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A method for batch detection of ltr-retrotransposons in plant genomes

A technology of retrotransposon and batch detection, which is applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problem that the program cannot be identified, and achieves the effect of fast speed, good effect and easy process flow.

Active Publication Date: 2016-09-28
JIANGSU ACAD OF AGRI SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the program can only look for relatively young LTR-retrotransposons
For elements with older insertion times, sequences with "GAP" (indicated by "N") in the middle of the transposon, and elements whose LTR sequence is inserted by other transposons, the program cannot identify

Method used

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  • A method for batch detection of ltr-retrotransposons in plant genomes
  • A method for batch detection of ltr-retrotransposons in plant genomes
  • A method for batch detection of ltr-retrotransposons in plant genomes

Examples

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Embodiment 1

[0042] Example 1. Establishment of a method for batch detection of plant genome LTR-retrotransposons

[0043] The flowchart of the method for batch detection of plant genome LTR-retrotransposons provided by the present invention is shown in figure 2 , including the following steps:

[0044] (1) Use the LTR_STRUC program based on the de novo search for the structural characteristics of transposons to identify relatively young LTR-retrotransposons in the genome to be tested (data set A), operate under the Windows system, and use the default parameter settings for analysis; then , using Perl script language programming (Script 1), follow the steps below to extract LTR-retrotransposon sequences (L1 data set) and LTRs sequences (B data set);

[0045] Extraction of LTR-retrotransposons and LTR sequence steps: put the script 1 under the LTRSTRUC folder, run the "perl abstract1.pl XXX1" command, where "XXX1" represents the file name of the A data set (for LTR_STRUC analysis has bee...

Embodiment 2

[0073] Example 2, using the method established in Example 1 to detect the Raymond cotton genome LTR-retrotransposon in batches

[0074] Enter the NCBI database (BioProject accession PRJNA171262) to download the genome sequence (13 chromosomes, 737.8Mb) of Gossypium raimondii L., upload it to the Windows system and the local Linux computing server, and perform LTR of the Gossypium raimondii L. genome - Detection of retrotransposons. During the detection process, the names, operating environments and addresses of commonly used programs involved are shown in Table 1. The specific operation steps of the detection method are as follows:

[0075] 1) Carry out with reference to step (1) of Example 1.

[0076] The LTR_STRUC program was used to identify LTR-retrotransposons in the Raymond cotton genome (Dataset A), operating under the Windows system with default parameter settings. Using Perl script language programming (script 1), extract 2247 LTR-retrotransposon sequence sets (L1 ...

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Abstract

The invention discloses a method for batch inspection of plant genome LTR-retrotransposon. An LTR_STRUC program based on structural characteristics and searching from the beginning, a CROSS_MATCH program based on homology searching and a CLUSTALW comparison program based on sequence similarity are comprehensively applied in the method for the batch inspection of the plant genome LTR-retrotransposon, and Perl scripting language programming and other methods are combined. Experimental results show that the method for the batch inspection of the plant genome LTR-retrotransposon is relatively systematic, the effect for detecting the direct repeat of the inserting sites of the plant genome LTR-retrotransposon is good, speed is high, and process operation is easy to achieve. According to the method, the frequently-used software for detecting the plant genome LTR-retrotransposon and the Perl scripting language programming are combined, and certain defects of the frequently-used software are made up. The method can play an important role in genome annotation and the batch inspection of the plant genome LTR-retrotransposon.

Description

technical field [0001] The invention belongs to the field of biotechnology, and relates to a method for batch detection of plant genome LTR-retrotransposons. Background technique [0002] In recent years, with the advancement of sequencing technology, especially the emergence of second-generation sequencing technology, the development of genomics is extremely rapid. Not only many model plants such as Arabidopsis and rice, but also other economic crops such as soybean, corn, cotton, etc. have also completed whole genome sequencing. By analyzing the genetic components of the genomes of these sequenced species, scientists have found almost unanimous findings: In addition to functional genes, plant genomes are mainly composed of various types of repetitive sequences, especially transposons and their derivatives. According to the different ways of transposition, transposons are divided into retroposons and DNA transposons. According to different structures, retrotransposons can...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/18G06F19/28
Inventor 杜建厂刘静徐珍珍倪万潮
Owner JIANGSU ACAD OF AGRI SCI
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