A method, device and storage medium for diploid assembly

A diploid and haplotype technology, applied in the fields of genomics, proteomics, instruments, etc., can solve the problems of limited application prospects, typing impact, and high genomic heterozygosity, and achieve the effect of overcoming difficulties in obtaining

Active Publication Date: 2022-07-22
BGI TECH SOLUTIONS
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  • Abstract
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Problems solved by technology

However, for diploid species with high heterozygosity, the genome heterozygosity of the parents will also be high, which will have a certain impact on typing
Moreover, parental samples or data are often not easy to obtain, which limits the application prospects of this technology

Method used

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  • A method, device and storage medium for diploid assembly
  • A method, device and storage medium for diploid assembly
  • A method, device and storage medium for diploid assembly

Examples

Experimental program
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Embodiment

[0085] In this case, a diploid assembly test was performed on the F1 generation high-heterozygous genome of hybrid maize. The parents of the hybrid maize were maize B73 and maize SK, respectively. The diploid genome size is about 4.5Gb. In this experiment, this example was based on PacBio HiFi data, Hi-C data, and gamete single-cell data to perform diploid assembly of this hybrid F1 individual. details as follows:

[0086] 1. Construction of the initial genome

[0087] In this example, the PacBio HiFi data of hybrid F1 individuals were obtained based on the parental genome sequence simulation. The genomic data of the parents are published public data.

[0088] The SK genome download address in this example is:

[0089] https: / / db.cngb.org / search / assembly / CNA0002536 / ;

[0090] The B73 genome download address is:

[0091] ftp: / / ftp.ensemblgenomes.org / pub / plants / release-50 / fasta / zea_mays / dna / ;

[0092] The download address of pbsim software is: https: / / github.com / pfaucon / P...

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Abstract

The present application discloses a method, device and storage medium for diploid assembly. The diploid assembly method of the present application utilizes the gamete single-cell data of the individual to be tested to assist in typing. The method of the present application can effectively realize the chromosome-level diploid assembly only by using the gamete single-cell data of the object to be processed, and does not need to use parental data, which overcomes the problem of difficulty in obtaining parental data; at the same time, the diploid assembly of the present application does not require Limited by the heterozygosity of diploid species, it solves the problem that different heterozygosity of diploid species limits the existing diploid assembly technology routes.

Description

technical field [0001] The present application relates to the technical field of genome assembly, and in particular, to a method, device and storage medium for diploid assembly. Background technique [0002] Humans and common eukaryotes are diploid organisms, containing two sets of chromosomes, inherited from the male parent and the female parent. Homologous chromosomal sequences from both parents have identical and different allelic sites, namely homozygous and heterozygous sites, respectively. [0003] Genome assembly has become an indispensable basic research method for genomics research. The existing genome assembly method is mainly haplotype assembly, that is, only the genotype of the paternal or maternal parent is randomly retained at the heterozygous site, so as to assemble a chimeric genome of a single ploidy. Haplotype assembly often ignores heterozygous allelic sequences, which not only discards the alleles of heterozygous loci, but also discards the genotype inf...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/20G16B20/20
CPCG16B30/20G16B20/20
Inventor 谢敏杨林峰陈世璇贺丽娟杨鑫邓天全
Owner BGI TECH SOLUTIONS
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