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      Genome sequencing and analysis of plant growth-promoting attributes from Leclercia adecarboxylata

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          Abstract

          Plant growth-promoting bacteria are ecological alternatives for fertilization, mainly for gramineous. Since plant x bacteria interaction is genotype and strain dependent, searching for new strains may contribute to the development of new biofertilizers. We aim to characterize plant growth-promoting capacity of Leclercia adecarboxylata strain Palotina, formerly isolated by our group in corn. A single isolated colony was taken and its genome was sequenced using Illumina technology. The whole genome was compared to other Leclercia adecarboxylata strains, and their biological and growth-promoting traits, such as P solubilization and auxin production, were tested. Following that, a 4.8 Mb genome of L. adecarboxylata strain Palotina was assembled and the functional annotation was carried out. This paper is the first to report the genes associated with plant growth promotion demonstrating in vitro indole acid production by this strain. These results project the endophyte as a potential biofertilizer for further commercial exploitation.

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          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

            The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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              The neighbor-joining method: a new method for reconstructing phylogenetic trees.

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              A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
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                Author and article information

                Journal
                Genet Mol Biol
                Genet Mol Biol
                gmb
                Genetics and Molecular Biology
                Sociedade Brasileira de Genética
                1415-4757
                1678-4685
                27 January 2021
                2021
                : 44
                : 1
                : e20200130
                Affiliations
                [1 ]Universidade Federal do Paraná, Labiogen-Laboratório de Bioquímica e Genética, Palotina, PR, Brazil.
                [2 ]Universidade Federal do Paraná, Departamento de Biociências, Palotina, PR, Brazil.
                [3 ]Universidade Federal do Paraná, Departamento de Bioquímica, Centro Politécnico, Jardim das Américas, Curitiba, PR, Brazil.
                Author notes
                [Send correspondence to ] Eliane Cristina Gruszka Vendruscolo. Universidade Federal do Paraná, Labiogen-Laboratório de Bioquímica e Genética, Rua Pioneiro, 2153, CEP: 85950-000, Palotina, PR, Brazil. E-mail: egvendru@ 123456gmail.com

                Associate Editor: Célia Maria de Almeida Soares

                Conflict of Interest: The authors declare that there is no conflict of interest.

                Author Contributions: ECGV conceived the project and wrote the manuscript. AS and AF conducted the laboratory experiments. DM performed the genomics data analysis. MFS did the corrections.

                Author information
                http://orcid.org/0000-0002-3287-0006
                Article
                00403
                10.1590/1678-4685-GMB-2020-0130
                7839631
                33503198
                ba49f1ba-d1e1-4506-b462-3b1d27255a53

                This is an open-access article distributed under the terms of the Creative Commons Attribution License

                History
                : 24 April 2020
                : 11 December 2020
                Page count
                Figures: 3, Tables: 4, Equations: 0, References: 58
                Categories
                Genetics of Microorganisms

                Molecular biology
                endophyte,leclercia,genome,plant growth promotion,strains
                Molecular biology
                endophyte, leclercia, genome, plant growth promotion, strains

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