Location: Animal Diseases Research
Project Number: 5348-32000-034-08
Start Date: Jan 01, 2014
End Date: Sep 30, 2015
Comparative and structural genomic analysis will be performed by a combination of (1) Genome and transcriptome sequencing through creation of libraries (Illumina paired end and mate pair; PacBio >8 Kb strand-specific RNAseq and sequencing (1 MiSeq Illumina run; 10 PacBio SMRT cells, ¼ Hi Seq channel); (2) Analysis through genome-guided transcriptome assembly, using Trinity; and (3) targeted analysis using comparative genomics and homologs to EF-1a and Tubulin alpha chain genes. Specifically for T. parva, (1) develop a host:parasite quantification assay with qPCR; (2) structural re-annotation of the genome using Trinity and generation of gene training set for ab initio gene finders; (3) perform training and running of serveral gene finders; (4) compile cross species evidence from other apicomplexan species; and (5) generation of new gene structures using a variety of combiners such as evidence Modeler and Glean.