Pan-genome Sequencing and Comparative Genomic Analysis of Atrazine-degrading Bacteria

doi:10.13560/j.cnki.biotech.bull.1985.2019-0360

Abstract

Abstract: Arthrobacter aurescens TC1 and Pseudomonas sp. ADP are currently the model strains of atrazine-degrading bacteria. Microbacterium sp. HBT4 was screened in this experiment for discovering the similarities and differences of biological information among the 3 bacterial genomes and predicting important genes. In this study,pan-genome sequencing was carried out by using small DNA library preparation and sequencing technology on Illumina Hiseq 4000 sequencing platform. Genome composition analysis,gene function annotation,gene mutation detection and comparative genomics analysis were carried out by using related software. The nucleotide composition,collinearity and variation differences between the isolated Microbacterium HBT4 and model strains were analyzed. The genome size of the strain was about 3.53 Mb. It was predicted that there were 3 397 coding genes,1.33% repetitive sequences and 63 non-coding RNA in the strain HBT4. There were 3 324 annotations of gene function in general database and 1 149 annotations of gene function in special database. SNP,Small InDel and horizontal transfer genes were found through analyzing variance among strains and no structural variation genes were found. The number and proportion of GO-annotated genes in the specific genes of the strain in cell components,molecular functions and biological processes were obtained. From KEGG metabolic pathway enrichment map,it was found that the dihydrothiosyllysine residue succinyltransferase encoded by the specific gene was located between the metabolic pathway of α-ketoglutaric acid and succinyl coenzyme A in the tricarboxylic acid cycle. The proportional distribution,phylogenetic tree and collinearity of the core genome and non-essential genome of the three strains were obtained. It was found that there were 986 common gene families among the three strains,and 1171 specific gene families strain HBT4. Compared with the two model strains,the strain HBT4 obtained in this study had both similarities and differences in gene family.

Key words: atrazine, Microbacterium sp. HBT4, pan-genome, comparative genome analysis, bioinformatics

WANG Ya-li, ZHU Shan-shan, YANG Feng-shan, MA Yu-kun, FU Hai-yan, LIU Chun-guang. Pan-genome Sequencing and Comparative Genomic Analysis of Atrazine-degrading Bacteria[J]. Biotechnology Bulletin, 2019, 35(7): 90-99.

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