Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii.

BACKGROUND: Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3. RESULTS: A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other. CONCLUSIONS: There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.

Theories for Understanding the Effect of Impact Assessment and Project Evaluation on the Practice of Science.

We examine the phenomenon of impact assessment in the practice of scientific research, paying attention to the context in which project evaluation is used in federally funded research on plant health in the United States. Our analysis, which is derived from systems theory, carries out a particular view of the research process. For the purposes of this review, our use of the term systems theory references the body of interdisciplinary work that deals with the organization and function of complex structures in nature and human society. Key concepts in this body of theory are that both the components and the interactions among components are important in understanding behavior and that, frequently, systems are seen to be hierarchical in structure. The aim of our analysis is to bring to the attention of the plant health community several concepts from the social sciences that might help in understanding how researchers have responded to the increased expectations from funders to provide project evaluations and impact assessments. We generate a synthesis of these theories, which have not previously been used in a unified way, to explain choices in response to newly imposed goals. Although our analysis is motivated by a specific disciplinary focus on plant health, the issues we discuss are general. Thus, we hope the review is useful to a wide range of scientists, science program managers, and policymakers.