title: Genome sequence of Coxiella endosymbiont of Rhipicephalus microplus
design: The three runs of Illumina HiSeq-1000 (accession SRX1668952, SRX1668960 and SRX1668961) sequencing reads that were generated from low cot and Cot 696 genomic DNA extracted from pooled collection of eggs from the f7, f10, f11 and f12 generation of the Rhipicephalus microplus Deutsch strain, along with the two runs of 454 GS FLX (accession SRX019998 and SRX019999) sequencing reads from the same Deutsch strain were used for assembling our partial Coxiella-like endosymbiont (CLE-Rm) genome. The raw sequence reads of R. microplus generated from Illumina and 454 sequencing platforms by Centre for Comparative Genomics, Murdoch University, Australia were submitted to SRA/NCBI as BioProjects with accessions PRJNA312025 (Biosample# SAMN04492774; WGS# LYUQ00000000) for illumina HiSeq-1000 reads, and, PRJNA46685 (Biosample# SAMN02953771; WGS# ADMZ00000000) for 454 GS FLX reads.  We are only submitting our assembly of the Coxiella-like endosymbiont genome (partial) derived from the aforementioned existing publicly available SRA metagenomics sequence data.All the runs of Illumina and 454 reads were merged independently and mapped against 38 Coxiella genome sequences existing in the NCBI/DDBJ/EMBL and NCBI contigs containing CLE sequences previously assembled from Illumina/PacBio/454 reads of R. microplus using BWA v0.7.12 to identify the Coxiella-related reads. Extant NCBI contigs (complete sequences) were identified by BLASTn using the CLE-genomes from R. turanicus, R. sanguineus and C. burnetii RSA 493. All the Illumina/454 mapped CLE-Rm reads against 38 Coxiella genome sequences and NCBI contigs were extracted using SAMtools v1.3.1 and subsequently these sequences were assembled into scaffolds independently using state-of-the-art assemblers, SPAdes v3.10.1, Velvet v1.2.10 and CLC Genomics Workbench v9.5.2. Tool CISA v1.3  was used to integrate the three de novo assemblies along with NCBI R. microplus contigs containing CLE sequences into a hybrid set of scaffolds, resulting in assemblies of superior contiguity and accuracy. These scaffolds were verified manually to exclude the overlapping regions.