De novo draft genome of Portunus trituberculatus and its Hox gene cluster

A De Novo draft genome of Portunus trituberculatus was initially assembled by using SOAPdenovo2 (v2.04) and and its gaps were filled by using Platanus v1.2.4. In order to reduce null bases to improve the quality of draft genome, we reassembled the final version of draft genome by Platanus (v1.2.4)-sole assembly, instead of using SOAPdenovo2. Mate Pair filtered reads were used for Scaffolding and gap closing in initial and final draft assembly cases. We annotated the final version of draft genome by using Seqping v0.1.33 pipeline. Ab initio gene models were constructed by GlimmerHMM v3.0.4, AUGUST v3.2.2, and SNAP (2012/05/17). Then consensus set of predicted genes was constructed by merging ab initio gene models with unigenes assembled from transcriptomic data which were successfully mapped to our draft scaffold sequences. For assessing our final version of draft genome, we conducted BUSCO analyses of 4 arthropod draft genome sequences (P. trituberculatus; current study, E. sinensis, N. denticulata, and D.pullex; datasets of 3 referred species were downloaded online publications) by using arthropoda_odb9 database. We further validated our final version of draft genome by manual curation of highly preserved Hox genes. These resulted in recovery of 85.6 % of arthropod core genes and the entire consensus set of 10 Hox genes.