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Title: High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain

Abstract

Ensifer meliloti 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 in this paper, the features of E. meliloti 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 Ensifer meliloti IAM 12611 T, Ensifer medicae A 321T and Ensifer numidicus ORS 1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as E. meliloti . 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 Ensifer strains, but ≤93%more » with nodC of Ensifer strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced E. meliloti strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In E. medicae strain WSM419, 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 E. medicae strains, which suggests genetic recombination between strain Mlalz-1 and E. medicae and the horizontal gene transfer of lpiA-acvB.« less

Authors:
 [1];  [2];  [3];  [4];  [2];  [1]; ORCiD logo [1];  [5];  [6];  [6];  [6];  [6];  [7];  [7];  [8];  [9];  [6];  [1]
  1. Murdoch Univ., WA (Australia). School of Veterinary and Life Sciences
  2. US Dept. of Agriculture (USDA)., Beltsville, MD (United States). Soybean Genomics and Improvement Lab., Beltsville Agricultural Research Center
  3. Univ. de La Laguna, Tenerife (Spain). Dept. de Bioquimica, Microbiologia, Biologia Celular y Genetica
  4. Univ. de Salamanca, Salamanca (Spain). Dept. de Microbiologia y Genetica and Inst. Hispanoluso de Investigaciones Agrarias (CIALE)
  5. Curtin Univ., Bentley, WA (Australia). Curtin Univ. Sustainability Policy Inst.
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
  8. Univ. of Jeddah, Jeddah (Saudi Arabia). Dept. of Biology
  9. Univ. of Jeddah, Jeddah (Saudi Arabia). Dept. of Biology
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1416926
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Root-nodule bacteria; Ensifer; Geba-Rnb; Medicago; lpiA-acvB operon

Citation Formats

Osman, Wan Adnawani Meor, van Berkum, Peter, León-Barrios, Milagros, Velázquez, Encarna, Elia, Patrick, Tian, Rui, Ardley, Julie, Gollagher, Margaret, Seshadri, Rekha, Reddy, T. B. K., Ivanova, Natalia, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Baeshen, Mohamed N., Baeshen, Naseebh Nabeeh, Kyrpides, Nikos, and Reeve, Wayne. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0270-2.
Osman, Wan Adnawani Meor, van Berkum, Peter, León-Barrios, Milagros, Velázquez, Encarna, Elia, Patrick, Tian, Rui, Ardley, Julie, Gollagher, Margaret, Seshadri, Rekha, Reddy, T. B. K., Ivanova, Natalia, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Baeshen, Mohamed N., Baeshen, Naseebh Nabeeh, Kyrpides, Nikos, & Reeve, Wayne. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. United States. doi:10.1186/s40793-017-0270-2.
Osman, Wan Adnawani Meor, van Berkum, Peter, León-Barrios, Milagros, Velázquez, Encarna, Elia, Patrick, Tian, Rui, Ardley, Julie, Gollagher, Margaret, Seshadri, Rekha, Reddy, T. B. K., Ivanova, Natalia, Woyke, Tanja, Pati, Amrita, Markowitz, Victor, Baeshen, Mohamed N., Baeshen, Naseebh Nabeeh, Kyrpides, Nikos, and Reeve, Wayne. Mon . "High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain". United States. doi:10.1186/s40793-017-0270-2. https://www.osti.gov/servlets/purl/1416926.
@article{osti_1416926,
title = {High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain},
author = {Osman, Wan Adnawani Meor and van Berkum, Peter and León-Barrios, Milagros and Velázquez, Encarna and Elia, Patrick and Tian, Rui and Ardley, Julie and Gollagher, Margaret and Seshadri, Rekha and Reddy, T. B. K. and Ivanova, Natalia and Woyke, Tanja and Pati, Amrita and Markowitz, Victor and Baeshen, Mohamed N. and Baeshen, Naseebh Nabeeh and Kyrpides, Nikos and Reeve, Wayne},
abstractNote = {Ensifer meliloti 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 in this paper, the features of E. meliloti 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 Ensifer meliloti IAM 12611 T, Ensifer medicae A 321T and Ensifer numidicus ORS 1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as E. meliloti . 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 Ensifer strains, but ≤93% with nodC of Ensifer strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced E. meliloti strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In E. medicae strain WSM419, 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 E. medicae strains, which suggests genetic recombination between strain Mlalz-1 and E. medicae and the horizontal gene transfer of lpiA-acvB.},
doi = {10.1186/s40793-017-0270-2},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {Mon Sep 25 00:00:00 EDT 2017},
month = {Mon Sep 25 00:00:00 EDT 2017}
}

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