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Method for comparative analysis of ancient chromosome evolution of sisoridae fishes

A technique for comparative analysis, chromosomes, applied in evolutionary biology, sequence analysis, instrumentation, etc.

Pending Publication Date: 2020-08-21
西藏自治区农牧科学院水产科学研究所
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  • Abstract
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Problems solved by technology

[0007] In order to overcome the difficulty of reconstructing the karyotype of the ancestors of the genus in Tibet and to study the large-scale recombination phenomenon on the chromosomes of the ancestors of the genus in Tibet, the present invention provides a kind of method that uses the relative species of the genus in Tibet as a reference, and infers its The method of ancestral karyotype can conduct an in-depth analysis of the karyotype of the ancestors of Tibetan fishes

Method used

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  • Method for comparative analysis of ancient chromosome evolution of sisoridae fishes
  • Method for comparative analysis of ancient chromosome evolution of sisoridae fishes

Examples

Experimental program
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Embodiment 1

[0026] Example 1: Material acquisition

[0027] In this experiment, a species of fish that is endemic to the Tibetan Plateau, the black-spotted catfish, was used as the research object. Adult female black-spotted catfish caught in the wild from the Yarlung Zangbo River. After recording the basic traits and indicators, take the fins and freeze them with liquid nitrogen for one hour, and store them in the refrigerator at -80°C.

Embodiment 2

[0028] Example 2: DNA extraction of P. black spot and third-generation long-segment genome sequencing and genome contig assembly The traditional phenol method was used to extract the genomic DNA of P. black spot. The specific method was to grind the sample into powder with liquid nitrogen. Add 1 mL of digestion solution and let stand at 37°C for 5 hours. After cooling down to room temperature, take 0.5 mL of phenol, mix and centrifuge at 4000×g for 10 min, and suck out the water phase. Add 0.5 mL of a mixture of phenol, chloroform and isoamyl alcohol for DNA extraction and extract twice again, extract the aqueous phase and add NaCl to a concentration of 0.3M. Add ethanol, centrifuge at 3000×g for 15 min, rinse twice with 70% ethanol, suck out the supernatant, and dry in the air. The powder sample was suspended in TE, NaCl was added to 100mM, RNase A was added to a concentration of 100ug / mL, and after being kept at 37°C for 3hrs, SDS was added to a final concentration of 0.2%....

Embodiment 3

[0030] Example 3: Hi-C tissue library construction, sequencing and chromosome assembly of P.

[0031]Take fresh P. black spot muscle tissue, use a cell sieve to obtain cell suspension. Use 37% formaldehyde for formaldehyde treatment. After being treated with SDS and Triton, centrifuge to remove the supernatant, resuspend the precipitate with restriction endonuclease buffer, add different amounts of restriction endonuclease HindⅢ-HF, and digest overnight at 37°C on a rotary mixer. After enzyme digestion, choose a low temperature of 23°C for end-filling labeling. Centrifuge the blunt-end product at 500g at 4°C for 2min at low temperature, remove the supernatant, resuspend the pellet with 1×T4 DNA Ligase Buffer, perform blunt-end ligation in a 250µL ligation system according to the amount of ligase of 1-2 Cohesive unit / μL, and ligate at 16°C for 4- 8h. Add NaCl with a final concentration of 200mmol / L and proteinase K at 1μg / μL to the ligation product, decompose the cross-link ...

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Abstract

The invention relates to a comparative analysis method for ancient chromosome evolution of sisoridae fishes. According to the invention, a comparative genomic technology is utilized to analyze the ancient chromosomes of the sisoridae fishes, and evolution research on the chromosomes of the sisoridae fishes is beneficial for exploring the evolution rule of the genomes of the sisoridae fishes and provides basic data for the evolution research and resource protection of the sisoridae fishes. The method provided by the invention comprises the steps of construction of the chromosome sequence of glyptosternon maculatum, phylogenetic analysis, comparison with the chromosomes of sibling species, ancient chromosome construction and the like. The method is suitable for the sisoridae fishes in Tibetan, and can be widely applied to resource investigation and protection research of the sisoridae fishes in the Qinghai-Tibet Plateau.

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] Biological evolution involves a wide range. The development and changes of biological macromolecules, genes and genomes, cells, biological individuals, biological groups, and even the entire biosphere on the earth are related to biological evolution, so biological structures at various levels have History of its origin and evolution. Discussing the origin process and evolution mode of these biological structures, and reconstructing their history are important aspects of the study of biological evolution. These studies will greatly improve human beings' understanding of life and themselves. [0003] Chromosomal variation In eukaryotic organisms, chromosomes are carriers of genetic material DNA. When the number of chromosomes changes (absence, in...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B30/20G16B10/00G16B40/00
CPCG16B30/10G16B30/20G16B10/00G16B40/00
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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