Plant Pan-genome Sequencing

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Genome sequences are the basis for studies of chromosome structure, the distribution of repetitive and coding sequences, and gene identification and annotation. Genomic information from different species permits comparative phylogenetic analyses to study the relationships between species, their origins, and evolutionary features. Plant genome dynamics and processes, such as amplification of transposable elements, gene tandem duplication, genomic rearrangements, and mutations, can lead to everything from single nucleotide polymorphisms (SNPs), and gene presence/absence variants (PAVs) to structural variants (SVs) providing the raw material for natural selection, phenotypic diversity and adaptation. The high level of genomic variation observed has led to the realization that a single reference genome does not represent diversity within a species and has led to the expansion of the concept of pan-genome. A pan-genome represents the genomic diversity of a species, including the core genes found in all individuals, as well as variable genes that are absent in some individuals.

Fig. 1. Schematic diagram showing the concept, construction methods, and research focus of pan-genomics. (Li et al., 2022)

Our plant pan-genome sequencing service

Based on a long-read sequencing technology platform, CD Genomics provides specialized plant pan-genome sequencing services to more accurately represent the genetic variation present in a species. By combining genomic data from multiple germplasm, our pangenomes can detect and annotate complex DNA polymorphisms, such as structural variation (SV). Currently, we have sequenced the pan-genomes of nearly dozens of species, including rice, soybean, maize, wheat, cucumber, chickpea, and tomato, to help our clients with crop breeding, adaptation, and evolution.

CD Genomics offers the following methods for constructing pan-genomes, enabling you to build comprehensive pan-genomes for your plant species of interest. We aim to integrate multiple genomes from a subset of germplasm and give biologists easy access to the integrated genetic information. Based on project needs, we will choose the most cost-effective solution for you.

	De Novo Assembly	Iterative Assembly	Graph-Based Assembly
Features	The most straightforward approach to constructing a pangenome is to assemble the genomes of multiple samples from scratch, followed by comparative analyses to detect all variant types and characterize identified genes as core or dispensable.	Starting with the construction of a single reference genome, reads from other samples are then sequentially mapped to the reference genome. Unmapped reads are assembled and added to the reference genome to construct a pan-genome of non-redundant sequences.	Graph-based assembly strategies for pan-genome construction use graphs to represent diversity and variation relative to a reference genome.
Advantages	Handles repetitive regions well	The cost of this method is lower than the de novo assembly method because each sample can be sequenced at a lower sequencing depth, allowing hundreds of samples to be combined.	Graph-based pan-genomes show significant improvements in mitigating reference bias compared to traditional linear genomes.
Disadvantages	Requires high depth sequencing reads to construct highly contiguous and accurate genome assemblies, which is costly for large plant genomes and hundreds of reference genomes for a single species).	Because there is no assembly process, iterative assembly methods have difficulty with genomes containing large numbers of repetitive regions and are unable to detect large SVs that are not spanned by a single short read segment.	Currently, the construction and application of graph-based pan-genomes are limited by the complexity of plant genomes, such as high repeat content and polyploidy, as well as the lack of common downstream analysis and graph visualization tools.

Advantages of plant pan-genome sequencing

Eliminates deviations from a single reference genome wherever possible and can present a near-complete view of diversity within a species.
Allows integration of multiple types of DNA variants into a single reference.
Helps to understand coding and non-coding variants.
With pan-genomics, researchers can use methods such as QTL analysis and GWAS to identify genetic variation associated with different traits, even large-scale structural variation.
Provides increasing information on genetic variation and new genes.

Our services can be applied to the following research areas

For genetic mapping of crop species.
For domestication and evolutionary studies.
For genome evolution studies.
For genotype database construction.
for crop molecular breeding.

Service workflow

Fig. 2. CD Genomics' plant pan-genome sequencing service process.

Our advantages and features

Comprehensive data analysis. From the identification of structural variants to the functional annotation of genes, our services cover genome-wide analysis.
Cutting-edge technology. We harness the power of long-read sequencing technology to identify the most elusive structural variants, ensuring the most accurate and insightful data for our clients.
Extensive experience. Our extensive experience covers a wide range of plant species, both cultivated and wild.
Personalized solutions. Whether the focus is on crop improvement, evolutionary studies, or functional genomics, we customize our services to deliver the best results.

CD Genomics, as an industry leader in agricultural genome solutions, will provide you with advanced pan-genome sequencing platforms and sequencing solutions for plants. If you are interested, please feel free to contact us.

Reference

Li, Wei, et al. Plant pan-genomics: Recent advances, new challenges, and roads ahead. Journal of Genetics and Genomics (2022).

For Research Use Only.

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