Next generation sequencing technologies allow us to assemble genomes in days, with the primary advantage of producing large volumes of inexpensive data. The introduction of these technologies is changing our ability to answer the fundamental question of genetics: what genotypes determine phenotypes. However, the blueprint provided by genome sequences is not sufficient to reveal gene function. A variety of methods have been developed, that use high throughput sequencing to analyze diverse biological phenomena, including RNA expression. Massive parallel sequencing of cDNA libraries allows us to study transcription with unprecedented detail. We have undertaken a comparative genomics/transcriptomics approach to identify genes responsible for two different phenotypes in Anaplasma marginale.A. marginale., a tick-borne pathogen in the Order Rickettsiales, is the most prevalent vector-borne pathogen of cattle. Although most pathogens in this Order are transmitted by arthropods, little is known about the microbial determinants of transmission. A. marginale provides unique tools for studying the determinants of transmission, with multiple strain sequences available that display distinct transmission phenotypes. The closed core A. marginale genome suggests that phenotypic differences are due to single nucleotide polymorphisms (SNPs). We combined DNA/RNA comparative genomic approaches and identified genes that segregate with transmissibility. Comparison of seven strains with different transmission phenotypes generated a list of SNPs affecting 18 genes and nine promoters. Transcriptional analysis verified two genes downstream from promoter SNPs as differentially transcribed. RNA-seq analysis confirmed the comparative genomics data and found 10 additional genes whose transcription between strains with distinct transmission efficiencies was significantly different. We identified 30 genes and two novel transcripts potentially involved in tick transmission.Transformation of bacterial pathogens with the green fluorescent protein (GFP) allows for dissection of the molecular mechanisms responsible for transmission and infection of vector-borne pathogens. A. marginale has been successfully transformed and is known to have a stable in vivo infection cycle. Like other GFP-transformed bacterial pathogens, this mutant replicates slower than wild type A. marginale. Whole genome transcriptional profiling allowed us to reveal genes and pathways whose transcription is altered in slow growing transformed A. marginale
