. Cytoscape v2. 8. 2 was used to visualize the networks and Photoshop was used to edit the images. GO analysis and Arabidopsis orthology prediction Because of the lack of citrus genome annotation for the Probesets in the Affymetrix chip, the Probesets were used for all analysis. They were annotated using Arabidopsis orthologs or homologs. The Probesets were annotated by searching against the Arabidopsis genome using the tool provided in HarvEST database. GO terms were assigned to the citrus Probesets based on their corresponding Ara bidopsis gene ID. For those without AtGID, general GO terms were assigned, biological process, molecular function, and cellular component. GO enrich ment analysis was performed using the hypergeometric statistical method with Hochberg FDR adjustment in the AgriCO website as described elsewhere.

Trypanosoma Cilengitide cruzi is a protozoan parasite of the order Kinetoplastida, and the causative agent of Chagas Disease, one of the so called neglected diseases that dis proportionately affect the poor. The disease is endemic in most Latin American countries, affecting in excess of 8 million people. Chagas disease has a variable clinical outcome. In its acute form it can lead to death, while in its chronic form, it is a debilitating disease producing different associated pathologies, mega colon, mega esophagus and cardiomyopathy, among others. These different clinical outcomes are the result of a complex inter play between environmental factors, the host genetic back ground and the genetic diversity present in the parasite population.

As a result, these different clinical manifesta tions have been suggested to be, at least in part, due to the genetic diversity of T. cruzi. The T. cruzi species has a structured population, with a predominantly clonal mode of reproduction, and a con siderable phenotypic diversity. Through the use of a number of molecular markers the population has been divided in a number of evolutionary lineages, also called discrete typing units. Some markers allow the distinction of two or three major lineages, while other experimen tal strategies, such as RAPD and multilocus isoenzyme electrophoresis support the distinction of six sub divisions originally designated as DTUs I, IIa, IIb, IIc, IId, and IIe. Recently, this nomenclature was revised as follows, TcI, TcII, TcIII, TcIV, TcV and TcVI.

Lineages TcV and TcVI have a very high degree of heterozygosity but otherwise very homogeneous population structures with low intralineage diversity. The currently favoured hypothesis suggests that these two lineages originated after either one or two inde pendent hybridization events between strains of DTUs TcII and TcIII. Knowledge of the genetic variation present in a genome or in a species is of central importance for a variety of reasons and applications, i to understand the evolutionary forces underlying the biological and pheno typic properties observed in an individual, ii to detect cases of apparent horizontal gene tr