Mengwei Yao, Wenman Li, Zihong Duan, Yinliang Zhang, Rong Jia
{"title":"Genome sequence of the white-rot fungus <i>Irpex lacteus</i> F17, a type strain of lignin degrader fungus.","authors":"Mengwei Yao, Wenman Li, Zihong Duan, Yinliang Zhang, Rong Jia","doi":"10.1186/s40793-017-0267-x","DOIUrl":"https://doi.org/10.1186/s40793-017-0267-x","url":null,"abstract":"<p><p><i>Irpex lacteus</i>, a cosmopolitan white-rot fungus, degrades lignin and lignin-derived aromatic compounds. In this study, we report the high-quality draft genome sequence of <i>I. lacteus</i> F17, isolated from a decaying hardwood tree in the vicinity of Hefei, China. The genome is 44,362,654 bp, with a GC content of 49.64% and a total of 10,391 predicted protein-coding genes. In addition, a total of 18 snRNA, 842 tRNA, 15 rRNA operons and 11,710 repetitive sequences were also identified. The genomic data provides insights into the mechanisms of the efficient lignin decomposition of this strain.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"55"},"PeriodicalIF":0.0,"publicationDate":"2017-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0267-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35416584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic <i>Sulfurovum lithotrophicum</i> 42BKT<sup>T</sup>.","authors":"Wooyoung Jeon, Lia Priscilla, Gyuyeon Park, Heeseok Lee, Narae Lee, Dongyup Lee, Hyuksung Kwon, Iksung Ahn, Changha Lee, Hongweon Lee, Jungoh Ahn","doi":"10.1186/s40793-017-0265-z","DOIUrl":"https://doi.org/10.1186/s40793-017-0265-z","url":null,"abstract":"<p><p>A sulfur-oxidizing chemolithoautotrophic bacterium, <i>Sulfurovum lithotrophicum</i> 42BKT<sup>T</sup>, isolated from hydrothermal sediments in Okinawa, Japan, has been used industrially for CO<sub>2</sub> bio-mitigation owing to its ability to convert CO<sub>2</sub> into C<sub>5</sub>H<sub>8</sub>NO<sub>4</sub><sup>-</sup> at a high rate of specific mitigation (0.42 g CO<sub>2</sub>/cell/h). The genome of <i>S. lithotrophicum</i> 42BKT<sup>T</sup> comprised of a single chromosome of 2217,891 bp with 2217 genes, including 2146 protein-coding genes and 54 RNA genes. Here, we present its complete genome-sequence information, including information about the genes encoding enzymes involved in CO<sub>2</sub> fixation and sulfur oxidation.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"54"},"PeriodicalIF":0.0,"publicationDate":"2017-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0265-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35401698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Diogo N Proença, William B Whitman, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Paula V Morais
{"title":"Draft genome sequence of the cellulolytic endophyte <i>Chitinophaga costaii</i> A37T2<sup>T</sup>.","authors":"Diogo N Proença, William B Whitman, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Paula V Morais","doi":"10.1186/s40793-017-0262-2","DOIUrl":"10.1186/s40793-017-0262-2","url":null,"abstract":"<p><p>Here we report the draft genome sequence of <i>Chitinophaga costai</i> A37T2<sup>T</sup> (=CIP 110584<sup>T</sup>, =LMG 27458<sup>T</sup>), which was isolated from the endophytic community of <i>Pinus pinaster</i> tree. The total genome size of <i>C. costaii</i> A37T2<sup>T</sup> is 5.07 Mbp, containing 4204 coding sequences. Strain A37T2<sup>T</sup> encoded multiple genes likely involved in cellulolytic, chitinolytic and lipolytic activities. This genome showed 1145 unique genes assigned into 109 Cluster of Orthologous Groups in comparison with the complete genome of <i>C. pinensis</i> DSM 2588<sup>T</sup>. The genomic information suggests the potential of the strain A37T2<sup>T</sup> to interact with the plant metabolism. As there are only a few bacterial genomes related to Pine Wilt Disease, this work provides a contribution to the field.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"53"},"PeriodicalIF":0.0,"publicationDate":"2017-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35402256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wah-Seng See-Too, Robson Ee, Yan-Lue Lim, Peter Convey, David A Pearce, Taznim Begam Mohd Mohidin, Wai-Fong Yin, Kok Gan Chan
{"title":"Complete genome of <i>Arthrobacter alpinus</i> strain R3.8, bioremediation potential unraveled with genomic analysis.","authors":"Wah-Seng See-Too, Robson Ee, Yan-Lue Lim, Peter Convey, David A Pearce, Taznim Begam Mohd Mohidin, Wai-Fong Yin, Kok Gan Chan","doi":"10.1186/s40793-017-0264-0","DOIUrl":"https://doi.org/10.1186/s40793-017-0264-0","url":null,"abstract":"<p><p><i>Arthrobacter alpinus</i> R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze proteins and cold-shock proteins, genes involved in bioremediation of xenobiotic compounds including naphthalene, and genes with chitinolytic and <i>N</i>-acetylglucosamine utilization properties and also plant-growth-influencing properties. In this genome report, we present a complete genome sequence of <i>A. alpinus</i> strain R3.8 and its annotation data, which will facilitate exploitation of potential novel cold-active enzymes.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"52"},"PeriodicalIF":0.0,"publicationDate":"2017-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0264-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35402255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Amir Ktari, Imen Nouioui, Teal Furnholm, Erik Swanson, Faten Ghodhbane-Gtari, Louis S Tisa, Maher Gtari
{"title":"Permanent draft genome sequence of <i>Frankia</i> sp. NRRL B-16219 reveals the presence of canonical <i>nod</i> genes, which are highly homologous to those detected in <i>Candidatus</i> Frankia Dg1 genome.","authors":"Amir Ktari, Imen Nouioui, Teal Furnholm, Erik Swanson, Faten Ghodhbane-Gtari, Louis S Tisa, Maher Gtari","doi":"10.1186/s40793-017-0261-3","DOIUrl":"https://doi.org/10.1186/s40793-017-0261-3","url":null,"abstract":"<p><p><i>Frankia</i> sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of <i>Ceanothus jepsonii</i> growing in the USA. Its host plant range includes members of <i>Elaeagnaceae</i> species. Phylogenetically, strain NRRL B-16219 is closely related to <i>\"Frankia discariae</i>\" with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for <i>Frankia</i>, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited. Since the first three <i>Frankia</i> genomes were sequenced, additional genome sequences covering more diverse strains have helped provide insight into the depth of the pangenome and attempts to identify bacterial signaling molecules like the rhizobial canonical <i>nod</i> genes. The genome sequence of <i>Frankia</i> sp. strain NRRL B-16219 was generated and assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content. Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes, 1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL B-16219 draft genome contained genes homologous to the rhizobial common nodulation genes clustered in two areas. The first cluster contains <i>nod</i>ACIJH genes whereas the second has <i>nod</i>AB and <i>nod</i>H genes in the upstream region. Phylogenetic analysis shows that <i>Frankia nod</i> genes are more deeply rooted than their sister groups from rhizobia. PCR-sequencing suggested the widespread occurrence of highly homologous <i>nod</i>A and <i>nod</i>B genes in microsymbionts of field collected <i>Ceanothus americanus</i>.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"51"},"PeriodicalIF":0.0,"publicationDate":"2017-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0261-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35332015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ruby Ponnudurai, Lizbeth Sayavedra, Manuel Kleiner, Stefan E Heiden, Andrea Thürmer, Horst Felbeck, Rabea Schlüter, Stefan M Sievert, Rolf Daniel, Thomas Schweder, Stephanie Markert
{"title":"Genome sequence of the sulfur-oxidizing <i>Bathymodiolus thermophilus</i> gill endosymbiont.","authors":"Ruby Ponnudurai, Lizbeth Sayavedra, Manuel Kleiner, Stefan E Heiden, Andrea Thürmer, Horst Felbeck, Rabea Schlüter, Stefan M Sievert, Rolf Daniel, Thomas Schweder, Stephanie Markert","doi":"10.1186/s40793-017-0266-y","DOIUrl":"https://doi.org/10.1186/s40793-017-0266-y","url":null,"abstract":"<p><p><i>Bathymodiolus thermophilus</i>, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic <i>Gammaproteobacteria</i> within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics. In this study, we report the first draft genome sequence of the sulfur-oxidizing symbiont of <i>B. thermophilus</i>, here tentatively named <i>Candidatus</i> Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045 protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate as energy sources and encodes the Calvin-Benson-Bassham cycle for CO<sub>2</sub> fixation. Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates oxaloacetate and succinate were absent, suggesting that these intermediates may be substituted by metabolites from external sources. We also detected a repertoire of genes associated with cell surface adhesion, bacteriotoxicity and phage immunity, which may perform symbiosis-specific roles in the <i>B. thermophilus</i> symbiosis.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"50"},"PeriodicalIF":0.0,"publicationDate":"2017-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0266-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35332014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Soraya Mendoza-Olazarán, José F Garcia-Mazcorro, Rayo Morfín-Otero, Licet Villarreal-Treviño, Adrián Camacho-Ortiz, Eduardo Rodríguez-Noriega, Paola Bocanegra-Ibarias, Héctor J Maldonado-Garza, Scot E Dowd, Elvira Garza-González
{"title":"Draft genome sequences of two opportunistic pathogenic strains of <i>Staphylococcus cohnii</i> isolated from human patients.","authors":"Soraya Mendoza-Olazarán, José F Garcia-Mazcorro, Rayo Morfín-Otero, Licet Villarreal-Treviño, Adrián Camacho-Ortiz, Eduardo Rodríguez-Noriega, Paola Bocanegra-Ibarias, Héctor J Maldonado-Garza, Scot E Dowd, Elvira Garza-González","doi":"10.1186/s40793-017-0263-1","DOIUrl":"https://doi.org/10.1186/s40793-017-0263-1","url":null,"abstract":"<p><p>Herein, we report the draft-genome sequences and annotation of two opportunistic pathogenic strains of <i>Staphylococcus cohnii</i> isolated from humans. One strain (SC-57) was isolated from blood from a male patient in May 2006 and the other (SC-532) from a catheter from a male patient in June 2006. Similar to other genomes of <i>Staphylococcus</i> species, most genes (42%) of both strains are involved in metabolism of amino acids and derivatives, carbohydrates and proteins. Eighty (4%) genes are involved in virulence, disease, and defense and both species show phenotypic low biofilm production and evidence of increased antibiotic resistance associated to biofilm production. From both isolates, a new Staphylococcal Cassette Chromosome <i>mec</i> was detected: <i>mec</i> class A, <i>ccr</i> type 1. This is the first report of whole genome sequences of opportunistic <i>S. cohnii</i> isolated from human patients.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"49"},"PeriodicalIF":0.0,"publicationDate":"2017-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0263-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35332013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jacqueline Hollensteiner, Anja Poehlein, Cathrin Spröer, Boyke Bunk, Anna E Sheppard, Philip Rosentstiel, Hinrich Schulenburg, Heiko Liesegang
{"title":"Complete Genome sequence of the nematicidal <i>Bacillus thuringiensis</i> MYBT18246.","authors":"Jacqueline Hollensteiner, Anja Poehlein, Cathrin Spröer, Boyke Bunk, Anna E Sheppard, Philip Rosentstiel, Hinrich Schulenburg, Heiko Liesegang","doi":"10.1186/s40793-017-0259-x","DOIUrl":"10.1186/s40793-017-0259-x","url":null,"abstract":"<p><p>10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by <i>cry</i>-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis of the genome revealed a large number of mobile elements involved in genome plasticity including 11 plasmids and 16 chromosomal prophages. Three different nematicidal toxin genes were identified and classified according to the Cry toxin naming committee as <i>cry</i>13Aa2, <i>cry</i>13Ba1, and <i>cry</i>13Ab1. Strikingly, these genes are located on the chromosome in close proximity to three separate prophages. Moreover, four putative toxin genes of different toxin classes were identified on the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with three closely related 10.1601/nm.5000 strains enabled determination of the pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons, mostly represented by phage genes, morons and cryptic genes.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"48"},"PeriodicalIF":0.0,"publicationDate":"2017-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35359983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lucas M Demey, Caitlin R Miller, Michael P Manzella, Rachel R Spurbeck, Sukhinder K Sandhu, Gemma Reguera, Kazem Kashefi
{"title":"The draft genome of the hyperthermophilic archaeon <i>Pyrodictium delaneyi</i> strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction.","authors":"Lucas M Demey, Caitlin R Miller, Michael P Manzella, Rachel R Spurbeck, Sukhinder K Sandhu, Gemma Reguera, Kazem Kashefi","doi":"10.1186/s40793-017-0260-4","DOIUrl":"10.1186/s40793-017-0260-4","url":null,"abstract":"<p><p><i>Pyrodictium delaneyi</i> strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06<sup>T</sup>, which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk. This makes <i>P. delaneyi</i> strain Hulk the first hyperthermophilic archaeon known to gain energy for growth by reduction of iron, nitrate, and sulfur-containing electron acceptors. Here we present the most notable features of the genome of <i>P. delaneyi</i> strain Hulk and identify genes encoding proteins critical to its respiratory versatility at high temperatures. The description presented here corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019 protein-coding genes, 53 RNA genes, and 1365 hypothetical genes.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"47"},"PeriodicalIF":0.0,"publicationDate":"2017-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5556600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35276349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vera Y Matrosova, Elena K Gaidamakova, Kira S Makarova, Olga Grichenko, Polina Klimenkova, Robert P Volpe, Rok Tkavc, Gözen Ertem, Isabel H Conze, Evelyne Brambilla, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tbk Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Hajnalka Daligault, Karen Davenport, Tracy Erkkila, Lynne A Goodwin, Wei Gu, Christine Munk, Hazuki Teshima, Yan Xu, Patrick Chain, Michael Woolbert, Nina Gunde-Cimerman, Yuri I Wolf, Tine Grebenc, Cene Gostinčar, Michael J Daly
{"title":"High-quality genome sequence of the radioresistant bacterium <i>Deinococcus ficus</i> KS 0460.","authors":"Vera Y Matrosova, Elena K Gaidamakova, Kira S Makarova, Olga Grichenko, Polina Klimenkova, Robert P Volpe, Rok Tkavc, Gözen Ertem, Isabel H Conze, Evelyne Brambilla, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tbk Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Hajnalka Daligault, Karen Davenport, Tracy Erkkila, Lynne A Goodwin, Wei Gu, Christine Munk, Hazuki Teshima, Yan Xu, Patrick Chain, Michael Woolbert, Nina Gunde-Cimerman, Yuri I Wolf, Tine Grebenc, Cene Gostinčar, Michael J Daly","doi":"10.1186/s40793-017-0258-y","DOIUrl":"10.1186/s40793-017-0258-y","url":null,"abstract":"<p><p>The genetic platforms of <i>Deinococcus</i> species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium <i>Deinococcus ficus</i> KS 0460 and its phenotypic characterization. <i>Deinococcus ficus</i> KS 0460 has been studied since 1987, first under the name <i>Deinobacter grandis</i>, then <i>Deinococcus grandis</i>. The <i>D. ficus</i> KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all <i>D. ficus</i> KS 0460 proteins, 79% and 70% had homologues in <i>Deinococcus radiodurans</i> ATCC BAA-816 and <i>Deinococcus geothermalis</i> DSM 11300, respectively. The most striking differences between <i>D. ficus</i> KS 0460 and <i>D. radiodurans</i> BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) <i>D. ficus</i> lacks nine enzymes of purine degradation present in <i>D. radiodurans</i>, and (ii) <i>D. ficus</i> contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that <i>D. radiodurans</i> lacks. Moreover, genes previously considered to be important to IR resistance are missing in <i>D. ficus</i> KS 0460, namely, for the Mn-transporter <i>nramp</i>, and proteins DdrF, DdrJ and DdrK, all of which are also missing in <i>Deinococcus deserti</i>. Otherwise, <i>D. ficus</i> KS 0460 exemplifies the <i>Deinococcus</i> lineage.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"46"},"PeriodicalIF":0.0,"publicationDate":"2017-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35290937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}