Using de novo sequencing to obtain the genomic information of microbes provides a fresh start for exploring the genetic structure and functions, studying the evolutionary origin of microbial populations, as well as developing potential applications of these abundant microbes in medicine, disease, agriculture, and environment. Novogene is at the forefront of de novo sequencing as it becomes more rapid and affordable. Novogene’s founder, Dr. Ruiqiang Li, is a leading genomics expert and a primary developer of the SOAPdenovo software package for genome assembly. Dr. Li and the Novogene team have contributed to many important publications on novel genome sequences, and we can provide you with the high level of expertise required for your specific project. For the microbial genome, Novogene offers de novo sequencing service using both PacBio and Illumina platforms. We provide multifaceted sequencing services including genome survey, frame map, complete map, and fine map tailored to different research needs. For each project, our scientists will design the best sequencing strategy utilizing an optimal combination of short reads and long-range sequencing information to achieve the most comprehensive de novo assembly results for your genome of interest.
The Novogene Advantage
- Highly experienced: We have completed over 2,000 microbial sequencing projects with 20 publications on top tier journals.
- Largest sequencing capacity: We have the largest Illumina and PacBio sequencing capacities in the world, allowing us to provide high quality data, fast turnaround, and affordable prices.
- DNA amount for survey: ≥ 1 µg
- DNA amount for genome de novo sequencing per library: ≥ 1 µg (for Illumina sequencing) and > 10 µg (for PacBio sequencing)
- DNA concentration: ≥ 50 ng/µL (for Illumina sequencing) and > 80 ng/µL (for PacBio sequencing)
- Purity: No degradation, no DNA contamination
Sequencing Strategy & Data Quality Guarantee
|Genome Characteristics||Sequencing Platform||Sequencing Strategy||Delivered Data Parameters||Application||Turnaround Time (TAT)|
|Bacterial frame map||HiSeq PE150||350 bp library ≥ 100X||-||Large scale samples, fast scanning||25 working days|
|Bacteria fine genome map||HiSeq PE150||350 bp library ≥ 100X 2 Kbp library ≥ 100X||≤30 scaffolds||Middle scale samples, somewhat fine mapping||35 working days|
|Bacteria complete genome map||PacBio||≥ 50X PacBio reads||1 Scaffold, 0 gap||Small number of samples, fine mapping||45 working days|
|Fungi survey||HiSeq PE150||350 bp library ≥ 100X||-||Estimate genome size and evaluate assembly difficulties||25 working days|
|Fungi frame genome map||HiSeq PE150||350 bp library ≥ 100X||-||Large amount of samples, frame mapping||35 working days|
|Fungi fine genome map||PacBio & HiSeq PE150||≥ 100X Illumina reads + ≥ 70X PacBio reads||Contig N50 ≥ 1Mb (genome size < 100 Mb) Contig N50 > 500Kb (genome size ≥ 500 Kb)||Small number of samples, fine mapping||55 working days|
The following study utilized Novogene's de novo sequencing services. Comparative genomics identifies the Magnaporthe oryzae avirulence effector AvrPi9 that triggers Pi9-mediated blast resistance in rice New Phytologist, 206: 1463-1475 (2015) Rice blast, caused by the fungus Magnaporthe oryzae, is a significant threat to stable rice production worldwide, and yet the virulence mechanisms of this fungus remain poorly defined. In this study, a virulent strain and an avirulent strain of Magnaporthe oryzae were sequenced using Novogene’s HiSeq platform, and the genomes were assembled de novo with our SOAPdenovo program. Comparative genomics revealed an insertion within the coding sequence of the avirulent effector AvrPi9 in the virulent strain, a disruption that turns off the rice Pi9-mediated blast-resistance mechanism. This study highlights the effectiveness of applying comparative genomics with de novo microbial sequencing data for elucidating key mechanisms in the pathogenesis of fungi. Figure. Genomic structure of the AvrPi9 locus in Magnaporthe oryzae