Haploid assemblies of Branchiostoma belcheri breed outbred isolate BF01. The genome project of Branchiostoma belcheri

The current whole-genome shotgun (WGS) assembly was sequenced from an single male of the Chinese amphioxus Branchiostoma belcheri. The draft diploid assembly (GenBank accession AYSR00000000) 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 both haploid assemblies from this original diploid assembly. The details and programs of HaploMerger are available here (https://github.com/mapleforest/HaploMerger). The haploid assembly with better quality is chosen as the reference haploid assembly (version: ref_bbv18h27), and the other haploid assembly is named as the alternative haploid assembly (version: alt_bbv18h27), which contains all other alleles not included in the reference haploid assembly. The reference haploid assembly version ref_bbv18h27 is based on the diploid assembly version 18 (GenBank accession AYSR00000000). This reference halpoid assembly (version ref_bbv18h27) is an improved version over the previous reference haploid assembly version bbv18h27 (GenBank accession AYSS00000000). The alternative haploid assembly version alt_bbv18h27 is also based on the diploid assembly version 18 (GenBank accession AYSR00000000). Reference: Shengfeng Huang, Zelin Chen, Xinyu Yan, Ting Yu, Guangrui Huang, Pierre Antoine Pontarotti, Qingyu Yan, Hongchen Zhao, Jie Li, Ping Yang, Ruihua Wang, Rui Li, Xin Tao, Ting Deng, Yiquan Wang, Guang Li, Qiujin Zhang, Sisi Zhou, Leiming You, Shaochun Yuan, Yonggui Fu, Fenfang Wu, Meiling Dong, Shangwu Chen, Anlong Xu. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nature communications. 2014 Dec 19; 5:5896.