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Tuesday, July 28 • 13:40 - 13:45
Genome Assembly of Microbes By Leveraging Evolutionary Relationships

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Microbial genomics has seen rapid improvements in the past decade primarily due to the development of novel algorithms capable of assembling the data generated by a variety of next-generation sequencing technologies, into a high quality genome. Depending on the sequencing technology, type of libraries, and the complexity of the genome, this has most often resulted in the generation of draft genomes. The completion of these microbial genomes however, have remained a challenge. Recent technologies capable of producing extremely long reads allow for the determination of the complete genomes of microbes. However, the cost-effectiveness of short-read technologies has resulted in the deposition of 4,68,154 (as of Dec 2019) permanent-draft genomes (i.e., genomes unlikely to be ever completed) in the NCBI database, while the number of complete genomes is only 16,814. Out of these 4,68,154 genomes, 2,62,766 were obtained from the surveillance project, which has increased drastically since 2017 from 13 to 5,883 in 2018 and 2,56,860 in the year 2019. Unfortunately, a large number of these organisms are unavailable in any culture collection for resequencing using long-read technologies, in order to complete the genome. With some exceptions, the short-read data of these genomes available in the short-read archive (SRA) contains information corresponding to the entire genome. When a closely related genome is available, this can be used as a reference to map the short-read data to determine the genome, and often times this performs better than a de novo assembly. We propose a workflow to use information from multiple-reference genomes to obtain an improved assembly (as compared to either single-reference mapping, single-reference-guided, or de novo assembly) of microbial genomes using short-read data from the SRA. It is envisaged that with the increase in the number of complete genomes of a given Genus of microbe in the NCBI, the information contained in the genomes of related microbes can be exploited to obtain an assembly with improved contiguity, and with no loss in strain-specific information, using the original short-read data from the SRA. A proof-of-concept using simulated short-read data sets of E. coli is presented to highlight the improvements in the final assembly guided by multiple reference genomes.


Urmi Shah

Research Intern, Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh.
Working as a research intern for the first time, under the guidance of Dr. Srikrishna Subramanian has been a great opportunity to learn and expand my horizon in the field of Genomics. I have worked on the project of improving a genome assembly of microbes. Looking at the increased... Read More →

Tuesday July 28, 2020 13:40 - 13:45 MSK
Zoom Conference https://zoom.us/j/94321101353?pwd=QlJBb09uM0NVVnVyK0FkbTJ3Nkcrdz09