Long Read Sequencing for New Reference Genomes Construction

Individual members of a species do not always share exactly the same genes. Therefore, our reliance on only one reference genome for relevant research is highly flawed. Long-read sequencing is a highly accurate and scalable technology with impressive throughput, forcing the scientific community to fundamentally rethink what is achievable and move away from outdated practices. CD Genomics is a leading global life sciences company, and we are continually expanding our solutions and improving our available resources to help scientists accelerate their basic research. Based on our advanced PacBio SMRT sequencing and ONT Nanopore sequencing, and years of sequencing experience, we are committed to delivering the best solutions to build new reference genomes to meet the project needs of our customers worldwide.

Introduction to Pan Genomics

During the evolution of species, each species has produced an extremely rich genetic variation, and the genome of a single individual does not cover all the genetic information of this species. A single individual genome does not cover all the genetic information of the species, or in the study of different subspecies or variants of the same species, the analysis of a single genome as a template cannot comprehensively reflect all the genetic information of the species at the gene level. Therefore, using a single reference genome of a species for research is an outdated concept. For example, representative germplasm resources of species are highly different from each other, the reference genome is not sufficiently representative of all the genetic information of the species, and low-depth resequencing yields limited differential information. There are usually two ideas for genome assembly, one is reference-based assembly and the other is de novo assembly. Reference-based assembly is suitable for resequencing, while de novo assembly is suitable for de novo species. Compared with reference-based assembly, de novo assembly reduces errors in the reference genome and biases in chromosome rearrangements, facilitates the discovery of genetic diversity in species, and promotes the development of Pan genomics.

What is Pan Genomics?

Pan genomics refers to all genes in the same species, including genes that are present in all individuals also called Core genome, as well as Dispensable genome that is specific to an individual.

Fig. 1. De novo assembly and polishing pipelines for benchmarking. (Zhang et al., 2022)

Solutions Offering at CD Genomics

CD Genomics provides professional Pan-Genome Analysis service to analyze the basic situation of core and non-core genes, to obtain more comprehensive and complete information on variant sites, to study the differences within species from the perspective of unique gene sequences, and to help you understand the molecular evolutionary mechanism of species formation and its relationship with natural selection. Here at CD Genomics, we use long-read sequencing to rapidly generate high-quality new reference genomes, even for the largest crop (maize) genomes and human genomes.

In addition, we can use long-read sequencing to assemble initial reference genomes for many non-model organisms. For example, Rickettsia rickettsii, Bacillus maculatus, Amphiprion cellaris spotted, Jurtina Maniola, Varanus komodoensis, Pavo cristatus, Panthera leo, and Eumeta heterochromatica, etc. We can also use long-read sequencing to construct RNA viral genomes while eliminating the need for traditional reverse transcription steps, including Mayaro virus, Venezuelan equine encephalitis virus, chikungunya virus, Zika virus, herpetic stomatitis Indiana virus, oropouche virus, influenza A, and human coronavirus.

Our strength lies in our ability to make genome assembly of genomes of all sizes less time-consuming and less costly. Our interdisciplinary team of experienced molecular biologists, cutting-edge genomics experts, and savvy bioinformaticians coordinate every phase of the project. This holistic approach encompasses everything from meticulous sample preparation and sequencing to nuanced data interpretation and analysis.

Significance of New Reference Genomes

The construction of new reference genomes is not just about filling knowledge gaps. It helps:

• Disease research: newly discovered genetic variants can shed light on disease pathways and potential therapeutic targets.
• Biodiversity and conservation: Understanding the genomes of lesser-known organisms contributes to conservation efforts and evolutionary adaptation research.

With its unparalleled expertise and cutting-edge technology, CD Genomics is a trusted partner in the genomics community, continually pushing the boundaries of what is possible in genome assembly and analysis. Our goal is to construct new reference genomes for more species. If you have any questions, please feel free to contact us. We look forward to working with you on projects of interest.

Related Services

PacBio SMRT Sequencing
Oxford Nanopore Sequencing
Pan-Genome Analysis