Transcriptome and secretome of two pythium species during infection and saprophytic growth
Date
2016
Authors
Ibarra Caballero, Jorge Rafael, author
Tisserat, Ned A., advisor
Leach, Jan, committee member
Hess, Ann, committee member
Jahn, Courtney, committee member
Journal Title
Journal ISSN
Volume Title
Abstract
In the first part of this dissertation, I describe how we obtained and analyzed the full complement of transcripts –the transcriptome- and the set of secreted proteins –the secretome- of Pythium irregulare and Pythium iwayamai isolates when they were infecting plant hosts and when they were growing saprophytically. Additionally, these two treatments were performed at two different temperatures (4˚ and 19˚C). The assembled transcriptomes were annotated, and a closer analysis of the expression profiles of transcripts coding for pathogenicity-related proteins is shown. Secreted proteins were semi-quantified and their likely functions were determined based on the annotation of the corresponding transcripts. In the second part of this document, I include four appendices. Each one is about a different project that I contributed to during my stay at the Department of Bioagricultural Sciences and Pest Management. An article has been publish for each project. For the study included in appendix 1, I used basic plant pathology and microbiology techniques to fulfill Koch’s postulates for a disease affecting Turkish filbert trees. I also used some molecular techniques to aid in the identification of the isolated bacteria. The work presented in appendix 2 was a follow-up of the previous one. We sequenced the genome of Xanthomonas arboricola pv. Corylina isolated from Turkish filbert leaves. Then, we iii assembled a draft genome of the bacterium. The assembled genome was annotated and the robustness of the assembly was verified. Appendix 3 includes the report about the genome assemblies of 3 different isolates of Lonsdalea quercina subsp. quercina. As in the previous work, the genomes were annotated and the robustness of the assemblies was verified. In appendix 4, the report of a study on the population structure of Geosmithia morbida is presented. This fungus and the walnut twig beetle Pityophthorus juglandis are associated with the Thousand Cankers disease of walnut and wingnut trees. There is big concern because the disease has moved from the western United States to the native range of a highly susceptible walnut species in the eastern USA. I contributed to this research in the analysis of the data, the statistical analyses and the writing of the paper.
Description
Zip file contains data files: SFile1_Pir_transcripts_seqs.fasta, SFile2_Piw_trancripts_seqs.fasta, ST1_RNASeq.csv, ST2_P174b_med4_P176med4.csv, ST3_P174b_wp4_P176wp4.csv, ST4_P174b_med19_P176med19.csv, ST5_P174b_wp19_P176wp19.csv, ST6_P174b_wp4_med4.csv, ST7_P174b_wp19_med19.csv, ST8_P176_wp4_med4.csv, ST9_P176wp19_med19.csv, ST10_P174a_med4_P191med4.csv, ST11_P174a_wp4_P191wp4.csv, ST12_P174a_med19_P191med19.csv, ST13_P174a_wp19_P191wp19.csv, ST14_P174a_wp4_med4.csv, ST15_P174a_wp19_med19.csv, ST16_P191_wp4_med4.csv, ST17_P191_wp19_med19.csv, ST18_P174b_proteins_table.csv, ST19_P176_proteins_table.csv, ST20_P174a_proteins_table.csv, ST21_P191_proteins_table.csv, ST22_Pir_other_proteins.csv, and. ST23_Piw_other_proteins.csv. Their contents are described in the text.
Rights Access
Subject
transcriptomics
Pythium
secretome
proteomics