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 Browsing for the lancelet genome Branchiostoma Belcheri (中国白氏文昌鱼)
The current whole-genome shotgun (WGS) assembly was sequenced from an individual male of the Chinese amphioxus (Branchiostoma belcheri). The draft diploid assembly was generated from a total of 100X raw shotgun and paired-end reads which included both 454 FLX titanium reads (~30X) and Illumina 115bp reads (~70X). The assembler Newbler and the assembler Celera were used in this task, especially, the newly developed algorithms (HaploMerger) is adopted to reconstruct a reference haploid assembly from the original diploid assembly.

The latest reference haploid assembly version, v18h27, 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a hybrid assembly method (both Illumina and 454 reads were used for de novo assembly), the HaploMerger2 (an unpublished updated version) algorithms for error correction and haploid assembly reconstruction.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.

Here you can browse the haploid genome (v7h2, v15h11 and v18h27), gene annotaion and supporting data on line, including the alternative polyadenylation sites.
  veiwer online
 Our Related Publication:
 [1]. Huang S, Tao X, Yuan S, et al. Discovery of an active RAG transposon illuminates the origins of V(D)J recombination. Cell. 2016, 166(1):102-114.
 [2]. Huang S, et al. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nat Commun. 2014, 5:5896.
 [3]. Chen Z, Huang S, et al. AliquotG: An Improved Heuristic Algorithm for Genome Aliquoting. Plos One. 2013, 8(5): e64279.
 [4]. Huang S, Chen Z, et al. HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res. 2012, 22(8): 1581-1588.
 

 

 Browsing for the lancelet genome Branchiostoma floridae (美国佛罗里达文昌鱼)
The genome sequencing of lancelet (Branchiostoma floridae) was completed and reported in 2008 ( Putnam NH, et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008, 453:1064-1071). Here, we provides the browsing for the predicted genes based on the released assembly (Branchiostoma_floridae_v1.allmasked, Branchiostoma_floridae_v2.assembly).
  viewer online
 
 

Augest 9, 2016. last modified
 
 
 
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