U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 Crops Pathology and Genetics Research: Davis, CA
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    Outreach Events
                        UC Davis Picnic Day
                                    Kinders go to College
                                    STEM Girls
                                    Future Scientist Program
                                    Agriculture Future of America
                                    Wallace-Carver Fellowship
                                    Young Scholars Program
                                    Annual Awards Banquet
                    About Us
                        About Us
                                    Our Mission
                                    Principal InvestigatorsSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Pacific West Area Davis, California Crops Pathology and Genetics Research Research Publications at this Location





- ARS National Programs
- Search for a scientific manuscript
- Search for a research project
- ARS Software
- Programs and Projects
- Collaborations
- Subjects of Investigation
- Publications
- Etiology and Biology of Tree Crop Diseases
- Rice Genetics
- Sustainable Floriculture
- Sustainable Viticulture

Title:   Author  item
                                            MORALES-CRUZ, ABRAHAM - University Of Californiaitem
                                            AMRINE, KATHERINE - University Of Californiaitem
                                            BLANCO-ULATE, BARBARA - University Of Californiaitem
                                            LAWRENCE, DANIEL - University Of Californiaitem
                                            TRAVADON, RENAUD - University Of Californiaitem
                                            ROLSHAUSEN, PHILIPPE - University Of Californiaitem
                                            Baumgartner, Kendraitem
                                            CANTU, DARIO - University Of California
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 5/6/2015
                                    Publication  Date: 6/19/2015
                                    Publication URL: http://www.biomedcentral.com/1471-2164/16/469Citation: Morales-Cruz, A., Amrine, K.C., Blanco-Ulate, B., Lawrence, D.P., Travadon, R., Rolshausen, P., Baumgartner, K., Cantu, D. 2015. Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens. Biomed Central (BMC) Genomics. 16:469.Interpretive Summary: The trunk diseases Eutypa dieback, Botryosphaeria dieback, Phomopsis dieback, and Esca threaten the longevity and productivity of grapevines worldwide. They are caused by fungi that are genetically unrelated, but nonetheless form chronic wood infections. Variation in their abilities to decompose the wood as a food source and in their production of compounds toxic to the grapevine are thought to contribute to the unique disease symptoms these fungi cause. We sequenced the genomes of six trunk pathogens: Diaporthe ampelina, Diplodia seriata, Eutypa lata, Neofusicoccum parvum, Phaeomoniella chlamydospora, and Togninia minima. In comparing their genomes, we focused on gene families that are likely to enhance the pathogen’s ability to infect grapevine wood: wood degradation, (nutrient uptake, and toxin production. For these comparisons between the genomes of the trunk pathogens, we examined the number of genes per gene family, the similarities/differences of genes within gene families, and the evolution of gene families over time. In the genomes of N. parvum, D. ampelina, and E. lata, we found an increase in total gene numbers within gene families associated with cell wall oxidative functions and secondary metabolic pathways, whereas D. seriata, P. chlamydospora, and T. minima appear to have actually ‘lost’ genes with these functions over time. This finding suggests that N. parvum, D. ampelina, and E. lata may produce more enzymes or toxins, which is consistent with the fact that infections of these three species (more so than the other three) spread quickly within a grapevine.  Gene families with significantly faster rates of gene gain can now provide a basis for further studies, to determine how the different trunk pathogens spread from one plant cell to the next and how resistant grape cultivars evade or tolerate the pathogens. In the short term, the genomes of the trunk pathogens are an important study tool for development of accurate diagnostic markers.
                                Technical Abstract: Trunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections, but variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we expanded genomic resources to three additional trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. The predicted proteomes were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, D. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will ultimately lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov