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Microorganisms
Volume 9
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10.3390/microorganisms9122428
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Article

Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022

by
Laura Baxter
1,2,*,
Proyash Roy
1,3,
Emma Picot
1,
Jess Watts
1,
Alex Jones
1,
Helen Wilkinson
1,
Patrick Schäfer
1,†,
Miriam Gifford
1 and
Beatriz Lagunas
1,*
1
School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
2
Bioinformatics Research Technology Platform, University of Warwick, Coventry CV4 7AL, UK
3
Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
*
Authors to whom correspondence should be addressed.
†
Current Address: Department of Biology II, Ulm University, 89069 Ulm, Germany.
Microorganisms 2021, 9(12), 2428; https://doi.org/10.3390/microorganisms9122428
Submission received: 20 September 2021 / Revised: 11 November 2021 / Accepted: 18 November 2021 / Published: 25 November 2021
(This article belongs to the Special Issue Genomics of Nitrogen-Fixing Plant Symbiotic Bacteria)
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Abstract

Here, we report an improved and complete genome sequence of Sinorhizobium (Ensifer) meliloti strain WSM1022, a microsymbiont of Medicago species, revealing its tripartite structure. This improved genome sequence was generated combining Illumina and Oxford nanopore sequencing technologies to better understand the symbiotic properties of the bacterium. The 6.75 Mb WSM1022 genome consists of three scaffolds, corresponding to a chromosome (3.70 Mb) and the pSymA (1.38 Mb) and pSymB (1.66 Mb) megaplasmids. The assembly has an average GC content of 62.2% and a mean coverage of 77X. Genome annotation of WSM1022 predicted 6058 protein coding sequences (CDSs), 202 pseudogenes, 9 rRNAs (3 each of 5S, 16S, and 23S), 55 tRNAs, and 4 ncRNAs. We compared the genome of WSM1022 to two other rhizobial strains, closely related Sinorhizobium (Ensifer) meliloti Sm1021 and Sinorhizobium (Ensifer) medicae WSM419. Both WSM1022 and WSM419 species are high-efficiency rhizobial strains when in symbiosis with Medicago truncatula, whereas Sm1021 is ineffective. Our findings report significant genomic differences across the three strains with some similarities between the meliloti strains and some others between the high efficiency strains WSM1022 and WSM419. The addition of this high-quality rhizobial genome sequence in conjunction with comparative analyses will help to unravel the features that make a rhizobial symbiont highly efficient for nitrogen fixation.
Keywords: rhizobium; Sinorhizobium; Ensifer; rhizobial genome; Medicago truncatula; WSM1022; WSM419; Sm1021; nitrogen fixation; nodulation; nodule rhizobium; Sinorhizobium; Ensifer; rhizobial genome; Medicago truncatula; WSM1022; WSM419; Sm1021; nitrogen fixation; nodulation; nodule

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MDPI and ACS Style

Baxter, L.; Roy, P.; Picot, E.; Watts, J.; Jones, A.; Wilkinson, H.; Schäfer, P.; Gifford, M.; Lagunas, B. Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022. Microorganisms 2021, 9, 2428. https://doi.org/10.3390/microorganisms9122428

AMA Style

Baxter L, Roy P, Picot E, Watts J, Jones A, Wilkinson H, Schäfer P, Gifford M, Lagunas B. Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022. Microorganisms. 2021; 9(12):2428. https://doi.org/10.3390/microorganisms9122428

Chicago/Turabian Style

Baxter, Laura, Proyash Roy, Emma Picot, Jess Watts, Alex Jones, Helen Wilkinson, Patrick Schäfer, Miriam Gifford, and Beatriz Lagunas. 2021. "Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022" Microorganisms 9, no. 12: 2428. https://doi.org/10.3390/microorganisms9122428

APA Style

Baxter, L., Roy, P., Picot, E., Watts, J., Jones, A., Wilkinson, H., Schäfer, P., Gifford, M., & Lagunas, B. (2021). Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022. Microorganisms, 9(12), 2428. https://doi.org/10.3390/microorganisms9122428

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