Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> WSM1022
Here, we report an improved and complete genome sequence of <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> strain WSM1022, a microsymbiont of <i>Medicago species</i>, revealing its tripartite structure. This improved genome sequence was generate...
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| Format: | Article |
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MDPI AG
2021-11-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/12/2428 |
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| author | Laura Baxter Proyash Roy Emma Picot Jess Watts Alex Jones Helen Wilkinson Patrick Schäfer Miriam Gifford Beatriz Lagunas |
| author_facet | Laura Baxter Proyash Roy Emma Picot Jess Watts Alex Jones Helen Wilkinson Patrick Schäfer Miriam Gifford Beatriz Lagunas |
| author_sort | Laura Baxter |
| collection | DOAJ |
| description | Here, we report an improved and complete genome sequence of <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> strain WSM1022, a microsymbiont of <i>Medicago species</i>, 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 <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> Sm1021 and <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>medicae</i> WSM419. Both WSM1022 and WSM419 species are high-efficiency rhizobial strains when in symbiosis with <i>Medicago truncatula</i>, 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. |
| first_indexed | 2024-03-10T03:32:50Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T03:32:50Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-f6f33a8a62df40f4b1fac72af11f81b62023-11-23T09:37:50ZengMDPI AGMicroorganisms2076-26072021-11-01912242810.3390/microorganisms9122428Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> WSM1022Laura Baxter0Proyash Roy1Emma Picot2Jess Watts3Alex Jones4Helen Wilkinson5Patrick Schäfer6Miriam Gifford7Beatriz Lagunas8School of Life Sciences, University of Warwick, Coventry CV4 7AL, UKSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UKSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UKSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UKSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UKSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UKSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UKSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UKSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, UKHere, we report an improved and complete genome sequence of <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> strain WSM1022, a microsymbiont of <i>Medicago species</i>, 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 <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> Sm1021 and <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>medicae</i> WSM419. Both WSM1022 and WSM419 species are high-efficiency rhizobial strains when in symbiosis with <i>Medicago truncatula</i>, 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.https://www.mdpi.com/2076-2607/9/12/2428rhizobium<i>Sinorhizobium</i><i>Ensifer</i>rhizobial genome<i>Medicago truncatula</i>WSM1022 |
| spellingShingle | Laura Baxter Proyash Roy Emma Picot Jess Watts Alex Jones Helen Wilkinson Patrick Schäfer Miriam Gifford Beatriz Lagunas Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> WSM1022 Microorganisms rhizobium <i>Sinorhizobium</i> <i>Ensifer</i> rhizobial genome <i>Medicago truncatula</i> WSM1022 |
| title | Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> WSM1022 |
| title_full | Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> WSM1022 |
| title_fullStr | Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> WSM1022 |
| title_full_unstemmed | Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> WSM1022 |
| title_short | Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont <i>Sinorhizobium</i> (<i>Ensifer</i>) <i>meliloti</i> WSM1022 |
| title_sort | comparative genomics across three ensifer species using a new complete genome sequence of the medicago symbiont i sinorhizobium i i ensifer i i meliloti i wsm1022 |
| topic | rhizobium <i>Sinorhizobium</i> <i>Ensifer</i> rhizobial genome <i>Medicago truncatula</i> WSM1022 |
| url | https://www.mdpi.com/2076-2607/9/12/2428 |
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