Microbial whole genome sequencing yields data that enables a comprehensive evaluation of all genetic features of an isolated microorganism. Shotgun sequencing strategy is a primary method of microbial whole genome sequencing. The sequencing steps do not need labor-intensive mapping and cloning, which saves tremendous time and money. Furthermore, high-throughput sequencing allows us to sequence hundreds of bacteria or viruses at the same time with the power of multiplexing. In whole genome shotgun sequencing, the whole genome is broken up into small fragments for sequencing, and then assembled together by computational method based on the overlapped regions, hence not requiring a reference genome. PacBio SMRT technology enables us to provide bacterial de novo whole genome sequencing and fungal de novo whole genome sequencing that generate more accurate and contiguous sequences.
Microbial whole genome sequencing is crucial for precise microbial identification, the generation of complete reference genomes (de novo sequencing), comparative genomic studies (re-sequencing), and genomic exploitation. Comparative genomic studies can identify individual genetic variations and large-scale structural variations within a population for which a reference genome is available. Evolutionary characteristics and phylogenetic relationships can be hence inferred. Microbial whole genome sequencing provides the possibility of gene finding and annotation. After multiple genes are explained, novel biochemical pathways that may be beneficial for medicine and biotechnology will likely be identified.
There are three ways to ensure the accuracy of genome assembly: (i) prior to assembly, correct sequences in the consensus sequence; (ii) correct the results of sequence assembly utilizing sequencing data; (iii) correct the results of sequence assembly utilizing high quality next generation sequencing data. After the three corrections, the accuracy of final sequence assembly can reach 99.99%.