Project description:Tomato is one of the most important crops for human consumption. Unfortunately, its production is affected by diseases caused by pathogens such as the actynomicete Clavibacter michiganensis subsp. michiganens (Cmm). This pathogen is the causal agent of the bacterial canker of tomato, considered one of the most devastating tomato diseases. To date, there are not resistant varieties of commercial tomato against Cmm. However, there are wild tomato species resistant to Cmm. Using massive sequencing, we obtained the transcriptomes of the wild tomato species Solanum arcanum LA2157 and the commercial tomato Solanum lycopersicum cv. Ailsa Craig at 8 and 24 hours after Cmm challenge. We identified potential tomato tolerance-related genes by three approaches: mapping the reads to S. lycopersicum reference genome SL3.0, performing a semi de novo transcriptome assembly and a de novo transcriptome assembly. Some functional groups such as oxylipin biosynthetic process response to wounding, response to cytokinin among others, were enriched in both tomato species, suggesting a similar response, however, genes that encode proteins such as the Polyphenol oxidase E, Ankyrin and Leucine Rich Repeat receptors were overexpressed mainly in the wild tomato species, suggesting a possible role in the defense response. Here, we uncovered new candidate genes potentially related to bacterial canker tomato defense.
Project description:Clavibacter michiganensis subsp. michiganensis is an important Gram-positive phytopathogenic bacteria that causes bacterial wilt and canker in tomato. The genome of the type strain, NCPPB382, has been sequenced and annotated, however comparative genomics suggests that certain regions are under- or misannotated. In order to improve the genome annotation, we have undertaken a proteogenomic study of this important pathogen. Samples were grown in culture and the proteome of the pellet and supernatant were analyzed separately using shotgun HPLC-MS/MS. These proteomics datasets were analyzed and a number of missing gene were found and a number of existing gene calls were modified.
Project description:The gram- positive bacterial pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) causes huge economic losses by infecting tomato plants worldwide. Cmm can be spread by contaminated seeds and transplants, penetrating the plant through natural openings or wounds and is transferred through the plant xylem. While in recent years significant progress has been made to elucidate plant responses to pathogenic gram-negative bacteria by gene expression studies, the molecular mechanisms that lead to disease symptoms caused by gram-positive bacteria like Cmm remain elusive. An indigenous virulent Cmm strain isolated from a farm crop of Pomodoro tomatoes in southern Greece was used for the infection of EKSTASIS F1 hybrid tomato seedlings. Here, we present the results of a deep RNA- sequencing (RNA-seq) analysis performed to characterize the dynamic expression profile of tomato genes upon Cmm infection.
