 X depth.

The genome assembly release v.1.0 was annotated using the JGI annotation pipeline. Gene models and associated transcripts/proteins are predicted or mapped using a variety of tools based on cDNA, protein homology and ab initio methods. The current release contains approximately 50817 gene models composed of known Branchiostoma floridae genes as well as support from available Branchiostoma floridae EST and cDNA data.

Approximately 95% of Branchiostoma floridae full-length cDNAs mapped to the v.1.0 assembly. Average gene length is 9.1 kb and average transcript length is 1.4 kb, with the average protein containing 451 amino acids. There are approximately 7 exons per gene averaging 204 bp each with intron spacing of 1.3 kb. Gene functions have been automatically assigned based on homology to known genes. Manual curation of these annotations will start shortly.

Assembly Release

v.1.0 (December 5, 2006): Approximately 6.5 Million shotgun reads were initially assembled using JAZZ. A high allelic polymorphism rate of 5-10% allowed the two haplotypes to be assembled separately at approximately 75% of genomic loci. There are a total of 3,032 scaffolds, with a total length of 923 Mb composed of 81,073 contigs. Half of the assembly is contained in 174 scaffolds, all at least 1.6 Mb in length. The length-weighted mean contig size (L50) is 26kb.

Collaborators

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.