Method for obtaining LMW-GS gene coding regions of wheat plants in batch from batch contig
A technology of gene coding and coding region, which is applied in the field of obtaining LMW-GS gene coding region in batches, and can solve the problems such as the difficulty of LMW-GS gene coding region.
Active Publication Date: 2019-12-31
HENAN INST OF SCI & TECH
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[0006] The purpose of the present invention is to overcome the problem of the difficulty in obtaining the LMW-GS gene coding region of wheat plants in batches from the contig assembled in batches of SeqMan
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[0018] Divided into the following three steps to achieve:
[0019] 1. Batch renaming of contig sequence identifiers and organizing them into the same fasta format file
[0020] After completing the SeqMan assembly of the LMW-GS gene PCR product PacBio sequencing results, the fasta format sequence of each contig (that is, the genomic DNA sequence of the LMW-GS gene) can be derived from SeqMan, and the sequence derived by the present invention is named: "Material number-- temp. fas". In the previous work of the present invention, in order to save time when SeqMan was assembled, the assembled contig was generally named as: "contig number in this material + space + the numbering of the corresponding reference gene (the LMW-GS gene number in Chinese Spring or Xiaoyan 54 )", after exporting the fasta sequence, the sequence identifier is: ">'contig number_the number of the corresponding reference gene'" (the space in the assembly name will automatically become an underscore after ex...
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The invention discloses a method for obtaining LMW-GS gene coding regions of wheat plants in batches from batch contig. The method is characterized in that a problem that the LMW-GS gene coding regions of different wheat plants are difficult to be acquired in batches from contig assembled from batch SeqMan is solved. According to contig sequences of LMW-GS genes in different wheat materials assembled by SeqMan, batch renaming of sequence identifiers is firstly performed, and the renamed sequence identifiers are sorted into files with a same fasta format; then, according to a conservative characteristic of an N end and a C end of the genes, 90 bp sequences at the two ends of published Chinese spring and Xiao Yan 54 LMW-GS gene coding regions are adopted as reference sequences and are compared with a corresponding contig sequence (a genome DNA sequence of an LMW-GS gene) which is assembled by SeqMan and corresponds to different wheat materials, and an initial position of a correspondingcoding region is found; and finally, coding region sequences are extracted in batches from the LMW-GS gene contig assembled from the SeqMan according to the initial position. Therefore, a good foundation is laid for functional research of the gene.
Description
technical field [0001] The invention belongs to the cross technical field of molecular biology and bioinformatics, and specifically relates to a method for obtaining LMW-GS gene coding regions in batches from batches of contigs. Background technique [0002] Proteins in wheat grain include albumin, globulin, gliadin and glutenin, among which albumin and globulin account for about 15%, which are metabolic proteins; glutenin and gliadin account for about 85%, which are the main components of wheat grain Storage protein is the main component of wheat gluten. The types and characteristics of storage proteins determine the quality of wheat flour processing. Wheat prolamin mainly affects the extensibility of dough, and glutenin mainly determines the elasticity of dough, including high molecular weight glutenin subunit (HMW-GS) and low molecular weight glutenin subunit (LMW-GS), respectively accounting for the total protein content of endosperm 10% and 40% or so. From the conten...
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Login to View More IPC IPC(8): G16B30/10G16B30/20G16B50/00
CPCG16B30/10G16B30/20G16B50/00
Inventor 张胜利李东方董松果朱启迪杨靖周岩
Owner HENAN INST OF SCI & TECH