Method for identifying pedigree-specific amplified gene family

A gene amplification and specific technology, applied in the field of biological information analysis, to achieve the effect of simple operation, small amount of data and good representation

Pending Publication Date: 2022-04-08
NANJING AGRICULTURAL UNIVERSITY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Currently, methods for identifying lineage-specifically amplified gene families have not been reported

Method used

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  • Method for identifying pedigree-specific amplified gene family
  • Method for identifying pedigree-specific amplified gene family
  • Method for identifying pedigree-specific amplified gene family

Examples

Experimental program
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Embodiment 1

[0040](1) In GDR (https: / / www.rosaceae.org / ), ensemblplants (http: / / plants.ensembl.org / index.html), and phytozome (https: / / phytozome-next.jgi.doe. gov / ) to download Rosaceae plants from these three websites: Potentilla micrantha, Tibetan strawberry (Fragaria nubicola), wild strawberry (Fagaria vesca), black raspberry (Rubus occidentalis), and Chinese rose (Rosa chinese). Apple subfamily: Malus baccata, European sweet cherry (Prunus avium), plum blossom (Prunus mume), plum (Prunus salicina), Tokyo cherry blossom (Prunusyedoensis). And non-Rosaceae plants: grape (Vitis vinifera), Arabidopsis (Athaliana), soybean (Glycine max), the genome data of these 13 species, and then according to the known evolutionary information, these 13 species are ranked according to the distance of evolution Sort the relationship;

[0041] (2) Use gffreader to extract the pep and cds sequences of the above-mentioned 13 species, change all pep sequence files to the Latin scientific name of the species...

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Abstract

The invention belongs to the technical field of biological information analysis, and provides a method for identifying a pedigree specific amplification gene family. The invention relates to a method for screening and identifying pedigree specific amplification genes appearing in different subfamilies by utilizing orthologous homology analysis. The method is easy to operate, the required data volume is small, analysis software operation is easy to learn, the screened genes have good representativeness, and a foundation is laid for wide-range identification and functional analysis of pedigree specific genes in the future.

Description

technical field [0001] The invention relates to the technical field of biological information analysis, in particular to a method for identifying lineage-specific amplified gene families. Background technique [0002] Lineage-specific genes refer to a large expansion of genes in a gene family in a certain plant. These amplified genes are called lineage-specific genes. These genes generally play an important role in the functional traits of the species. Likewise, gene families that have undergone substantial expansion within a subfamily can be referred to as lineage-specifically expanded genes. The massive expansion of these genes would have played an important role in the divergence of species in this family. Therefore, the identification of such genes has important implications for understanding plant evolution and adaptation. Currently, no methods for identifying lineage-specific amplified gene families have been reported. Contents of the invention [0003] To overc...

Claims

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Application Information

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IPC IPC(8): G16B25/10G16B30/10G16B35/20G16B40/00
Inventor 王长泉孙婧睿刘金义孙晶晶陆俊
Owner NANJING AGRICULTURAL UNIVERSITY
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