We report here the complete genome sequence of Mesorhizobium sophorae ICMP 19535T. This strain was isolated from Sophora microphylla root nodules and can nodulate and fix nitrogen with this host and also with Sophora prostrata, Sophora longicarinata, and Clianthus puniceus. The genome consists of 8.05 Mb

Andrews, M.

De Meyer, S.E.

Nguyen, D.T.

Wang, P.

English

We report here the complete genome sequence of Mesorhizobium sophorae ICMP 19535(T). This strain was isolated from Sophora microphylla root nodules and can nodulate and fix nitrogen with this host and also with Sophora prostrata, Sophora longicarinata, and Clianthus puniceus. The genome consists of 8.05 Mb

De Meyer, Sofie

Dung Tuan Nguyen, Dung Tuan Nguyen

Wang, Penghao

Andrews, Mitchell

Ghent University Academic Bibliography

Complete genome sequence of Mesorhizobium sophorae ICMP 19535(T), a highly specific, nitrogen-fixing symbiont of New Zealand endemic Sophora spp.

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Complete Genome Sequence ofMesorhizobium sophorae ICMP 19535T, aHighly Specific, Nitrogen-Fixing Symbiontof New Zealand Endemic Sophora spp.Sofie E. De Meyer,a,b Dung Tuan Nguyen,c Penghao Wang,a Mitchell AndrewscCentre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia, Australiaa; Laboratory ofMicrobiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgiumb; Faculty ofAgriculture and Life Sciences, Lincoln University, Lincoln, New ZealandcABSTRACT We report here the complete genome sequence of Mesorhizobium so-phorae ICMP 19535T. This strain was isolated from Sophora microphylla root nodulesand can nodulate and fix nitrogen with this host and also with Sophora prostrata,Sophora longicarinata, and Clianthus puniceus. The genome consists of 8.05 Mb.Most legume species (plant family Leguminosae) can fix atmospheric nitrogen viasymbiotic bacteria (“rhizobia”) in root nodules, which can give them an advan-tage under low-nitrogen soil conditions (1, 2). New Zealand is geographically isolated,and this separation has given rise to a unique native flora (3). There are four genera ofindigenous legumes on the main New Zealand islands, and all of them are in thesubfamily Papilionoideae and all nodulate. These genera are Carmichaelia, Clianthus,and Montigena in the tribe Galegeae, and Sophora is within the tribe Sophoreae (4, 5).Forty-eight rhizobial isolates from four New Zealand native Sophora spp. sampled ateight different field sites were separated into eight groups and three individual isolateson the basis of their concatenated recA, glnII, and rpoB gene sequences, while showingalmost identical unique nodA and nodC gene sequences (6). Seven of these groups havebeen formally identified as new species, one of which is Mesorhizobium sophorae ICMP19535T (7, 8). This relationship between New Zealand native Sophora spp. and Mesorhi-zobium spp. with specific nodulation gene sequences is highly specific (9).Genomic DNA was isolated using the GENTRA Pure-Gene kit (Qiagen). The genomesequence was determined using the PacBio RS II (Pacific Biosciences) platform atChunLab, Inc. (South Korea). Raw sequences were assembled with PacBio SMRT Analysisversion 2.0 software (Pacific Biosciences). Gene prediction was performed using tRNA-scan version 1.3.1 (10) for the tRNA search, Cmsearch (INFERNAL version 1.0.2) andRfam version 12.0 for the rRNA and noncoding RNA searches, and gPilerCR version1.06 (11) and CRT1.2 (12) for the clustered regularly interspaced short palindromicrepeat (CRISPR) searches. Functional annotation was performed by a homologysearch against the KEGG (13), SEED (14), Swissprot (15), and eggNOG (16) databases.In total, 8,049,106 bp of sequence information was obtained with a total of 24 contigs.The average contig size was 334,479 bp, with the largest being 1,626,386 bp and theshortest 14,820 bp. The genome features an average GC content of 62.22%, and the N50value was 666,711 bp. A total of 7,659 protein-coding sequences and 6 rRNAs and 58tRNAs were predicted.The genomic sequence comparison against other sequenced Mesorhizobium strainsindicated that around 70% of the sequences of ICMP 19535T are highly conserved.However, ICMP 19535T demonstrated segments of unique sequences and genomicsrearrangements. The closest strains that were matched to ICMP 19535T include theReceived 3 August 2017 Accepted 31 August2017 Published 26 October 2017Citation De Meyer SE, Nguyen DT, Wang P,Andrews M. 2017. Complete genomesequence of Mesorhizobium sophorae ICMP19535T, a highly specific, nitrogen-fixingsymbiont of New Zealand endemic Sophoraspp. Genome Announc 5:e00958-17. https://doi.org/10.1128/genomeA.00958-17.Copyright © 2017 De Meyer et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Sofie E. De Meyer,sofdemey@outlook.com.PROKARYOTEScrossmVolume 5 Issue 43 e00958-17 genomea.asm.org 1 on November 5, 2017 by MURDOCH UNIVESRITY LIBhttp://genomea.asm.org/Downloaded from rhizobia Mesorhizobium ciceri bv. biserrulae WSM1284 and Mesorhizobium loti NZP2037.Preliminary sequence analysis revealed that the ICMP 19535T genome contains manykey genes known to be associated with legume symbiosis. A number of clusters ofnodulation genes (nod) were identified, and, interestingly, one cluster of nod genes islocated on a genomic island that contains multiple nif genes, which are known toencode enzymes involved in nitrogen fixation. Moreover, a cluster of fix genes wasdiscovered. Further analysis of the genome will lead to a better understanding of thestrain’s genomic mechanisms that regulate nodulation and nitrogen fixation associatedwith native New Zealand legume symbioses.Accession number(s). This whole-genome shotgun project has been deposited atDDBJ/ENA/GenBank under accession number NNRI00000000. The version describedhere is the first version, NNRI01000000.REFERENCES1. The Legume Phylogeny Working Group (LPWG). 2017. A new subfamilyclassification of the Leguminosae based on a taxonomically comprehen-sive phylogeny. Taxon 66:44 –77. https://doi.org/10.12705/661.3.2. Andrews M, Raven JA, Lea PJ. 2013. Do plants need nitrate? The mech-anisms by which nitrogen form affects plants. Ann Appl Biol 163:174 –199. https://doi.org/10.1111/aab.12045.3. McGlone MS, Duncan RP, Heenan PB. 2001. Endemism, species selectionand the origin and distribution of the vascular plant flora of NewZealand. J Biogeogr 28:199 –216. https://doi.org/10.1046/j.1365-2699.2001.00525.x.4. Wagstaff SJ, Heenan PB, Sanderson MJ. 1999. Classification, origins, andpatterns of diversification in New Zealand Carmichaelinae (Fabaceae).Am J Bot 86:1346 –1356. https://doi.org/10.2307/2656781.5. Heenan PB, De Lange PJ, Wilton AD. 2001. Sophora (Fabaceae) in NewZealand: taxonomy, distribution, and biogeography. N Z J Bot 39:17–53.https://doi.org/10.1080/0028825X.2001.9512715.6. Tan HW, Heenan PB, De Meyer SE, Willems A, Andrews M. 2015. Diversenovel mesorhizobia nodulate New Zealand native Sophora species. SystAppl Microbiol 38:91–98. https://doi.org/10.1016/j.syapm.2014.11.003.7. De Meyer SE, Tan HW, Heenan PB, Andrews M, Willems A. 2015. Me-sorhizobium waimense sp. nov. isolated from Sophora longicarinata rootnodules and Mesorhizobium cantuariense sp. nov. isolated from Sophoramicrophylla root nodules. Int J Syst Evol Microbiol 65:3419 –3426. https://doi.org/10.1099/ijsem.0.000430.8. De Meyer SE, Tan HW, Andrews M, Heenan PB, Willems A. 2015. Me-sorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Me-sorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov.and Mesorhizobium kowhaii sp. nov. isolated from Sophora root nodulesin New Zealand. Int J Syst Evol Microbiol 66:786 –795. https://doi.org/10.1099/ijsem.0.000796.9. Andrews M, Andrews ME. 2017. Specificity in legume-rhizobia symbio-ses. Int J Mol Sci 18:705. https://doi.org/10.3390/ijms18040705.10. Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan andsnoGPS Web servers for the detection of tRNAs and snoRNAs. NucleicAcids Res 33:W686 –W689. https://doi.org/10.1093/nar/gki366.11. Edgar RC. 2007. PILER-CR: fast and accurate identification of CRISPR repeats.BMC Bioinformatics 8:18. https://doi.org/10.1186/1471-2105-8-18.12. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugen-holtz P. 2007. CRISPR recognition tool (CRT): a tool for automatic detec-tion of clustered regularly interspaced palindromic repeats. BMC Bioin-formatics 8:209. https://doi.org/10.1186/1471-2105-8-209.13. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014.Data, information, knowledge and principle: back to metabolism inKEGG. Nucleic Acids Res 42:D199 –D205. https://doi.org/10.1093/nar/gkt1076.14. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M,de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED,Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R,Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F,Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD,Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y,Zagnitko O, Vonstein V. 2005. The subsystems approach to genomeannotation and its use in the project to annotate 1000 genomes. NucleicAcids Res 33:5691–5702. https://doi.org/10.1093/nar/gki866.15. UniProt Consortium. 2015. UniProt: a hub for protein information. NucleicAcids Res 43:D204–D212. https://doi.org/10.1093/nar/gku989.16. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J,Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, BorkP. 2014. eggNOG v4.0: nested orthology inference across 3686 organ-isms. Nucleic Acids Res 42:D231–D239. https://doi.org/10.1093/nar/gkt1253.De Meyer et al.Volume 5 Issue 43 e00958-17 genomea.asm.org 2 on November 5, 2017 by MURDOCH UNIVESRITY LIBhttp://genomea.asm.org/Downloaded from 

Complete genome sequence of Mesorhizobium sophorae ICMP 19535T, a highly specific, nitrogen-fixing symbiont of New Zealand endemic Sophora spp

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Complete genome sequence of Mesorhizobium sophorae ICMP 19535T, a highly specific, nitrogen-fixing symbiont of New Zealand endemic Sophora spp

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