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Comparative analysis of 454 pyrosequencing data from coffee transcriptomes

Year: 2011
Type: dissertation
Abstract: Understanding the mechanisms beyond the resistance of coffee plants (Coffea spp.) to leaf rust (caused by Hemileia vastatrix) is of vital importance for breeding coffee varieties with durable resistance. However, loss of resistance due to the appearance of new rust races is occurring, but some genotypes are still resistant to all known H. vastatrix races, such as HDT832/2. Previous studies show that the resistance to H. vastatrix in this genotype shares common immunity components with the nonhost resistance. 454 pyrosequencing transcriptomic data representing HDT832/2 host and nonhost resistance, along a healthy plant control, were analyzed with the purpose of better understanding this resistance. Expressed sequence tags (ESTs) are a very common and interesting solution for transcriptomic studies because they lack the non-expressed part of the genome. The small amount of reads generated for this project present a limitation that has not an established solution. To analyze this dataset, two different assembly strategies (individual assembly versus global assembly) and two different assemblers (Newbler versus MIRA) were used, and the results of all four assemblies are reported and analyzed. Assemblies were compared by assessing the number of transcripts shared by the three libraries, by a blast searches against NCBI nr protein and Coffea spp. EST databases and searching for previously studied genes. Overall the global assembly strategy performed better than the individual strategy, and Newbler performed better than MIRA in most but not all parameters. Here we provide a good strategy for small budget transcriptome projects to optimize their data and we present an annotated transcriptome of coffee line HDT832/2 resistance response to rust in host and nonhost interactions.
Language: English
Open Access status: green
OpenAlex ID: W2284064489
Cites: 35
Cited by: 2
Related to: 10