ABSTRACT Previously, we assembled a model bacterial community of maize roots. Here, we report the complete genome sequences of the seven strains composing the community

Kolter, Roberto

Niu, Ben

Harvard University - DASH 

Complete Genome Sequences ofSeven Strains Composing a ModelBacterial Community of Maize RootsThe Harvard community has made thisarticle openly available.  Please share  howthis access benefits you. Your story mattersCitation Niu, Ben, and Roberto Kolter. 2017. “Complete Genome Sequencesof Seven Strains Composing a Model Bacterial Community of MaizeRoots.” Genome Announcements 5 (36): e00997-17. doi:10.1128/genomeA.00997-17. http://dx.doi.org/10.1128/genomeA.00997-17.Published Version doi:10.1128/genomeA.00997-17Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:34491839Terms of Use This article was downloaded from Harvard University’s DASHrepository, and is made available under the terms and conditionsapplicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAAComplete Genome Sequences of SevenStrains Composing a Model BacterialCommunity of Maize RootsBen Niu,* Roberto KolterDepartment of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USAABSTRACT Previously, we assembled a model bacterial community of maize roots.Here, we report the complete genome sequences of the seven strains composingthe community.As two key components of the biosphere on our planet, plants and microbessometimes evolve with each other. Plants serve as a “home” for microbes, one inwhich they live and interact with other organisms. In return, microbes can affect thegrowth and health of their plant hosts (1). In a previous study, aided by host selection,we built a model bacterial community for maize root comprising strains belonging toseven species (Stenotrophomonas maltophilia AA1, Ochrobactrum pituitosum AA2, Cur-tobacterium pusillum AA3, Enterobacter cloacae AA4, Chryseobacterium indologenes AA5,Herbaspirillum frisingense AA6, and Pseudomonas putida AA7) (2). This model commu-nity is able to colonize maize roots and exhibits a clear protective effect on hosts bysuppressing the growth of phytopathogens. Here, we announce the complete genomesequences of the seven strains composing this model bacterial community of maizeroots.The genome sequences of the seven strains were determined by the PacBiosingle-molecule real-time (SMRT) sequencing technology at the University of DelawareDNA Sequencing and Genotyping Center. The genomic DNA of each strain wasextracted from pure cultures grown overnight in tryptic soy broth (BD) using thecetyltrimethylammonium bromide-based extraction protocol (3), including proteinaseK and RNase treatments. The SMRTbell template preparation kit (Paciﬁc Biosciences,Menlo Park, CA, USA) was used according to the PacBio standard protocol (20-kbtemplate preparation using the BluePippin size-selection system). After DNA sizeselection, the SMRT cells were run on a PacBio RS II instrument (Paciﬁc Biosciences)using a P4-C2 chemistry combination. Adaptor trimming, quality ﬁltering, and assemblywere performed using the hierarchical genome assembly process pipeline (4). Theassembly resulted in 49,930 to 87,018 reads with mean lengths of 10,932 bp to12,808 bp and N50 read lengths of 14,762 bp to 17,399 bp for the seven strains.The genome sequences for ﬁve of the strains— Stenotrophomonas maltophilia AA1,Enterobacter cloacae AA4, Chryseobacterium indologenes AA5, Herbaspirillum frisingenseAA6, and Pseudomonas putida AA7—contain one contig, while those of Ochrobac-trum pituitosum AA2 and Curtobacterium pusillum AA3 are composed of four and twocontigs, respectively. Three of the four contigs of AA2 are chromosomes, while theremaining one is a putative plasmid. The two contigs of AA3 are one chromosome andone putative plasmid, respectively. The genome size of the seven strains ranges from4,541,048 bp (AA3) to 6,137,024 bp (AA7). The chromosome of AA3 possesses thehighest GC content, 70.87%, while the lowest GC content is for the genome of AA5,35.88%. The number of coding sequences ranges from 4,138 (AA1) to 5,490 (AA2). Allthe genome sequences have been annotated by the Rapid Annotation using Subsys-tem Technology (RAST) server version 2.0 (5–7). These genome sequences provide usReceived 9 August 2017 Accepted 10 August2017 Published 7 September 2017Citation Niu B, Kolter R. 2017. Completegenome sequences of seven strainscomposing a model bacterial community ofmaize roots. Genome Announc 5:e00997-17.https://doi.org/10.1128/genomeA.00997-17.Copyright © 2017 Niu and Kolter. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Ben Niu,niuben2004@126.com.* Present address: Ben Niu, College of LifeScience, Northeast Forestry University, Harbin,Heilongjiang, China.PROKARYOTEScrossmVolume 5 Issue 36 e00997-17 genomea.asm.org 1with an overview of the functional genes related to the plant-associated activity of themodel bacterial community and should serve as a useful guide and resource for futurestudies of bacterial interspecies interactions and bacterial community-plant interaction.Accession number(s). This genome sequencing project has been deposited atGenBank under the accession no. CP018756, CP018779 to CP018786, CP018845, andCP018846.ACKNOWLEDGMENTSWe thank Olga Shevchenko at the University of Delaware Sequencing and Geno-typing Center for performing the PacBio sequencing and assembling the sequences.B.N. was supported, in part, by a China Green Health Agriculture PostdoctoralFellowship. R.K. was supported by NIH grant GM58218.REFERENCES1. Berendsen RL, Pieterse CM, Bakker PA. 2012. The rhizosphere microbiomeand plant health. Trends Plant Sci 17:478–486. https://doi.org/10.1016/j.tplants.2012.04.001.2. Niu B, Paulson JN, Zheng X, Kolter R. 2017. Simpliﬁed and representativebacterial community of maize roots. Proc Natl Acad Sci U S A 114:E2450–E2459. https://doi.org/10.1073/pnas.1616148114.3. Wilson K. 1987. Preparation of genomic DNA from bacteria. Curr ProtocMol Biol Chapter 2:Unit 2.4.4. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A,Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Non-hybrid, ﬁnished microbial genome assemblies from long-read SMRT se-quencing data. Nat Methods 10:563–569. https://doi.org/10.1038/nmeth.2474.5. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K,Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL,Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD,Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. TheRAST server: rapid annotations using subsystems technology. BMCGenomics 9:75. https://doi.org/10.1186/1471-2164-9-75.6. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA,Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R.2014. The SEED and the Rapid Annotation of microbial genomes usingSubsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. https://doi.org/10.1093/nar/gkt1226.7. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R,Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA, Stevens R,Vonstein V, Wattam AR, Xia F. 2015. RASTtk: a modular and extensibleimplementation of the RAST algorithm for building custom annotationpipelines and annotating batches of genomes. Sci Rep 5:8365. https://doi.org/10.1038/srep08365.Niu and KolterVolume 5 Issue 36 e00997-17 genomea.asm.org 2

Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community of Maize Roots

https://dash.harvard.edu/bitstream/1/34491839/1/5589546.pdf

Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community of Maize Roots

Abstract

Similar works

Full text

Available Versions

Harvard University - DASH