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Method for constructing rosaceae original chromosome

A chromosome and Rosaceae technology, applied in the field of bioinformatics, can solve problems such as the difficulty of comparative genome research

Active Publication Date: 2012-07-11
BEIJING FORESTRY UNIVERSITY +1
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  • Summary
  • Abstract
  • Description
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Problems solved by technology

Compared with mammals, paleogenomics is less studied in plants, because angiosperms have undergone multiple genome duplications, large segment duplications, diploidization, small-scale rearrangements and gene duplication events, Makes comparative genomic studies in monocots and dicots quite difficult

Method used

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  • Method for constructing rosaceae original chromosome
  • Method for constructing rosaceae original chromosome
  • Method for constructing rosaceae original chromosome

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Embodiment 1

[0027] 1. Collection of apple, strawberry and plum genome data. Obtain apple gene CDS sequence and gene location information on chromosome from http: / / www.rosaceae.org / projects / apple_genome; download strawberry gene CDS sequence, gene on chromosome from http: / / www.strawberrygenome.org / Location information: CDS sequence and gene location information on chromosomes were obtained by whole-genome sequencing of plum blossoms.

[0028] 2. Identification of homologous genes. Cumulative identity percentage (CIP: cumulative identity percentage) and cumulative alignment length percentage (CALP: cumulative alignment length percentage) of two gene alignments. It is calculated according to the alignment result of the gene blastn of the alignment species (query) and the gene of the reference species (subject) and the length of the alignment gene. Align the CIP of gene A and reference gene B=∑(N AB / L AB )×100, where N AB is the length of each alignment of gene A and gene B, L AB is t...

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Abstract

The invention provides a method for constructing a rosaceae original chromosome on the basis of bioinformatics methods and the application of the method. The method comprises the steps as follows: known gene data of apples, strawberries and plum blossom which belong to rosaceae are compared, homologous genes are identified, the relation between chromosomes of reference species is determined, and the relation between the chromosomes of sequenced species and the reference species is determined, so that the rosaceae original chromosome is constructed, and the history that the sequenced species evolve from ancestor chromosomes is determined.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a method for constructing a Rosaceae primitive chromosome and its application. Background technique [0002] Paleogenomics is the creation of primitive genomes based on the genes of existing species, and is the study of the structure of primitive genomes. In silico collinearity studies, mammalian primitive genes are reconstructed by modest reshuffling of chromosome segments. Compared with mammals, paleogenomics has been less studied in plants because angiosperms undergo multiple whole-genome duplications, large-scale duplications, diploidization, small-scale rearrangements and gene duplication events, This makes comparative genomic studies in monocotyledonous and dicotyledonous plants rather difficult. In the past few decades, comparative genomics research has made great progress in monocotyledonous plants, especially in grasses. Jerome salse predicted five primitive chromosomes ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68
Inventor 张启翔孙丽丹黄邦清陈文彬程堂仁杨炜茹王佳
Owner BEIJING FORESTRY UNIVERSITY
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