Fu, Shuhua (2015-05). Genomic and Transcriptomic Studies on Non-Model Organisms. Doctoral Dissertation. Thesis uri icon

abstract

  • As the advance in high-throughput sequencing enables the generation of large volumes of genomic information, it provides researchers the opportunity to study non-model organisms even in the absence of a fully sequenced genome. The hugely advantageous progress calls for powerful sequencing assembly algorithms as these technologies also raise challenging assembly problems: (1) Some RNA products are highly expressed but others may have much lower expression level. (2) Data cannot easily be represented as linear structure, due to post-transcriptional modification like alternative splicing. (3) Conserved sequences in domains in gene families can result in assembly errors, (4) Sequencing errors due to technique limitations. Useful assembly algorithms are required to overcome the difficulties above. In these studies, there is often a need to identify similar transcripts in non-model organisms to transcripts found in related organisms. The traditional approach to address this problem is to perform de novo transcriptome assemblies to obtain predicted transcripts for these organisms and then employ similarity comparison algorithms to identify them. I observe it is possible to obtain a more complete set of similar transcripts from transcriptome assembly by making use of evolutionary information. I apply new algorithms to study non-model organisms which play an important role in applied biology. Moreover, improvement of sequencing technologies and application of current algorithms also help to study interkingdom signals between blow flies and bacteria community. With current computational tools, I annotate genomes of Proteus mirabilis and Providencia stuartii, which play an important role in bacteria-insect interaction. The study shows significant features of these strains isolated, which provides useful information to develop and test hypothesis in related interactions in insects and bacteria.
  • As the advance in high-throughput sequencing enables the generation of large volumes of genomic information, it provides researchers the opportunity to study non-model organisms even in the absence of a fully sequenced genome. The hugely advantageous progress calls for powerful sequencing assembly algorithms as these technologies also raise challenging assembly problems: (1) Some RNA products are highly expressed but others may have much lower expression level. (2) Data cannot easily be represented as linear structure, due to post-transcriptional modification like alternative splicing. (3) Conserved sequences in domains in gene families can result in assembly errors, (4) Sequencing errors due to technique limitations. Useful assembly algorithms are required to overcome the difficulties above. In these studies, there is often a need to identify similar transcripts in non-model organisms to transcripts found in related organisms. The traditional approach to address this problem is to perform de novo transcriptome assemblies to obtain predicted transcripts for these organisms and then employ similarity comparison algorithms to identify them. I observe it is possible to obtain a more complete set of similar transcripts from transcriptome assembly by making use of evolutionary information. I apply new algorithms to study non-model organisms which play an important role in applied biology.

    Moreover, improvement of sequencing technologies and application of current algorithms also help to study interkingdom signals between blow flies and bacteria community. With current computational tools, I annotate genomes of Proteus mirabilis and Providencia stuartii, which play an important role in bacteria-insect interaction. The study shows significant features of these strains isolated, which provides useful information to develop and test hypothesis in related interactions in insects and bacteria.

publication date

  • May 2015