EN
Animals and Plants Whole Genome Sequencing
Plant & Animal whole-genome sequencing refers to the DNA sequencing of a species with known genome sequences, and then complete individual or group analysis. Through sequence alignment, a large amount of Variation information can be detected, including SNP, Insertion/Deletion sites, Structure Variation sites, Copy Number Variation sites, etc., thus, to obtain the genetic variation map of different individuals of the same species. Using whole genome sequencing technology can help quickly identify genetic variations related to the important traits of animals and plants, which can be used in molecular breeding to shorten breeding time.
Advantage 01
Rolling circle amplification constructs DNB sequencing library, PCR-free resequencing detects InDels more accurately. No worries about index hopping. Low duplication rate without manual intervention.
Advantage 02
DNBSEQ-T20 has ultra-high throughput, short cycles, and high cost-effectiveness.
Applications
Target Trait Gene Mining
Group Genetics Research
Variation Graph Construction
Molecular Markers Development and Marker-Assisted Selection Breeding
Species/Variety Identificaition
Census of Core Animal and Plant
Technical procedure
Technical parameters
Sample requirements
Genomic DNA, no degradation or slight degradation.
Sample requirement (single time)
≥ 1ug
Sample concentration
≥ 12.5ng/uL
Recommended data volume
Individual resequencing is recommended to be more than 30X, group resequencing is recommended to be more than 10 X.
Case Analysis
3K Rice Sequencing & Pan-genome Research
Research background
Research Strategy
The 3,010 rice samples (from 89 countries and regions around the world) represent about 95% of the core germplasm diversity of 780,000 rice species worldwide. By whole genome resequencing, with an average sequencing depth of 14X per sample, a total of 32Mb of high-quality SNPs and InDels were detected using the resequencing data. The structure and differentiation of cultivated rice populations in Asia were described in a more detailed and accurate way. The traditional 5 populations were increased to 9, namely, indica rice populations in East Asia (China), indica rice in South Asia, indica rice in Southeast Asia and modern indica rice varieties. Three japonica rice populations, namely temperate japonica rice, tropical japonica rice and subtropical japonica rice in Southeast Asia, as well as Aus and fragrant rice from India and Bangladesh. This study reveals for the first time a large number of microstructural (> 100bp) variations (SVs, including translocations, deletions, inversions, and duplicates) among cultivated rice cultivars in Asia. The SVs of 453 strains with sequencing depth > 20X were studied. The phylogenetic tree constructed by SVs is similar to that of SNPS. A large number of SVs may be the genetic basis of different degrees of hybrid sterility and hybrid decay of XI and GJ. The pan-genome of Asian cultivated rice was constructed, including 12,770 (62.1%) core gene families and 9,050 (37.9%) distributed gene families. 12,000 new full-length genes and thousands of incomplete ones were discovered. The core genes are ancient, and most of the new genes appear younger and shorter in length.
Initially, 3,024 rice samples were sequenced, 14 samples were filtered out for quality control, and 3,010 rice samples were retained for research. The 3K RG sequencing data alignment to the reference genome Nipponbare for detection of SNPs and InDels. The pan-genome was constructed by the Nipponbare genome sequence and the newly assembled genome sequence without redundancy. Perform SVs and PAVs analysis on 453 rice materials with sequencing depth > 20X and alignment depth > 15X.a. PAVs gene family b. The components of a pan-genome and a separate genomec. Simulated pan-genome and core genome based on 500 randomly selected rice genomesd. Proportion of core and distributed gene familiese. Average difference in the number of gene families between two strainsf. 5733 Main group unbalanced gene family characteristics
