Polyploid organism genome diploidization degree quantitative evaluation method

A quantitative evaluation and genomics technology, applied in genomics, bioinformatics, proteomics, etc., can solve problems such as quantitative evaluation of the degree of diploidization of polyploid genomes

Active Publication Date: 2020-08-25
西藏自治区农牧科学院水产科学研究所
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  • Application Information

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Problems solved by technology

However, there is currently no method that can quantitatively assess the degree of diploidization of polyploid genomes using polyploid genome sequences

Method used

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  • Polyploid organism genome diploidization degree quantitative evaluation method
  • Polyploid organism genome diploidization degree quantitative evaluation method
  • Polyploid organism genome diploidization degree quantitative evaluation method

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0027] Embodiment 1: material preparation

[0028] In this experiment, Schizothorax, a unique fish in the Tibetan Plateau, was used as the research object. Female Schizothorax adults caught in the wild from Yajiang, Tibet. Based on previous studies, Schizothorax is a polyploid fish with a tetraploid karyotype. After recording the basic traits and indicators, take the fins and freeze them with liquid nitrogen for one hour, and store them in a -80 degree refrigerator.

Embodiment 2

[0029] Example 2: Schizothorax DNA extraction and high-pass sequencing

[0030] Frozen Schizothorax is expected to be ground in a single weight until ground to a powder. Afterwards, add 1 mL of digestion buffer so that the buffer fully contacts the ground sample and submerges. Place the entire sample in a 1.5 mL centrifuge tube and let stand at 37 °C for 5 h. Afterwards, cool the digestion solution to room temperature, take 0.5 mL of equilibrated phenol, mix gently and centrifuge at 3000-5000×g for 10 min, and suck out the aqueous phase. Add 0.5 mL of a mixture of phenol: chloroform: isoamyl alcohol (25:24:1 by volume) and extract twice again, extract the aqueous phase and add NaCl to a concentration of 0.3M. Add 3 times the volume of ethanol to make the solvents mix with each other, centrifuge at 3000×g for 10 min, rinse twice with 70% ethanol, suck out the supernatant, and dry in the air. The obtained sample was suspended in TE, NaCl was added to 100 mM, RNase A was added...

Embodiment 3

[0032] Example 3: Estimate the heterozygosity of the genome based on the results of genome resequencing

[0033] According to the genome resequencing results, after quality control and filtering by Fastqc and HTQC software, the number of Kmers of each type was calculated according to the Kmers with a read length of 17 bp, and the distribution of different Kmers was constructed. Using the method of Kmer distribution, the genomic characteristics information such as genome size and heterozygosity of Schizothorax was obtained. In this project, the calculated Schizothorax genome size is 2.2Gb, and the heterozygosity is 0.71%.

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Abstract

The invention relates to a polyploid organism genome diploidization degree quantitative evaluation method, which comprises the following steps: 1) evaluating the heterozygosity of a genome according to the Kmer analysis result of the genome; 2) constructing a polyploid genome characteristic model according to the heterozygosity characteristics of the genome; 3) simulating polyploid genomes with different diploidization degrees on the basis of the polyploid genome characteristic model; and 4) evaluating the accuracy of polyploid diploidization rate estimation, and calculating to obtain the diploidization degree of the polyploid genome. According to the method, resequencing data is used for polyploid genome diploidization analysis for the first time, the cost is low, and the method is suitable for polyploid genome research of animals and plants.

Description

【Technical field】 [0001] The invention relates to a biological genome analysis technology, in particular to a method for quantitatively evaluating the diploid degree of a polyploid biological genome. 【Background technique】 [0002] Polyploidy is a method of genome evolution, the state of doubling of chromosomal data in animal and plant genomes. Genome polyploidy is found mainly in plants and in some animals, notably roundworm and amphibian genomes. In diploid plant and animal genomes, there are two copies (2N) of each chromosome, one from the father and one from the mother. The core of the gametes of diploid species is haploid, that is, half of the karyotype of a diploid somatic cell. Among the many types of polyploidy, according to the state of chromosome doubling, polyploidy is divided into triploid (3N), tetraploid (4N) and so on. But in nature, tetraploid polyploidy is more common. [0003] Polyploidy is the result of the doubling of chromosomes in the biological gen...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/00G16B30/00
CPCG16B20/00G16B30/00
Inventor 刘海平牟振波肖世俊
Owner 西藏自治区农牧科学院水产科学研究所
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