Optimize the experimental and computational processes to achieve low-cost assembly of the core genomes of large genomic crops such as wheat.

On June 21st, the journal Nucleic Acids Research published an online paper entitled CGT-seq: epigenome-guided de Novo assembly of the core genome for-the-group for-go-population-with-si-s- research paper by zhang Yiyi Research Group of the Institute of Molecular Plant Sciences of the Chinese Academy of Sciences in collaboration with the Tong Yiping Research Group of the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences.
work to develop and optimize the experimental and computational processes to achieve low-cost assembly of the core genomes of large genomic crops such as wheat.
Ph.D. students Qi Meifang, Li Zixuan and Liu Chunmei were the co-first authors, and the rice experimental materials and data were helped by Lin Hongxuan, a researcher at the Institute of Plant Ecology.
related work has been supported by the Class A Pilot and Natural Science Genetics Project of the Chinese Academy of Sciences. The high genetic polymorphism of
plants provides abundant genetic resources for molecular breeding, and the fundamental method for determining important agronomic traits lies in comparing the relationship between genetic polymorphism and phenotype between different groups or cultivation and wild species.
However, many economic species have experienced long-term domestication, with complex and large genomes.
for example, the current widespread cultivation of wheat is 6 x, the whole genome has 17Gb, and the widely cultivated barley, cotton, corn, peanuts and soybeans have a Gb-scale genome, even with low coverage required for heavy sequencing experiments at a very high cost.
, there are still many large-scale unsequenceed large-scale economic species, the cost of whole genome sequencing is very high, especially for the population level of research whole genome sequencing is not realistic.
how to effectively characterize the genetic diversity of large genome polymorphic groups is a challenging task.
Because many studies do not need to know all the base sequences of the genome, various low-cost alternative sequencing techniques have been developed for large genome species.
the basic principle is usually selective sequencing of whole genome sequences, but these methods generally require high information on the existing genome sequence, and for groups with large genetic variations, technologies that rely on reference genomes, including exosome sequencing, and even genome-wide resequencing, significantly underestimate polymorphism.
, the development of simplified genome sequencing methods that do not rely on the direct capture of genes and regulatory region sequences by reference genomes is of great value for the study of groups with high polymorphisms.
the theoretical basis of this method lies in the regulation of gene activity of the important epigenetic modification in the gene and promoter region (Figure A-B), through the immunocoprecipitation technology and optimization of the splicing scheme to effectively obtain the gene and nearby sequence (Figure C).
the fragments obtained from the core genome assembly of wheat Chinese spring varieties are highly consistent with the gene region (Figure D), and new genes (Figure E-F), regulatory regions (Figure G) and polymorphic sites (Figure H-J) can be efficiently excavated.
the patent editing method, the advantage of this method is not to rely on reference genome sequence, directly capture genes and regulatory region sequences, thereby greatly reducing the cost of group core genome stitching, and effectively improve the efficiency of molecular genetics and population genetics research in large genome species.
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