Efficient method for actinomycete genome splicing

A technology for actinomycetes and genomes, used in the analysis of two-dimensional or three-dimensional molecular structures, special data processing applications, instruments, etc.

Inactive Publication Date: 2017-05-31
SHANGHAI PASSION BIOTECHNOLOGY CO LTD
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  • Abstract
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  • Claims
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Problems solved by technology

[0009] In view of the above-mentioned deficiencies in the prior art, the present invention provides an efficient method for splicing actinomycete genomes, aiming at solving the problem of how to obtain relatively complete splicing results of actinomycete genomes

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  • Efficient method for actinomycete genome splicing

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Embodiment

[0042] The experimental material is a strain of Streptomyces (a type of actinomycetes) with a reference genome size of 7M.

[0043] (1) The third-generation sequencing platform PacBio RSⅡ was used to build and sequence actinomycetes. The size of the library insert was 10K, and the read length mode was the standard mode.

[0044] (2) The second-generation sequencing platform Illumina Miseq performed library sequencing on actinomycetes. The size of the library insert was 400 bp, and the sequencing read length mode was 251 bp.

[0045] (3) The off-machine data of the Pacbio RSⅡ platform was spliced, and the software used was HGAP.3 (SMRT Analysis2.3.0).

[0046] (4) The off-machine data of the Illumina MiSeq platform was spliced, and the software used was Newbler (version2.7).

[0047] (5) Perform MUMmer (release 3.23) analysis on the splicing results of the two platforms to obtain the connection relationship between the sequences, and connect the sequences based on the connecti...

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Abstract

The invention discloses an efficient method for actinomycete genome splicing. The method includes the steps that A, actinomycete is subjected to database building sequencing through a third-generation sequencing platform; B, the actinomycete is subjected to database building sequencing through a second-generation sequencing platform; C, stopping data of the third-generation sequencing platform is spliced; D, stopping data of the second-generation sequencing platform is spliced; E, the splicing results of the two platforms are subjected to collinearity analysis to obtain the connecting relationships between all sequences, and the sequences are connected depending on the relationships; F, the connecting result is corrected through the stopping data of the second-generation sequencing platform. According to the efficient method for actinomycete genome splicing, the advantages of third-generation sequencing and the advantages of second-generation sequencing are combined, the complete actinomycete genome splicing results are obtained, and the genomics basis is provided for revealing the physiological and biochemical characteristics and the metabolic rule of actinomycete genome splicing.

Description

technical field [0001] The invention belongs to the category of bioinformatics, relates to the field of genome splicing, and in particular relates to an efficient method for genome splicing of actinomycetes. Background technique [0002] Actinomycetes are a group of prokaryotes, which belong to Gram-positive bacteria, and are named for their radial colonies. [0003] Most of the actinomycetes are saprophytic bacteria, which are widely distributed in the soil and are generally aerobic. A few are symbiotic with certain plants, and some are parasitic bacteria that can cause disease. The parasitic bacteria are generally anaerobic bacteria. Actinomycetes have a musty smell, which can make water and food taste bad. Some actinomycetes can also make cotton wool products or paper mildew like mold. Actinomycetes mainly promote the decay of animal and plant remains in the soil. There are also pathogenic bacteria in actinomycetes, such as actinomycetes bovis, which can invade the tiss...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22G06F19/16
CPCG16B15/00G16B30/00
Inventor 肖岚叶伟星姜丽荣孙子奎
Owner SHANGHAI PASSION BIOTECHNOLOGY CO LTD
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