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Genomic Analysis of Fungal Species Causing Ascochyta Blight in Field Pea

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Genomic Analysis of Fungal Species Causing Ascochyta Blight in Field Pea Department of Environment and Agriculture School of Science and Engineering Genomic Analysis of Fungal Species Causing Ascochyta Blight in Field Pea Chala Jefuka Turo This thesis is presented for the Degree of Doctor of Philosophy of Curtin University February 2016 School of Science and Engineering Declaration To the best of my knowledge and belief this thesis contains no material previously published by any other person except where due acknowledgment has been made. This thesis contains no material which has been accepted for the award of any other degree or diploma in any university. Signature: ____________________Date: ____________________ Acknowledgements I would like to express my appreciation to my initial principal supervisor Dr Judith Lichtenzveig for providing me the opportunity to study at Curtin University. Thank you for remarkable mentorship, encouragement and patience during my study. Special thanks go to my principal supervisor, Dr James Hane, for his tremendous mentorship and invaluable inputs. I am thankful for teaching me bioinformatics from the scratch to advanced computational biology, guidance and advice throughout writing my thesis. I have no words to explain, without you, it would have been impossible to produce this thesis. I am thankful to my co-supervisor, Dr Bernadette Henares, for your supervision, teaching quantitative PCR techniques and commenting the thesis. I would also like to thank my chair of supervisory committee, Professor Mark Gibberd, for evaluating my research progress, encouragement and serving committee members, particularly in the event of hardship situations. My special thanks extends to Dr Kate Trinajstic for serving as the chair of my supervisory committee toward the end of my studies. I am grateful to Julie Lawrence for teaching me molecular laboratory methods and for provision of technical assistances. I extend my special thanks to Lydia Kupsky, who taught me how to perform florescent microscopy. I’m indebted to invaluable technical and moral support obtained from Lina Farfan Caceres from start to end of my thesis. I am also grateful for bioinformatics support obtained from Robert Syme and Angela Williams. I would like to thank Francis Kessie, Robert Lee, Winnie Liu, Johannes Debler, Christy Grime, Bahram Sharifnabi and Fiona Kamphuis for various inputs and assistances provided. I would like to extend my gratitude to all CCDM staff members for their kind collaboration. I’m grateful to support from Julie Craig, from the International Sponsored Student Unit, for logistics arrangements and support. I am thankful to Australian Government for providing me a scholarship opportunity. I am also grateful to the financial assistance obtained from the Department of Environment and Agriculture, Curtin University. Finally, I would like express my appreciation to my beloved wife Aklil Knifu Kelifa, who always supports me in every moment and in all aspects throughout my studies. i Abstract The fungal pathogen Peyronellaea pinodes, Peyronellaea pinodella, Ascochyta pisi and Phoma koolunga are the most destructive fungal pathogens of field pea. Whole genome sequencing, comparative and in planta transcriptome studies were pursued to test the hypothesis that these pathogens secrete effectors as part of their pathogenicity arsenal. The genome of isolates of P. pinodes (2), P. pinodella (2), A. pisi (3) and Ph. koolunga (2) were completely sequenced and evaluated. In planta transcriptomes of P. pinodes, P. pinodella and Ph. koolunga were obtained as part of effector prediction. The genome assemblies varied between 29 and 33 Mbp with equilibrated GC content (51- 53%). The synteny relationship between P. pinodes and other fungal pathogens is congruent to their established evolutionary relationship. Genome analysis uncovered plant cell wall de-polymerization strategies evolved by ascochyta blight pathogens to establish themselves in their host. Heterologous expression confirmed that necrosis- inducing proteins (NLP) from Didymellaceae elicited cell-death only to dicots. This cytotoxic NLP is absent from cereal pathogens analysed suggesting niche adaptive evolution of Didymellaceae pathogens. About 223, 226 and 123 effector candidates were predicted from P. pinodes, P. pinodella and Ph. koolunga, respectively. In planta expressed effectors might play crucial role during infection. Further functional analysis will lead to development of novel pea breeding techniques. The availability of these genome data have contributed to scare molecular data available for studying host pathogen interaction. It is perceived that public availability of these data will increase public research engagement, hasten integration of available host and pathogen genome resources and boost pea improvement programs. ii Contents ......................................................................................................... Page Acknowledgements ...............................................................................................i Abstract ............................................................................................................... ii List of Tables .....................................................................................................vii List of Figures ..................................................................................................... ix Abbreviations ...................................................................................................... xi 1. General Introduction ................................................................................. 1 2. Molecular Basis of Ascochyta Blight Pathogens of Field Pea in the genomic Era ............................................................................................................ 5 2.1 Introduction .................................................................................................... 5 2.2 Molecular basis of interaction between plants and pathogens .......................... 5 2.3 Taxonomy and relatedness of ascochyta blight pathogens of field pea ............ 7 2.4 Infection and disease development in ascochyta blight pathogens of field pea 8 2.5 Population structure of ascochyta blight pathogens of pea (ABPFP) ............. 11 2.6 Host specificity of ascochyta blight pathogens of field pea ........................... 12 2.7 Molecular mechanisms of pathogenicity (effectors in ABPFP) ..................... 13 2.8 Phytoalexin detoxification is associated to virulence .................................... 15 2.9 Suppressors interfere with host defence via the jasmonic acid signalling pathway .................................................................................................. 17 2.10 Phytotoxic metabolites in ascochyta blight pathogens of field pea ........... 18 3. Genome Sequencing and Comparative Analysis of Peyronellaea pinodes, P. pinodella, Ph. koolunga and Ascochyta pisi ........................................ 22 3.1 Introduction .................................................................................................. 22 3.2 Materials and Methods ................................................................................. 25 3.2.1 Genome data acquisition and genome assembling ................................... 25 3.2.2 Repeat identification and repeat-induced point mutation (RIP) analysis .. 29 3.2.3 Gene finding ........................................................................................... 29 3.2.4 Functional annotation.............................................................................. 30 3.2.5 Comparative genomic analysis ................................................................ 30 3.2.5.1 Synteny and read mapping analysis ......................................................... 30 3.2.5.2 Analysis of secondary metabolite gene clusters ....................................... 31 3.2.5.3 Carbohydrate active enzyme (CAZymes) annotation ............................... 32 3.3 Results and Discussion ................................................................................. 33 3.3.1 Phylogenetic relatedness of ascochyta blight pathogens of field pea ........ 33 iii 3.3.2 Genome sequence assembly statistics ...................................................... 35 3.3.3 Repeat content of the genome assembly .................................................. 36 3.3.4 Gene content of genome assemblies ........................................................ 40 3.3.5 Comparative genomics ............................................................................ 41 3.3.5.1 RIP like activities are unusual in ascochyta blight pathogens of field pea 41 3.3.5.2 Synteny relationship between P. pinodes and other pathogens................. 44 3.3.5.3 Defining core protein sequences in Didymellaceae.................................. 51 3.3.5.4 Functional annotation abundance in P. pinodes ....................................... 53 3.3.5.5 Secondary metabolite gene clusters in ascochyta blight pathogens of field pea ................................................................................................... 55 3.3.5.6 Genomes of Didymellaceae, pathogens of field pea are enriched with carbohydrate activnzyme ........................................................................ 61 3.3.5.7 Pectin degradation is a common host adaptation mechanism in ascochyta blight pathogens of field pea ................................................................... 63 3.4 Conclusion ..................................................................................................
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