show Abstracthide AbstractThe current whole-genome shotgun (WGS) assembly was sequenced from an single male of the Chinese amphioxus Branchiostoma belcheri. The draft diploid assembly was generated from a total of ~73X raw shotgun and paired-end reads which included both 454 FLX titanium reads (~23X) and Illumina 2x115bp reads (~50X). Both the assembler Newbler and the assembler CABOGv6.1 were used in this task. The initial diploid assembly is fragmented and highly polymorphic (~4% heterozygosity). We developed novel algorithms (HaploMerger) to reconstruct a reference haploid assembly from the original diploid assembly. The details and programs of HaploMerger are available here (http://mosas.sysu.edu.cn/genome/download_softwares.php). The new reference assembly (version: bbv18h27) were created by using an pipeline that combines hierachical scaffolding, a hybrid assembly method (both Illumina and 454 reads were used for de novo assembly), the HaploMerger 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. An alternative haploid assembly is also provided, which contains all other alleles not included in the reference assembly.