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Method for constructing rosaceae original chromosome

A chromosome and Rosaceae technology, applied in the field of bioinformatics to avoid interference and expand homologous regions

Active Publication Date: 2013-10-09
BEIJING FORESTRY UNIVERSITY +1
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  • Abstract
  • Description
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Problems solved by technology

The traditional method of constructing the original chromosome is based on molecular markers such as SSR and RAPD, and obtains a small number of homologous segments to construct a low-density Rosaceae original chromosome; another disadvantage of the traditional method of constructing the original chromosome is that it is only based on the results of Blast comparison. Set corresponding thresholds, identify homologous genes between species, and apply one-to-many homologous genes within a species and between species and reference species, which is likely to cause cross-interference in homologous regions, and is limited to traditional software such as Mcsan to obtain homologous genes. Collinear regions with small source regions

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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

[0030] 1. Collection of genome data of apple, strawberry and plum blossom. from http: / / www.rosaceae.org / projects / apple_genome Obtain the apple gene CDS sequence and gene location information on the chromosome; download the strawberry gene CDS sequence and gene location information on the chromosome from http: / / www.strawberrygenome.org / ; positioning information. 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 comparison result of the comparison species (query) gene and the reference species (subject) gene blastn and the length of the comparison gene. Compare the CIP of gene A and reference gene B=∑(N AB / L AB )×100, where N AB is the length of each alignment between gene A and gene B, L AB is the length of gene A and gene B participating in the alignment; CALP of ge...

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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 the original chromosome of Rosaceae and its application. Background technique [0002] Paleogenomics is the creation of original genomes based on the genes of existing species, and is the study of the original genome structure. Reconstruction of mammalian primitive genes by modest reshuffling of chromosomal segments in silico synteny studies. 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, This makes comparative genomic studies in monocots and dicots quite difficult. In the past few decades, comparative genomics research has made great progress in monocots, especially grasses. Jerome salse predicted the 5 original chromosomes of Poaceae by using the genetic information of whe...

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Application Information

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Patent Type & Authority Patents(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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