Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production
Tóm tắt
Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organism prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy’s IMG database to facilitate easy genome exploration by the scientific community without the need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.
Tài liệu tham khảo
citation_journal_title=New Phytol; citation_title=Heterocyst and akinete differentiation in cyanobacteria; citation_author=DG Adams, PS Duggan; citation_volume=144; citation_issue=1; citation_publication_date=1999; citation_pages=3-33; citation_doi=10.1046/j.1469-8137.1999.00505.x; citation_id=CR1
citation_journal_title=PLoS ONE; citation_title=Towards a synthetic chloroplast; citation_author=CM Agapakis, H Niederholtmeyer, RR Noche, TD Lieberman, SG Megason, JC Way, PA Silver; citation_volume=6; citation_issue=4; citation_publication_date=2011; citation_pages=e18877; citation_doi=10.1371/journal.pone.0018877; citation_id=CR2
citation_journal_title=Nat Genet; citation_title=Gene ontology: tool for the unification of biology. The Gene Ontology Consortium; citation_author=M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock; citation_volume=25; citation_issue=1; citation_publication_date=2000; citation_pages=25-29; citation_doi=10.1038/75556; citation_id=CR3
citation_journal_title=BMC Genom; citation_title=The RAST Server: rapid annotations using subsystems technology; citation_author=RK Aziz, D Bartels, AA Best, M DeJongh, T Disz, RA Edwards, K Formsma, S Gerdes, EM Glass, M Kubal, F Meyer, GJ Olsen, R Olson, AL Osterman, RA Overbeek, LK McNeil, D Paarmann, T Paczian, B Parrello, GD Pusch, C Reich, R Stevens, O Vassieva, V Vonstein, A Wilke, O Zagnitko; citation_volume=9; citation_publication_date=2008; citation_pages=75; citation_doi=10.1186/1471-2164-9-75; citation_id=CR4
citation_journal_title=ISME J; citation_title=Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms; citation_author=JG Caporaso, CL Lauber, WA Walters, D Berg-Lyons, J Huntley, N Fierer, SM Owens, J Betley, L Fraser, M Bauer, N Gormley, JA Gilbert, G Smith, R Knight; citation_volume=6; citation_issue=8; citation_publication_date=2012; citation_pages=1621-1624; citation_doi=10.1038/ismej.2012.8; citation_id=CR5
Castenholz RW (2015) General characteristics of the cyanobacteria. Bergey’s Man Syst Archaea Bacteria. doi:
10.1002/9781118960608.cbm00019
citation_journal_title=Nucleic Acids Res; citation_title=IMG/M: integrated genome and metagenome comparative data analysis system; citation_author=IA Chen, VM Markowitz, K Chu, K Palaniappan, E Szeto, M Pillay, A Ratner, J Huang, E Andersen, M Huntemann, N Varghese, M Hadjithomas, K Tennessen, T Nielsen, NN Ivanova, NC Kyrpides; citation_publication_date=2016; citation_id=CR7
citation_journal_title=Nat Methods; citation_title=Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data; citation_author=CS Chin, DH Alexander, P Marks, AA Klammer, J Drake, C Heiner, A Clum, A Copeland, J Huddleston, EE Eichler, SW Turner, J Korlach; citation_volume=10; citation_issue=6; citation_publication_date=2013; citation_pages=563-569; citation_doi=10.1038/nmeth.2474; citation_id=CR8
citation_journal_title=Mol Biol Evol; citation_title=Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes; citation_author=KH Chu, J Qi, ZG Yu, V Anh; citation_volume=21; citation_issue=1; citation_publication_date=2004; citation_pages=200-206; citation_doi=10.1093/molbev/msh002; citation_id=CR9
citation_journal_title=New Phytol; citation_title=Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus
; citation_author=A Cormier, K Avia, L Sterck, T Derrien, V Wucher, G Andres, M Monsoor, O Godfroy, A Lipinska, MM Perrineau, Y Peer, C Hitte, E Corre, SM Coelho, JM Cock; citation_publication_date=2016; citation_id=CR10
citation_journal_title=Nat Biotechnol; citation_title=Genome sequence of the recombinant protein production host Pichia pastoris
; citation_author=K Schutter, YC Lin, P Tiels, A Hecke, S Glinka, J Weber-Lehmann, P Rouze, Y Peer, N Callewaert; citation_volume=27; citation_issue=6; citation_publication_date=2009; citation_pages=561-566; citation_doi=10.1038/nbt.1544; citation_id=CR11
citation_journal_title=Science; citation_title=Real-time DNA sequencing from single polymerase molecules; citation_author=J Eid, A Fehr, J Gray, K Luong, J Lyle, G Otto, P Peluso, D Rank, P Baybayan, B Bettman, A Bibillo, K Bjornson, B Chaudhuri, F Christians, R Cicero, S Clark, R Dalal, A Dewinter, J Dixon, M Foquet, A Gaertner, P Hardenbol, C Heiner, K Hester, D Holden, G Kearns, X Kong, R Kuse, Y Lacroix, S Lin, P Lundquist, C Ma, P Marks, M Maxham, D Murphy, I Park, T Pham, M Phillips, J Roy, R Sebra, G Shen, J Sorenson, A Tomaney, K Travers, M Trulson, J Vieceli, J Wegener, D Wu, A Yang, D Zaccarin, P Zhao, F Zhong, J Korlach, S Turner; citation_volume=323; citation_issue=5910; citation_publication_date=2009; citation_pages=133-138; citation_doi=10.1126/science.1162986; citation_id=CR12
citation_journal_title=Nat Biotechnol; citation_title=The minimum information about a genome sequence (MIGS) specification; citation_author=D Field, G Garrity, T Gray, N Morrison, J Selengut, P Sterk, T Tatusova, N Thomson, MJ Allen, SV Angiuoli, M Ashburner, N Axelrod, S Baldauf, S Ballard, J Boore, G Cochrane, J Cole, P Dawyndt, P Vos, C dePamphilis, R Edwards, N Faruque, R Feldman, J Gilbert, P Gilna, FO Glockner, P Goldstein, R Guralnick, D Haft, D Hancock, H Hermjakob, C Hertz-Fowler, P Hugenholtz, I Joint, L Kagan, M Kane, J Kennedy, G Kowalchuk, R Kottmann, E Kolker, S Kravitz, N Kyrpides, J Leebens-Mack, SE Lewis, K Li, AL Lister, P Lord, N Maltsev, V Markowitz, J Martiny, B Methe, I Mizrachi, R Moxon, K Nelson, J Parkhill, L Proctor, O White, SA Sansone, A Spiers, R Stevens, P Swift, C Taylor, Y Tateno, A Tett, S Turner, D Ussery, B Vaughan, N Ward, T Whetzel, IS Gil, G Wilson, A Wipat; citation_volume=26; citation_issue=5; citation_publication_date=2008; citation_pages=541-547; citation_doi=10.1038/nbt1360; citation_id=CR13
citation_journal_title=Nat Methods; citation_title=Direct detection of DNA methylation during single-molecule, real-time sequencing; citation_author=BA Flusberg, DR Webster, JH Lee, KJ Travers, EC Olivares, TA Clark, J Korlach, SW Turner; citation_volume=7; citation_issue=6; citation_publication_date=2010; citation_pages=461-465; citation_doi=10.1038/nmeth.1459; citation_id=CR14
citation_journal_title=PLoS ONE; citation_title=Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032; citation_author=J Gioia, S Yerrapragada, X Qin, H Jiang, OC Igboeli, D Muzny, S Dugan-Rocha, Y Ding, A Hawes, W Liu, L Perez, C Kovar, H Dinh, S Lee, L Nazareth, P Blyth, M Holder, C Buhay, MR Tirumalai, Y Liu, I Dasgupta, L Bokhetache, M Fujita, F Karouia, PE Moorthy, J Siefert, A Uzman, P Buzumbo, A Verma, H Zwiya, BD McWilliams, A Olowu, KD Clinkenbeard, D Newcombe, L Golebiewski, JF Petrosino, WL Nicholson, GE Fox, K Venkateswaran, SK Highlander, GM Weinstock; citation_volume=2; citation_issue=9; citation_publication_date=2007; citation_pages=e928; citation_doi=10.1371/journal.pone.0000928; citation_id=CR15
citation_journal_title=Mar Drugs; citation_title=Next generation sequencing of Actinobacteria for the discovery of novel natural products; citation_author=JP Gomez-Escribano, S Alt, MJ Bibb; citation_publication_date=2016; citation_id=CR16
Herdman M, Castenholz RW, Rippka R (2015) Cyanobacteria/Subsection IV/Subsection IV.I/Form-Nostoc. Bergey’s Manual of Systematics of Archaea and Bacteria. doi:
10.1002/9781118960608.gbm00459
citation_journal_title=J Bacteriol; citation_title=Cyanobacterial cell walls: news from an unusual prokaryotic envelope; citation_author=E Hoiczyk, A Hansel; citation_volume=182; citation_issue=5; citation_publication_date=2000; citation_pages=1191-1199; citation_doi=10.1128/JB.182.5.1191-1199.2000; citation_id=CR18
citation_journal_title=BMC Bioinform; citation_title=Prodigal: prokaryotic gene recognition and translation initiation site identification; citation_author=D Hyatt, GL Chen, PF Locascio, ML Land, FW Larimer, LJ Hauser; citation_volume=11; citation_publication_date=2010; citation_pages=119; citation_doi=10.1186/1471-2105-11-119; citation_id=CR19
citation_journal_title=Genome Biol; citation_title=An expanded evaluation of protein function prediction methods shows an improvement in accuracy; citation_author=Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, CS Funk, I Kahanda, KM Verspoor, A Ben-Hur, CE Koo, D Penfold-Brown, D Shasha, N Youngs, R Bonneau, A Lin, SM Sahraeian, PL Martelli, G Profiti, R Casadio, R Cao, Z Zhong, J Cheng, A Altenhoff, N Skunca, C Dessimoz, T Dogan, K Hakala, S Kaewphan, F Mehryary, T Salakoski, F Ginter, H Fang, B Smithers, M Oates, J Gough, P Toronen, P Koskinen, L Holm, CT Chen, WL Hsu, K Bryson, D Cozzetto, F Minneci, DT Jones, S Chapman, D Bkc, IK Khan, D Kihara, D Ofer, N Rappoport, A Stern, E Cibrian-Uhalte, P Denny, RE Foulger, R Hieta, D Legge, RC Lovering, M Magrane, AN Melidoni, P Mutowo-Meullenet, K Pichler, A Shypitsyna, B Li, P Zakeri, S ElShal, LC Tranchevent, S Das, NL Dawson, D Lee, JG Lees, I Sillitoe, P Bhat, T Nepusz, AE Romero, R Sasidharan, H Yang, A Paccanaro, J Gillis, AE Sedeno-Cortes, P Pavlidis, S Feng, JM Cejuela, T Goldberg, T Hamp, L Richter, A Salamov, T Gabaldon, M Marcet-Houben, F Supek, Q Gong, W Ning, Y Zhou, W Tian, M Falda, P Fontana, E Lavezzo, S Toppo, C Ferrari, M Giollo, D Piovesan, SC Tosatto, A Pozo, JM Fernandez, P Maietta, A Valencia, ML Tress, A Benso, S Carlo, G Politano, A Savino, HU Rehman, M Re, M Mesiti, G Valentini, JW Bargsten, AD Dijk, B Gemovic, S Glisic, V Perovic, V Veljkovic, N Veljkovic, ESDC Almeida, RZ Vencio, M Sharan, J Vogel, L Kansakar, S Zhang, S Vucetic, Z Wang, MJ Sternberg, MN Wass, RP Huntley, MJ Martin, C O’Donovan, PN Robinson, Y Moreau, A Tramontano, PC Babbitt, SE Brenner, M Linial, CA Orengo, B Rost, CS Greene, SD Mooney, I Friedberg, P Radivojac; citation_volume=17; citation_issue=1; citation_publication_date=2016; citation_pages=184; citation_doi=10.1186/s13059-016-1037-6; citation_id=CR20
citation_journal_title=Nat Prod Rep; citation_title=Unique marine derived cyanobacterial biosynthetic genes for chemical diversity; citation_author=K Kleigrewe, L Gerwick, DH Sherman, WH Gerwick; citation_volume=33; citation_issue=2; citation_publication_date=2016; citation_pages=348-364; citation_doi=10.1039/C5NP00097A; citation_id=CR21
citation_journal_title=Genome Biol; citation_title=Reducing assembly complexity of microbial genomes with single-molecule sequencing; citation_author=S Koren, GP Harhay, TP Smith, JL Bono, DM Harhay, SD McVey, D Radune, NH Bergman, AM Phillippy; citation_volume=14; citation_issue=9; citation_publication_date=2013; citation_pages=R101; citation_doi=10.1186/gb-2013-14-9-r101; citation_id=CR22
citation_journal_title=Genome Biol; citation_title=Versatile and open software for comparing large genomes; citation_author=S Kurtz, A Phillippy, AL Delcher, M Smoot, M Shumway, C Antonescu, SL Salzberg; citation_volume=5; citation_issue=2; citation_publication_date=2004; citation_pages=R12; citation_doi=10.1186/gb-2004-5-2-r12; citation_id=CR23
citation_journal_title=Mol Microbiol; citation_title=The morphogene AmiC2 is pivotal for multicellular development in the cyanobacterium Nostoc punctiforme
; citation_author=J Lehner, Y Zhang, S Berendt, TM Rasse, K Forchhammer, I Maldener; citation_volume=79; citation_issue=6; citation_publication_date=2011; citation_pages=1655-1669; citation_doi=10.1111/j.1365-2958.2011.07554.x; citation_id=CR24
citation_journal_title=Nucleic Acids Res; citation_title=tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence; citation_author=TM Lowe, SR Eddy; citation_volume=25; citation_issue=5; citation_publication_date=1997; citation_pages=955-964; citation_doi=10.1093/nar/25.5.0955; citation_id=CR25
citation_journal_title=J Biotechnol; citation_title=Cyanobacterial biofuel production; citation_author=IM Machado, S Atsumi; citation_volume=162; citation_issue=1; citation_publication_date=2012; citation_pages=50-56; citation_doi=10.1016/j.jbiotec.2012.03.005; citation_id=CR26
citation_journal_title=Nucleic Acids Res; citation_title=The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions; citation_author=VM Markowitz, E Szeto, K Palaniappan, Y Grechkin, K Chu, IM Chen, I Dubchak, I Anderson, A Lykidis, K Mavromatis, NN Ivanova, NC Kyrpides; citation_volume=Database issue; citation_issue=1; citation_publication_date=2008; citation_pages=D528-D533; citation_id=CR27
citation_journal_title=Nucleic Acids Res; citation_title=The integrated microbial genomes system: an expanding comparative analysis resource; citation_author=VM Markowitz, IM Chen, K Palaniappan, K Chu, E Szeto, Y Grechkin, A Ratner, I Anderson, A Lykidis, K Mavromatis, NN Ivanova, NC Kyrpides; citation_volume=38; citation_issue=Database issue; citation_publication_date=2010; citation_pages=D382-D390; citation_doi=10.1093/nar/gkp887; citation_id=CR28
citation_journal_title=Nucleic Acids Res; citation_title=IMG: the Integrated Microbial Genomes database and comparative analysis system; citation_author=VM Markowitz, IM Chen, K Palaniappan, K Chu, E Szeto, Y Grechkin, A Ratner, B Jacob, J Huang, P Williams, M Huntemann, I Anderson, K Mavromatis, NN Ivanova, NC Kyrpides; citation_volume=40; citation_issue=Database issue; citation_publication_date=2012; citation_pages=D115-D122; citation_doi=10.1093/nar/gkr1044; citation_id=CR29
citation_journal_title=Nat Chem Biol; citation_title=Minimum information about a biosynthetic gene cluster; citation_author=MH Medema, R Kottmann, P Yilmaz, M Cummings, JB Biggins, K Blin, I Bruijn, YH Chooi, J Claesen, RC Coates, P Cruz-Morales, S Duddela, S Dusterhus, DJ Edwards, DP Fewer, N Garg, C Geiger, JP Gomez-Escribano, A Greule, M Hadjithomas, AS Haines, EJ Helfrich, ML Hillwig, K Ishida, AC Jones, CS Jones, K Jungmann, C Kegler, HU Kim, P Kotter, D Krug, J Masschelein, AV Melnik, SM Mantovani, EA Monroe, M Moore, N Moss, HW Nutzmann, G Pan, A Pati, D Petras, FJ Reen, F Rosconi, Z Rui, Z Tian, NJ Tobias, Y Tsunematsu, P Wiemann, E Wyckoff, X Yan, G Yim, F Yu, Y Xie, B Aigle, AK Apel, CJ Balibar, EP Balskus, F Barona-Gomez, A Bechthold, HB Bode, R Borriss, SF Brady, AA Brakhage, P Caffrey, YQ Cheng, J Clardy, RJ Cox, R Mot, S Donadio, MS Donia, WA Donk, PC Dorrestein, S Doyle, AJ Driessen, M Ehling-Schulz, KD Entian, MA Fischbach, L Gerwick, WH Gerwick, H Gross, B Gust, C Hertweck, M Hofte, SE Jensen, J Ju, L Katz, L Kaysser, JL Klassen, NP Keller, J Kormanec, OP Kuipers, T Kuzuyama, NC Kyrpides, HJ Kwon, S Lautru, R Lavigne, CY Lee, B Linquan, X Liu, W Liu, A Luzhetskyy, T Mahmud, Y Mast, C Mendez, M Metsa-Ketela, J Micklefield, DA Mitchell, BS Moore, LM Moreira, R Muller, BA Neilan, M Nett, J Nielsen, F O’Gara, H Oikawa, A Osbourn, MS Osburne, B Ostash, SM Payne, JL Pernodet, M Petricek, J Piel, O Ploux, JM Raaijmakers, JA Salas, EK Schmitt, B Scott, RF Seipke, B Shen, DH Sherman, K Sivonen, MJ Smanski, M Sosio, E Stegmann, RD Sussmuth, K Tahlan, CM Thomas, Y Tang, AW Truman, M Viaud, JD Walton, CT Walsh, T Weber, GP Wezel, B Wilkinson, JM Willey, W Wohlleben, GD Wright, N Ziemert, C Zhang, SB Zotchev, R Breitling, E Takano, FO Glockner; citation_volume=11; citation_issue=9; citation_publication_date=2015; citation_pages=625-631; citation_doi=10.1038/nchembio.1890; citation_id=CR30
citation_journal_title=Microbiol Mol Biol Rev; citation_title=Regulation of cellular differentiation in filamentous cyanobacteria in free-living and plant-associated symbiotic growth states; citation_author=JC Meeks, J Elhai; citation_volume=66; citation_issue=1; citation_publication_date=2002; citation_pages=94-121; citation_doi=10.1128/MMBR.66.1.94-121.2002; citation_id=CR31
citation_journal_title=Photosynth Res; citation_title=An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium; citation_author=JC Meeks, J Elhai, T Thiel, M Potts, F Larimer, J Lamerdin, P Predki, R Atlas; citation_volume=70; citation_issue=1; citation_publication_date=2001; citation_pages=85-106; citation_doi=10.1023/A:1013840025518; citation_id=CR32
citation_journal_title=Bioinformatics; citation_title=Infernal 1.0: inference of RNA alignments; citation_author=EP Nawrocki, DL Kolbe, SR Eddy; citation_volume=25; citation_issue=10; citation_publication_date=2009; citation_pages=1335-1337; citation_doi=10.1093/bioinformatics/btp157; citation_id=CR33
citation_journal_title=Nucleic Acids Res; citation_title=The SEED and the rapid annotation of microbial genomes using Subsystems Technology (RAST); citation_author=R Overbeek, R Olson, GD Pusch, GJ Olsen, JJ Davis, T Disz, RA Edwards, S Gerdes, B Parrello, M Shukla, V Vonstein, AR Wattam, F Xia, R Stevens; citation_volume=42; citation_issue=Database issue; citation_publication_date=2014; citation_pages=D206-D214; citation_doi=10.1093/nar/gkt1226; citation_id=CR34
citation_journal_title=Nucleic Acids Res; citation_title=SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB; citation_author=E Pruesse, C Quast, K Knittel, BM Fuchs, W Ludwig, J Peplies, FO Glockner; citation_volume=35; citation_issue=21; citation_publication_date=2007; citation_pages=7188-7196; citation_doi=10.1093/nar/gkm864; citation_id=CR35
citation_journal_title=Stand Genomic Sci; citation_title=Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil; citation_author=MC Rice, JM Norton, F Valois, A Bollmann, PJ Bottomley, MG Klotz, HJ Laanbroek, Y Suwa, LY Stein, L Sayavedra-Soto, T Woyke, N Shapiro, LA Goodwin, M Huntemann, A Clum, M Pillay, N Kyrpides, N Varghese, N Mikhailova, V Markowitz, K Palaniappan, N Ivanova, D Stamatis, TB Reddy, CY Ngan, C Daum; citation_volume=11; citation_publication_date=2016; citation_pages=46; citation_doi=10.1186/s40793-016-0168-4; citation_id=CR36
Rippka R, Castenholz RW, Herdman M (2015) Cyanobacteria/subsection IV. Bergey’s Man Syst Archaea Bacteria. doi:
10.1002/9781118960608.gbm00450
citation_journal_title=J Biotechnol; citation_title=Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants; citation_author=L Rosgaard, AJ Porcellinis, JH Jacobsen, NU Frigaard, Y Sakuragi; citation_volume=162; citation_issue=1; citation_publication_date=2012; citation_pages=134-147; citation_doi=10.1016/j.jbiotec.2012.05.006; citation_id=CR38
citation_journal_title=BMC Genom; citation_title=Analysis of the early heterocyst Cys-proteome in the multicellular cyanobacterium Nostoc punctiforme reveals novel insights into the division of labor within diazotrophic filaments; citation_author=G Sandh, M Ramstrom, K Stensjo; citation_volume=15; citation_publication_date=2014; citation_pages=1064; citation_doi=10.1186/1471-2164-15-1064; citation_id=CR39
citation_journal_title=Proc Natl Acad Sci USA; citation_title=Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event; citation_author=BE Schirrmeister, JM Vos, A Antonelli, HC Bagheri; citation_volume=110; citation_issue=5; citation_publication_date=2013; citation_pages=1791-1796; citation_doi=10.1073/pnas.1209927110; citation_id=CR40
citation_journal_title=Nat Biotechnol; citation_title=The expanding scope of DNA sequencing; citation_author=J Shendure, E Lieberman Aiden; citation_volume=30; citation_issue=11; citation_publication_date=2012; citation_pages=1084-1094; citation_doi=10.1038/nbt.2421; citation_id=CR41
citation_journal_title=PLoS ONE; citation_title=
Bacillus pumilus SAFR-032 genome revisited: sequence update and re-annotation; citation_author=VG Stepanov, MR Tirumalai, S Montazari, A Checinska, K Venkateswaran, GE Fox; citation_volume=11; citation_issue=6; citation_publication_date=2016; citation_pages=e0157331; citation_doi=10.1371/journal.pone.0157331; citation_id=CR42
citation_journal_title=FEMS Yeast Res; citation_title=Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function; citation_author=M Valli, NE Tatto, A Peymann, C Gruber, N Landes, H Ekker, GG Thallinger, D Mattanovich, B Gasser, AB Graf; citation_publication_date=2016; citation_id=CR43
citation_journal_title=Nucleic Acids Res; citation_title=antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters; citation_author=T Weber, K Blin, S Duddela, D Krug, HU Kim, R Bruccoleri, SY Lee, MA Fischbach, R Muller, W Wohlleben, R Breitling, E Takano, MH Medema; citation_volume=43; citation_issue=W1; citation_publication_date=2015; citation_pages=W237-W243; citation_doi=10.1093/nar/gkv437; citation_id=CR44
Whitman WB (2015) Cyanobacteria/subsection IV/subsection IV.I In: Bergey’s Man Syst Archaea Bacteria. doi:
10.1002/9781118960608.gbm00451
citation_journal_title=Proc Natl Acad Sci USA; citation_title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya; citation_author=CR Woese, O Kandler, ML Wheelis; citation_volume=87; citation_issue=12; citation_publication_date=1990; citation_pages=4576-4579; citation_doi=10.1073/pnas.87.12.4576; citation_id=CR46
citation_journal_title=Nat Rev Genet; citation_title=A beginner’s guide to eukaryotic genome annotation; citation_author=M Yandell, D Ence; citation_volume=13; citation_issue=5; citation_publication_date=2012; citation_pages=329-342; citation_doi=10.1038/nrg3174; citation_id=CR47
citation_journal_title=J Exp Bot; citation_title=Cyanobacterial-based approaches to improving photosynthesis in plants; citation_author=J Zarzycki, SD Axen, JN Kinney, CA Kerfeld; citation_volume=64; citation_issue=3; citation_publication_date=2013; citation_pages=787-798; citation_doi=10.1093/jxb/ers294; citation_id=CR48