Method for polyploidy genome survey

A genomic and polyploid technology, applied in the field of molecular biology, can solve the problems of low evaluation accuracy of polyploid species, and achieve the effect of improving the evaluation accuracy

Pending Publication Date: 2020-07-14
武汉古奥基因科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] In order to overcome the problem of low accuracy of polyploid species assessment in current genome feature assessment methods, the present invention provides a polyploid genome survey method, which can accurately assess the genome features of polyploid species and improve the accuracy of assessment. The technical solution is as follows:

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  • Method for polyploidy genome survey

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Embodiment 1

[0047]A method for polyploid genome survey, which specifically includes the following steps:

[0048] Step 1. Genomic DNA extraction and sequencing:

[0049] (1) Cut 10mg of tissue into a 2ml centrifuge tube, cut it with surgical scissors (sterilized with alcohol), and then break it with a homogenizer;

[0050] (2) add 400ul of ACL solution and 20ul of proteinase K;

[0051] (3) Shake and mix for 1 minute, and then place it at 55°C for 3 hours. During this period, take out and mix evenly every half an hour, which is helpful for full cracking. The fully cracked sample should be clear and transparent;

[0052] (4) Take out the sample and shake it evenly when it is lowered to room temperature;

[0053] (5) Add 300ul of Ext solution and 300ul of AB solution to the treated sample in turn, shake vigorously, and then centrifuge at 12000rmp for 5min. The solution will be layered, the upper layer is the blue extraction layer, the lower layer is the transparent water phase, there may...

Embodiment 2

[0078] A method for polyploid genome survey, which specifically includes the following steps:

[0079] Step 1. Genomic DNA extraction and sequencing:

[0080] (1) Cut 7mg of tissue into a 2ml centrifuge tube, cut it with surgical scissors (sterilized with alcohol), and then break it with a homogenizer;

[0081] (2) add 400ul of ACL solution and 20ul of proteinase K;

[0082] (3) Shake and mix for 1 minute, and then place it at 55°C for 3 hours. During this period, take out and mix evenly every half an hour, which is helpful for full cracking. The fully cracked sample should be clear and transparent;

[0083] (4) Take out the sample and shake it evenly when it is lowered to room temperature;

[0084] (5) Add 300ul of Ext solution and 300ul of AB solution to the treated sample in turn, shake vigorously, and then centrifuge at 12000rmp for 5min. The solution will be layered, the upper layer is the blue extraction layer, the lower layer is the transparent water phase, there may...

Embodiment 3

[0109] A method for polyploid genome survey, which specifically includes the following steps:

[0110] Step 1. Genomic DNA extraction and sequencing:

[0111] (1) Cut 10mg of tissue into a 2ml centrifuge tube, cut it with surgical scissors (sterilized with alcohol), and then break it with a homogenizer;

[0112] (2) add 400ul of ACL solution and 20ul of proteinase K;

[0113] (3) Shake and mix for 2 minutes, and then place it at 55°C for 3 hours. During this period, take out and mix evenly every half an hour, which is helpful for full cracking. The fully cracked sample should be clear and transparent;

[0114] (4) Take out the sample and shake it evenly when it is lowered to room temperature;

[0115] (5) Add 300ul of Ext solution and 300ul of AB solution to the treated sample in turn, shake vigorously, and then centrifuge at 12000rmp for 6min. The solution will be layered, the upper layer is the blue extraction layer, the lower layer is the transparent water phase, there m...

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Abstract

The invention discloses a method for polyploidy genome survey and belongs to the technical field of molecular biology. By adopting the method, genome characteristic information of a polyploidy speciescan be accurately obtained through an updating algorithm. The method specifically comprises the following steps: performing genome DNA extraction and sequencing; performing quality control on genomesequencing data; evaluating characteristics of a polyploidy genome; and analyzing ploidy variation of the polyploidy genome. The method already takes complex relationships of genome sequences of polyploidy species into account when being designed, analysis methods aiming at sizes, heterozygosis rates and homologous rates of the genomes of the polyploidy species are specifically designed, and the problem that a conventional method is high in polyploidy genome evaluation fault rate can be effectively avoided. By adopting the method for polyploidy genome survey, survey analysis on any eukaryon polyploidy genome can be theoretically implemented, so that the method for polyploidy genome survey can be widely applied to polyploidy genome evaluation, and accurate and effective analysis methods areprovided for application to evaluation on sizes, heterozygosis rates and homologous rates of polyploidy genomes, and the like.

Description

technical field [0001] The invention belongs to the technical field of molecular biology, and in particular relates to a method for polyploid genome survey. Background technique [0002] Genome survey refers to the use of next-generation sequencing technology to effectively evaluate information such as genome size, heterozygosity, and repeat sequence ratio by counting K-mer frequencies without a reference genome to evaluate the genome characteristics of species. Assemble (assemble from scratch) for reference. The whole genome shotgun method (Whole-Genome-Shotgun, WGS) is commonly used in large-scale genome sequencing, and there are many genomes with high duplication and high heterozygosity. Such genomes will significantly increase the difficulty of genome assembly, resulting in incomplete and fragmented results, and the genome size of this species cannot be accurately estimated based on repetitive sequence information obtained only by sequencing. In addition, when the geno...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12N15/10C12Q1/6869G16B20/10G16B25/00G16B40/10G16B50/30
CPCC12N15/1003C12Q1/6869G16B40/10G16B25/00G16B20/10G16B50/30C12Q2535/122
Inventor 袁晓辉刘海平肖世俊
Owner 武汉古奥基因科技有限公司
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