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 Introduction for the Chinese Amphioxus Genome Sequencing Project Show or Hide gene list
  The current whole-genome shotgun (WGS) assembly was sequenced from a single male adult of the Chinese amphioxus Branchiostoma belcheri. The draft diploid assembly was generated from ~100X raw shotgun and paired-end reads which included both 454 FLX titanium reads (~30X) and Illumina GAIIx 2x115bp reads (~70X). The assembler Newbler and the Celera assembler were used in this task.

The diploid assembly is fragmented and highly polymorphic (~5% heterozygosity). We developed novel algorithms (HaploMerger) to reconstruct a reference haploid assembly from the original diploid assembly. The HaploMerger package is available here in our web site (Softwares Page).

The new reference assembly version, bbv18h27(diploid assembly version 18; haploid assembly version 27) were created by using a pipeline that combines hierachical scaffolding, a hybrid assembly method (both Illumina and 454 reads were used for de novo assembly), the HaploMerger (an unpublished updated version) algorithms for error correction and haploid assembly reconstruction. The new reference assembly has a size of ~426Mb, with scaffold and contig N50 sizes at 2.3Mb and 46 Kb, respectively.

NOTE : The reference haploid genome assembly has been also deposited in NCBI under the genome project accession No. PRJNA214454. This deposited sequence is slightly different from the original genome assembly presented on this website, because small changes have been made to the deposited assembly in order to meet NCBI's guidelines for genome submission. Also note that NCBI uses their own annotation pipeline to predict protein genes.


 Released Data
  Unless otherwise noted, all files are in FASTA format and compressed with Gnu Zip (gzip). To uncompress files: on Mac use StuffIt, on PC use WinZip or WinRAR.
*The download Links will be available after you read and accept the data release policy !
   Released: Branchiostoma.belcheri draft (haploid) genome Released 3 (internal tracking ID: bbv18)
 [ A1 ]. Branchiostoma.belcheri_v18h27.r3_alt_genome.softmasked.fa.gz
  Description:Branchiostoma.belcheri_v18h27.r3_alt_genome.softmasked.fa.gz: repeat masked
 [ A2 ]. Branchiostoma.belcheri_v18h27.r3_alt_cds.fa.gz
 [ A3 ]. Branchiostoma.belcheri_v18h27.r3_alt_protein.fa.gz
 [ A4 ]. Branchiostoma.belcheri_v18h27.r3_alt_annotation.gff3.gz
 [ A5 ]. Branchiostoma.belcheri_v18h27.r3_alt.fixed.agp.gz
 [ B1 ]. Branchiostoma.belcheri_v18h27.r3_ref_genome.softmasked.fa.gz
  Description:Branchiostoma.belcheri_v18h27.r3_ref_genome.softmasked.fa.gz: repeat masked
 [ B2 ]. Branchiostoma.belcheri_v18h27.r3_ref_cds.fa.gz
 [ B3 ]. Branchiostoma.belcheri_v18h27.r3_ref_protein.fa.gz
 [ B4 ]. Branchiostoma.belcheri_v18h27.r3_ref_annotation.gff3.gz
 [ B5 ]. Branchiostoma.belcheri_v18h27.r3_ref.fixed.agp.gz
 [ B6 ]. Branchiostoma.belcheri_v18h27.r3_degenerate.fa.gz
 [ C1 ]. Branchiostoma.belcheri_r3_transposon_elements.fa.gz
   Released: Branchiostoma.belcheri draft (haploid) genome Released 2 (internal tracking ID: bbv15)
 [ 1 ]. Branchiostoma.belcheri_v15h11.r2_genome.softmasked.fa.gz
  Description:Branchiostoma.belcheri_v15h11.r2_genome.softmasked.fa.gz: repeat masked
 [ 2 ]. Branchiostoma.belcheri_v15h11.r2_mRNA.fa.gz
  Description: Branchiostoma.belcheri_v15h11.r2_mRNA.fa.gz
 [ 3 ]. Branchiostoma.belcheri_v15h11.r2_protein.fa.gz
  Description: Branchiostoma.belcheri_v15h11.r2_protein.fa.gz
   Released: Branchiostoma.belcheri draft (haploid) genome Released 1 (internal tracking ID: bbv7)
 [ 1 ]. Branchiostoma.belcheri_HapV2_genome.fa.gz
  Description: The reference haploid assembly, soft-masked.
 [ 2 ]. Branchiostoma.belcheri_degenerate_genome.fa.gz
  Description: degenerate contigs (contigs that can not be incorporated into the assembly by the assember).
 [ 3 ]. Branchiostoma.belcheri_HapV2_proteins.fa.gz
  Description: The non-redundant protein set for the reference haploid assembly.
 [ 4 ]. Branchiostoma.belcheri_degenerate_proteins.fa.gz
  Description: The non-redundant protein set for degenerate contigs (contigs that can not be incorporated into the assembly by the assember).
 [ 5 ]. Branchiostoma.belcheri_HapV2_cds.fa.gz
  Description: The non-redundant transcript set for the reference haploid assembly.
 [ 6 ]. Branchiostoma.belcheri_degenerate_cds.fa.gz
  Description: The non-redundant transcript set for degenerate contigs (contigs that can not be incorporated into the assembly by the assember).

[Leiming You, et al. The Journal of Biological Databases and Curation. 2019, doi:10.1093/database/baz056] LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.

March 19, 2019. last modified
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