Abstract
This research undertook the systematic analysis of the Klebsiella sp. D5A genome and identification of genes that contribute to plant growth-promoting (PGP) traits, especially genes related to salt tolerance and wide pH adaptability. The genome sequence of isolate D5A was obtained using an Illumina HiSeq 2000 sequencing system with average coverages of 174.7× and 200.1× using the paired-end and mate-pair sequencing, respectively. Predicted and annotated gene sequences were analyzed for similarity with the Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme database followed by assignment of each gene into the KEGG pathway charts. The results show that the Klebsiella sp. D5A genome has a total of 5,540,009 bp with 57.15% G + C content. PGP conferring genes such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, siderophore production, acetoin and 2,3-butanediol synthesis, and N2 fixation were determined. Moreover, genes putatively responsible for resistance to high salinity including glycine-betaine synthesis, trehalose synthesis and a number of osmoregulation receptors and transport systems were also observed in the D5A genome together with numerous genes that contribute to pH homeostasis. These genes reveal the genetic adaptation of D5A to versatile environmental conditions and the effectiveness of the isolate to serve as a plant growth stimulator.
Highlights
Feature Size G +C content (%) Number of CDSs Gene density Average CDS length tRNA rRNA Number of genes with assigned function Number of genes without assigned function
A total of four rRNAs comprising two 5S rRNAs, a single 16S rRNA, and a single 23S rRNA togther with 73 tRNA genes representing 37 amino acids were identified in the D5A genome
We identified genes in the D5A genome attributable to the production of indole3-acetic acid (IAA), solubilization of phosphate, synthesis of sideropheres, acetoin and 2,3-butanediol, suppression of pathogenic fungi, resistance to oxidative stress, and ability to break down toxic compounds and other abiotic stresses (Table S1)
Summary
Feature Size (bp) G +C content (%) Number of CDSs Gene density Average CDS length (bp) tRNA rRNA Number of genes with assigned function Number of genes without assigned function. The genes that contribute to the beneficial activity of PGPR and especially salt tolerance and pH adaptability remain to be studied in detail. We report the complete genome sequence of Klebsiella sp. D5A to help reveal the complex biological mechanisms of D5A as a PGPR. The genomic analysis in this study includes comparison of the PGP traits to four closely related and representative PGPR strains that have been studied previously, namely K. variicola 34218 (originally misclassified as K. pneumoniae and clustered with K. variicola by Garza-Ramos et al.)[23], K. variicola At-2219,20 and K. variicola DX12020, K. pneumoniae MGH7857818. Comparisons among the completely sequenced Klebsiella genomes will help to offer new insights into evolutionary changes in Klebsiella spp. and highlight the genes that may contribute to their plant growth-promoting properties
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