Abstract
Leifsonia sp. ku-ls is an endophytic bacterial strain colonizing in high numbers the stem and leaf of the high-yielding and widely grown indica rice cultivar RP Bio-226. Whole genome sequencing of this strain using Illumina Hiseq-2500 system resulted in generation of 10,103,994 paired-end reads of 150 nucleotides length. De novo assembly of the reads with A5MySeq resulted in 51 scaffolds. Kmer analysis with KAT estimated the genome size as 3.83 Mbp with 70% GC content. Annotation of the genome resulted in identification of 3930 protein-coding genes, 45 tRNA genes, and 3 rRNA genes. Detailed analysis of the genes predicted resulted in identification of host beneficial genes which include genes associated with hormone production, nitrogen metabolism, and stress response. There is an elaborate defense against oxidative stress present in this bacterium which also can mitigate plant oxidative stress resulting from disease/abiotic stress. Comparison of this endophytic bacterial genome with non-endophytic Leifsonia sp. showed presence of additional genes, increase in copy number of some of the genes and regulators. Many genes with eukaryotic-like domains have also been identified in this bacterium.
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Data availability
The dataset submitted to NCBI include the assembled scaffolds of endophytic Leifsonia sp. ku-ls in Fasta format. The genome sequence can be accessed under the accession number QKXI00000000 at NCBI. Users can download and use the data freely for research purpose only with acknowledgment to us, and quoting this paper as a reference to the data.
References
An SQ, Lu GT, Su HZ, Li RF, He YQ, Jiang BL, Tang DJ, Tang JL (2011) Systematic mutagenesis of all predicted gntR genes in Xanthomonas campestris pv. campestris reveals a GntR family transcriptional regulator controlling hypersensitive response and virulence. Mol Plant-Microbe Interact 24(9):1027–1039. https://doi.org/10.1094/MPMI-08-10-0180
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Asif H, Studholme DJ, Khan A, Aurongzeb M, Khan IA, Azim MK (2016) Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard. Gene Mol Boil 39:465–473. https://doi.org/10.1590/1678-4685-GMB-2015-0186
Assis RAB, Polloni LC, Patané JSL, Thakur S, Felestrino ÉB, Diaz-Caballero J, Digiampietri LA, Goulart LR, Almeida NF, Nascimento R, Dandekar AM, Zaini PA, Setubal JC, Guttman DS, Moreira LM (2017) Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. Sci Rep 7:16133. https://doi.org/10.1038/s41598-017-16325-1
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75 http://RAST.nmpdr.org
Battu L, Reddy MM, Goud BS, Ulaganathan K, Kandasamy U (2017a) Genome inside genome: NGS based identification and assembly of endophytic Sphingopyxis granuli and Pseudomonas aeruginosa genomes from rice genomic reads. Genomics 109:141–146. https://doi.org/10.1016/j.ygeno.2017.02.002
Battu L, Reddy MM, Goud BS, Ulaganathan K, Ulaganathan K (2017b) Assembly of genomic reads of elite indica rice cultivar onto 2101 reference bacterial genomes for identification of co-sequenced endophytic bacteria. Data Brief 12:305–312. https://doi.org/10.1016/j.dib.2017.03.036
Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin biotechnol 27:30–37. https://doi.org/10.1016/j.copbio.2013.09.012
Brinkman AB, Ettema TJ, De Vos WM, Van Der Oost J (2003) The Lrp family of transcriptional regulators. Mol Microbiol 48:287–294. https://doi.org/10.1046/j.1365-2958.2003.03442.x
Bruggemann H, Cazalet C, Buchrieser C (2006) Adaptation of Legionella pneumophila to the host environment: role of protein secretion, effectors and eukaryotic-like proteins. Curr Opin Microbiol 9:86–94. https://doi.org/10.1016/j.mib.2005.12.009
Brumbley SM, Petrasovits LA, Birch RG, Taylor PW (2002) Transformation and transposon mutagenesis of Leifsonia xyli subsp. xyli, causal organism of ratoon stunting disease of sugarcane. Mol Plant Microbe Interact 15:262–268
Carvalho TLG, Balsemão-Pires E, Saraiva RM, Ferreira PCG, Hemerly AS (2014) Nitrogen signalling in plant interactions with associative and endophytic diazotrophic bacteria. J Exp Bot 65:5631–5642. https://doi.org/10.1093/jxb/eru319
Chaturvedi H, Singh V, Gupta G (2016) Potential of bacterial endophytes as plant growth promoting factors. J Plant Pathol Microbiol 7:2. https://doi.org/10.4172/2157-7471.1000376
Chaudhry V, Sharma S, Bansal K, Patil PB (2017) Glimpse into the genomes of rice endophytic bacteria: diversity and distribution of firmicutes. Front Microbial 7:2115. https://doi.org/10.3389/fmicb.2016.02115
Coil D, Jospin G, Darling AE (2015) A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589. https://doi.org/10.1093/bioinformatics/btu661
Coutinho BG, Licastro D, Mendonça-Previato L, Cámara M, Venturi V (2015) Plant-influenced gene expression in the rice endophyte Burkholderia kururiensis M130. Mol Plant-Microbe Interact 28:10–21. https://doi.org/10.1094/MPMI-07-14-0225-R
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J (2016) InterPro in 2017—beyond protein family and domain annotations. Nucleic Acids Res 45:190–199. https://doi.org/10.1093/nar/gkw1107
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31:439–441. https://doi.org/10.1093/nar/gkg006 http://rfam.wustl.edu/
Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43:895–914. https://doi.org/10.1139/m97-131
Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbial 16:463–471. https://doi.org/10.1016/j.tim.2008.07.008
Hassan HM, Troxell B (2013) Transcriptional regulation by ferric uptake regulator (Fur) in pathogenic bacteria. Front Cell Infect Microbial 3:59. https://doi.org/10.3389/fcimb.2013.00059
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P (2016) eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 44:286–293. https://doi.org/10.1093/nar/gkv1248 http://eggnog.embl.de
Jehl MA, Arnold R, Rattei T (2010) Effective—a database of predicted secreted bacterial proteins. Nucleic Acids Res 39:591–595. https://doi.org/10.1093/nar/gkq1154
Jofré E, Lagares A, Mori G (2004) Disruption of dTDP-rhamnose biosynthesis modifies lipopolysaccharide core, exopolysaccharide production, and root colonization in Azospirillum brasilense. FEMS Microbiol Lett 231:267–275. https://doi.org/10.1016/S0378-1097(04)00003-5
Koomnok C, Teaumroong N, Rerkasem B, Lumyong S (2007) Diazotroph endophytic bacteria in cultivated and wild rice in Thailand. ScienceAsia 33:429–435
Kulski JK (2016) Next-generation sequencing-an overview of the history, tools, and “Omic” applications. In: Next Generation Sequencing-Advances, Applications and Challenges Intech. https://doi.org/10.5772/61964DO-10
Kyrpides NC, Ouzounis CA (1995) The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus. Trends Biochem Sci 20:140–141. https://doi.org/10.1016/S0968-0004(00)88988-4
Larran S, Simon MR, Moreno MV, Siurana MS, Perelló A (2016) Endophytes from wheat as biocontrol agents against tan spot disease. Biol Control 92:17–23. https://doi.org/10.1016/j.biocontrol.2015.09.002
Liaqat F, Eltem R (2016) Identification and characterization of endophytic bacteria isolated from in vitro cultures of peach and pear rootstocks. 3 Biotech 6:1–8. https://doi.org/10.1007/s13205-016-0442-6
Lowe TM, Chan PP (2016) tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:54–57. https://doi.org/10.1093/nar/gkw413 http://trna.ucsc.edu/tRNAscan-SE/
Mapleson D, Garcia Accinelli G, Kettleborough G, Wright J, Clavijo BJ (2017) KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies. Bioinformatics 33:574–576. https://doi.org/10.1093/bioinformatics/btw663 https://github.com/TGAC/KAT
Martin M (2011) Cutadapt removes sequences from high-throughput sequencing reads. EMBnet 17:10–12. https://doi.org/10.14806/ej.17.1.200
Matsubara K, Ohnishi K, Kirltani K (1992) Nucleotide sequences and characterization of liv genes encoding components of the high-affinity branched-chain amino acid transport system in Salmonella typhimurium. J Biochem 112:93–101. https://doi.org/10.1093/oxfordjournals.jbchem.a123872
Miethke M, Monteferrante CG, Marahiel MA, van Dijl JM (2013) The Bacillus subtilis EfeUOB transporter is essential for high-affinity acquisition of ferrous and ferric iron Biochim. Biophys Acta Mol Cell Res 1833:2267–2278
Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A (2018) Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34:142–150. https://doi.org/10.1093/bioinformatics/bty266 http://bioinf.spbau.ru/quast
Mills L, Leaman TM, Taghavi SM, Shackel L, Dominiak BC, Taylor PWJ, Fegan M, Teakle DS (2001) Leifsonia xyli-like bacteria are endophytes of grasses in eastern Australia Aust. Plant Pathol 30:145. https://doi.org/10.1071/AP01003
Mitter B, Petric A, Shin MW, Chain PS, Hauberg-Lotte L, Reinhold-Hurek B, Nowak J, Sessitsch A (2013) Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Front Plant Sci 4:120. https://doi.org/10.3389/fpls.2013.00120
Moriya Y, Itoh M, Okuda S, Kanehisa M (2007) KAAS: KEGG automatic annotation server. Genome Inform 35:182–185. https://doi.org/10.1093/nar/gkm321 http://www.genome.jp/kegg/kaas/
Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497. https://doi.org/10.1111/j.1399-3054.1962.tb08052.x
Nishiguchi MK, Doukakis P, Egan M, Kizirian D, Phillips A, Prendini L, Rosenbaum HC, Torres E, Wyner Y, DeSalle R, Giribet G (2002) DNA isolation procedures. In: Techniques in Molecular Systematics and Evolution. Birkhäuser, Basel
Partida-Martinez LP, Heil M (2011) The microbe-free plant: fact or artifact? Front Plant Sci 2:100. https://doi.org/10.3389/fpls.2011.00100
Patankar AV, González JE (2009) Orphan LuxR regulators of quorum sensing. FEMS Microbiol Rev 33:739–756. https://doi.org/10.1111/j.1574-6976.2009.00163.x
Prasetya E (2015) Endophytic bacteria inducing antibacterial synthesis of the bark of Raru (Cotylelobium melanoxylon). Eur J Exp Biol 5:20–26
Reddy MM, Ulaganathan K (2015a) Draft genome sequence of Oryza sativa elite indica cultivar RP Bio-226. Front Plant Sci 6:896. https://doi.org/10.3389/fpls.2015.00896
Reddy MM, Ulaganathan K (2015b) RNA-Seq analysis of urea nutrition responsive transcriptome of Oryza sativa elite indica cultivar RP Bio 226. Genomics Data 6:112–113. https://doi.org/10.1016/j.gdata.2015.08.025
Reddy MM, Ulaganathan K (2016) Mitochondrial genome sequence of Oryza sativa indica cultivar RP Bio-226. Curr Sci 111:258–260
Schaefer AL, Lappala CR, Morlen RP, Pelletier DA, Lu TY, Lankford PK, Harwood CS, Greenberg EP (2013) LuxR-and LuxI-type quorum-sensing circuits are prevalent in members of the Populus deltoides microbiome. Appl Environ Microbiol 79:5745–5752. https://doi.org/10.1128/AEM.01417-13
Sessitsch A, Hardoim P, Döring J, Weilharter A, Krause A, Woyke T, Mitter B, Hauberg-Lotte L, Friedrich F, Rahalkar M, Hurek T (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36. https://doi.org/10.1094/MPMI-08-11-0204
Sheibani-Tezerji R, Rattei T, Sessitsch A, Trognitz F, Mitter B (2015) Transcriptome profiling of the endophyte PsJN indicates sensing of the plant environment and drought stress. MBio. 6:621–615. https://doi.org/10.1128/mBio.00621-15
Subramoni S, Gonzalez JF, Johnson A, Péchy-Tarr M, Rochat L, Paulsen I, Loper JE, Keel C, Venturi V (2011) Bacterial subfamily of LuxR regulators that respond to plant compounds. Appl Environ Microbiol 77:4579–4588
Sundaram RM, Vishnupriya MR, Biradar SK, Laha GS, Reddy GA, Rani NS et al (2007) Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 160:411–422
Tamosiune I, Baniulis D, Stanys V (2017) Role of endophytic bacteria in stress tolerance of agricultural plants: diversity of microorganisms and molecular mechanisms. In: Kumar V, Kumar M, Sharma S, Prasad R (eds) Probiotics in agroecosystem. Springer, Singapore
Tripathy BC, Oelmüller R (2012) Reactive oxygen species generation and signaling in plants. Plant Signal Behav 7:1621–1633. https://doi.org/10.4161/psb.22455
Truyens S, Weyens N, Cuypers A, Vangronsveld J (2015) Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ Microbiol Rep 7:40–50. https://doi.org/10.1111/1758-2229.12181
Vaishnav A, Shukla AK, Sharma A et al (2018) Endophytic bacteria in plant salt stress tolerance: current and future prospects. J Plant Growth Regul. https://doi.org/10.1007/s00344-018-9880-1
van der Ploeg R, Mäder U, Homuth G, Schaffer M, Denham EL, Monteferrante CG, Miethke M, Marahiel MA, Harwood CR, Winter T, Hecker M, Antelmann H, van Dijl JM (2011) Environmental salinity determines the specificity and need for tat-dependent secretion of the YwbN protein in Bacillus subtilis. PLoS One 6:e18140. https://doi.org/10.1371/journal.pone.0018140
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS (2005) BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 33:455–459. https://doi.org/10.1093/nar/gki593 http://wishart.biology.ualberta.ca/basys
Walitang DIC, Kim K, Kim Y, Kang YK, Kim ST (2018) The influence of host genotype and salt stress on the seed endophytic community of salt-sensitive and salt-tolerant rice cultivars. BMC Plant Biol 18:51
Wu S, Zhu Z, Fu L, Niu B, Li W (2011a) WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12:444. https://doi.org/10.1186/1471-2164-12-444 http://weizhongli-lab.org/metagenomic-analysis
Wu X, Monchy S, Taghavi S, Zhu W, Ramos J, Van der Lelie D (2011b) Comparative genomics and functional analysis of niche specific adaptation in Pseudomonas putida. FEMS Microbiol Rev 35:299–323. https://doi.org/10.1111/j.1574-6976.2010.00249.x
Zeng X, Saxild HH, Switzer RL (2000) Purification and characterization of the DeoR repressor of Bacillus subtilis. J Bacteriol 182:1916–1922. https://doi.org/10.1128/JB.182.7.1916-1922.2000
Acknowledgments
Latha Battu thanks the University Grants Commission, New Delhi, for UGC-BSR-RFSMS Senior Research Fellowship.
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This work was funded through the DST-Purse program of Osmania University.
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Battu, L., Ulaganathan, K. Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls. Funct Integr Genomics 20, 237–243 (2020). https://doi.org/10.1007/s10142-019-00713-z
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DOI: https://doi.org/10.1007/s10142-019-00713-z