Wan Adnawani Meor Osman, Peter van Berkum, Milagros León-Barrios, Encarna Velázquez, Patrick Elia, Rui Tian, Julie Ardley, Margaret Gollagher, Rekha Seshadri, T B K Reddy, Natalia Ivanova, Tanja Woyke, Amrita Pati, Victor Markowitz, Mohamed N Baeshen, Naseebh Nabeeh Baeshen, Nikos Kyrpides, Wayne Reeve
{"title":"Ensifer meliloti Mlalz-1 的高质量基因组序列草案，这是一种在西班牙加那利群岛兰萨罗特岛采集的 Medicago laciniata (L.) miller 的微共生体。","authors":"Wan Adnawani Meor Osman, Peter van Berkum, Milagros León-Barrios, Encarna Velázquez, Patrick Elia, Rui Tian, Julie Ardley, Margaret Gollagher, Rekha Seshadri, T B K Reddy, Natalia Ivanova, Tanja Woyke, Amrita Pati, Victor Markowitz, Mohamed N Baeshen, Naseebh Nabeeh Baeshen, Nikos Kyrpides, Wayne Reeve","doi":"10.1186/s40793-017-0270-2","DOIUrl":null,"url":null,"abstract":"<p><p>10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of <i>Medicago laciniata</i> (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host <i>M. laciniata</i>. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 <sup>T</sup>, 10.1601/nm.1334 A 321<sup>T</sup> and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 <sup>T</sup>, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of <i>M. laciniata</i> requires a specific <i>nodC</i> allele, and the <i>nodC</i> gene of strain Mlalz-1 shares ≥98% sequence identity with <i>nodC</i> of <i>M. laciniata</i>-nodulating 10.1601/nm.1328 strains, but ≤93% with <i>nodC</i> of 10.1601/nm.1328 strains that nodulate other <i>Medicago</i> species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response <i>lpiA-acvB</i> operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, <i>lpiA</i> is essential for enhancing survival in lethal acid conditions. The second copy of the <i>lpiA-acvB</i> operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of <i>lpiA-acvB</i>.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"58"},"PeriodicalIF":0.0000,"publicationDate":"2017-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613336/pdf/","citationCount":"0","resultStr":"{\"title\":\"High-quality draft genome sequence of <i>Ensifer meliloti</i> Mlalz-1, a microsymbiont of <i>Medicago laciniata</i> (L.) miller collected in Lanzarote, Canary Islands, Spain.\",\"authors\":\"Wan Adnawani Meor Osman, Peter van Berkum, Milagros León-Barrios, Encarna Velázquez, Patrick Elia, Rui Tian, Julie Ardley, Margaret Gollagher, Rekha Seshadri, T B K Reddy, Natalia Ivanova, Tanja Woyke, Amrita Pati, Victor Markowitz, Mohamed N Baeshen, Naseebh Nabeeh Baeshen, Nikos Kyrpides, Wayne Reeve\",\"doi\":\"10.1186/s40793-017-0270-2\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of <i>Medicago laciniata</i> (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host <i>M. laciniata</i>. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 <sup>T</sup>, 10.1601/nm.1334 A 321<sup>T</sup> and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 <sup>T</sup>, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of <i>M. laciniata</i> requires a specific <i>nodC</i> allele, and the <i>nodC</i> gene of strain Mlalz-1 shares ≥98% sequence identity with <i>nodC</i> of <i>M. laciniata</i>-nodulating 10.1601/nm.1328 strains, but ≤93% with <i>nodC</i> of 10.1601/nm.1328 strains that nodulate other <i>Medicago</i> species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response <i>lpiA-acvB</i> operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, <i>lpiA</i> is essential for enhancing survival in lethal acid conditions. The second copy of the <i>lpiA-acvB</i> operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of <i>lpiA-acvB</i>.</p>\",\"PeriodicalId\":21965,\"journal\":{\"name\":\"Standards in Genomic Sciences\",\"volume\":\"12 \",\"pages\":\"58\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2017-09-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613336/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Standards in Genomic Sciences\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1186/s40793-017-0270-2\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2017/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q3\",\"JCRName\":\"Biochemistry, Genetics and Molecular Biology\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Standards in Genomic Sciences","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1186/s40793-017-0270-2","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2017/1/1 0:00:00","PubModel":"eCollection","JCR":"Q3","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.
10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T, 10.1601/nm.1334 A 321T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.
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