Evolution of Promoter sequences in the fungal Pathogen Zymoseptoria tritici

Kumar, Avneesh

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Evolution of Promoter sequences in the fungal Pathogen Zymoseptoria tritici

Kumar, A. (2017). Evolution of Promoter sequences in the fungal Pathogen Zymoseptoria tritici. Master Thesis, Christian-Albrechts-Universität zu Kiel, Kiel.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0001-5468-C Version Permalink: https://hdl.handle.net/21.11116/0000-0005-1D2B-C

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Creators:
Kumar, Avneesh¹, Author
Stukenbrock, Eva H.¹, Referee

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1Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2068284

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Abstract: In previous studies, transcription profiling of Z. tritici early infection stages in compatible (wheat) and non-compatible host (Brachypodium distachyon) were compared, which showed that genes expressing specifically while infecting wheat were under positive selection along Zymoseptoria. tritici lineage (Kellner et al. 2014). In continuation with the previous study, this study focusses on putative promoter evolution of Z. tritici in terms of nucleotide diversity and neutrality of sequence evolution as Tajima’s Pi and Tajima’s D respectively.
The aim of this study was to address the underlying genetic and genomic basis of transcriptional variation in Z. tritici focusing on evolution in promoter sequences. For this purpose, de-novo assemblies of 26 Z. tritici isolates were created. The Dutch isolate IPO323 was used as a reference for further analysis. De-novo assembly was followed by multiple genome alignments. The generated alignment was further filtered and processed using MafFilter program. Furthermore, sequence diversity statistics and neutrality test were calculated for each promoter and their corresponding genes. Different correlation studies were carried out, including correlation between Tajima’s Pi of promoters with Tajima’s Pi of genes, Tajima’s D of promoters with Tajima’s D of genes, Tajima’s Pi of promoters with the distance of promoters from telomeres and Tajima’s Pi of promoters with the expression level (FPKM) of their corresponding genes. The same correlation studies were also performed considering the effector-coding genes of the Z. tritici genome.
Positive correlation was observed between nucleotide diversity of promotes and their corresponding genes. It was also found that Tajima’s D of promoters and their corresponding genes were positively correlated. Negative correlation was observed between nucleotide diversity of promoters and their distance from telomeres, similarly, negative correlation was observed between nucleotide diversity of promoters and expression level of their corresponding genes. Significantly low nucleotide diversity in promoters was observed for genes which were highly expressed only during biotrophic and lifestyle transition phase of infection.

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Language(s): eng - English

Dates: Accepted: 2107-05Date issued: 2017-05

Publication Status: Issued

Pages: 73

Publishing info: Kiel : Christian-Albrechts-Universität zu Kiel

Table of Contents: Table of Contents
1. Summary ....................................................................................................................................... 1
2. Introduction ................................................................................................................................... 2
2.1. Origin of Z. tritici .................................................................................................................. 3
2.2. Genome organization of Z. tritici .......................................................................................... 3
2.3. Z. tritici infection Cycle ........................................................................................................ 3
2.4. Role of Promoters in Regulation of Gene Expression .......................................................... 5
2.5. Properties of Eukaryotic Promoters ...................................................................................... 6
2.6. Why promoter evolution should be studied .......................................................................... 8
2.7. Population genomics Study ................................................................................................... 8
2.8. Nucleotide Diversity and neutrality test ................................................................................ 9
2.9. Aim of the study .................................................................................................................. 11
3. Material and Methods ................................................................................................................. 12
3.1. Assembly of Z. tritici isolates.............................................................................................. 12
3.2. Multiple genome alignments ............................................................................................... 12
3.3. Processing multiple genome alignment using MaFilter ...................................................... 12
3.4. Predicting fungal effector proteins using EffectorP ............................................................ 13
3.5. Statistical analysis ............................................................................................................... 13
3.6. Correlation study ................................................................................................................. 14
4. Results......................................................................................................................................... 16
4.1. De-novo assembly of short Illumina reads .......................................................................... 16
4.2. Filtering of multiple genome alignment .............................................................................. 16
4.3. Genetic diversity and test of neutrality................................................................................ 17
4.4. Negative correlation between nucleotide diversity of promoters and level of gene expression....................................................................................................................................... 22
5. Discussion ................................................................................................................................... 25
6. Conclusion and future prospects ................................................................................................. 28
7. Bibliography ............................................................................................................................... 29
8. Acknowledgement ...................................................................................................................... 35
9. Supplementary Data .................................................................................................................... 36

Rev. Type: -

Identifiers: Other: Dipl/12917

Degree: Master

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