Pipeline publication

[…] mon sequence AGCT and identify the site at which MdBV proviral segments excise from the M. demolitor genome [35]. WIMs were previously mapped for three segments by inverse PCR [35]. The locations of WIM sites for all proviral segments in the M. demolitor genome were obvious from read mapping data, and segment beginning and end coordinates were given to AGCT sites where circularization occurs. Host Integration Motifs (HIMs) were also identified previously by PCR methods and sequencing as the site where MdBV DNAs in virions integrate into the genome of infected host cells [35]. The twelve HIM sequences identified by these approaches were aligned and made into a Hidden Markov Model (hmm) using HMMER hmmbuild (http://hmmer.janelia.org). This hmm was used as a query in a HMMER hmmsearch against the scaffolds of interest to identify HIM motifs in all correctly assembled old and new segments. Sequence motifs were aligned using MUSCLE and maximum likelihood phylogenetic trees were built using phylogeny.fr with the HKY+I+G model and 100 bootstrap replicates [94]., Sets of orthologous genes were identified using orthomcl and four datasets: 1) all protein-coding sequences from M. demolitor, 2) all protein sequences from G. flavicoxis BV segments and flanking regions of the wasp genome, 3) same information from 2 for G. indiensis, and 4) protein coding sequences from nudivirus-gene containing regions of C. congregata [27], [41], [95]. Groups of orthologous genes (syntenic) in the genome were identified using the orthomcl output with orthocluster [96]. Syntenic regions were viewed with Gbrowse syn. Assembly of the M. demolitor genome initially suggested the nudivirus-like gene cluster contained two identical duplications absent from the nudivirus-like gene cluster identified in the wasp C. congregata [27]: Cc50C22.3/HzNVorf94-like/38K and 27b-like/Cc50C22.6. Given the identical nature of these predicted duplications, we assessed whether they were correct by primer walking and Sanger sequencing these domains. Resequencing showed that these genes were not duplicated. The above information was then used to make figures that included modifications of pictorial representations of M. demolitor genes on scaffolds generated by Gbrowse [97], [98]., We thank Sarah Thomas for assistance with PCR assays, Kavita Bitra for genomic DNA preparation, and Spencer Johnson for estimating the size of the M. demolitor genome.] […]

Pipeline specifications

Software tools HMMER, MUSCLE, OrthoCluster, GBrowse_syn, GBrowse
Organisms Human poliovirus 1 Mahoney, Viruses, Microplitis demolitor, Microplitis demolitor bracovirus