Draft genome sequences of symbiotic and nonsymbiotic Rhizopus microsporus strains CBS 344.29 and ATCC 62417

Genome Announcements

Volumn 3, Issue 1, 2015, Pages

  Horn, Fabian ^a   Üzüm, Zerrin ^a   Möbius, Nadine ^a   Guthke, Reinhard ^a   Linde, Jörg ^a   Hertweck, Christian ^a  

^a HANS KNÖLL INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85007178923     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.01370-14     Document Type: Article

References (25)

1. Scherlach K, Graupner K, Hertweck C. 2013. Molecular bacteria-fungi interactions: effects on environment, food, and medicine. Annu Rev Microbiol 67:375-397. http://dx.doi.org/10.1146/annurev-micro-092412-155702.
2. Lackner G, Hertweck C. 2011. Impact of endofungal bacteria on infection biology, food safety, and drug development. PLoS Pathog 7:e1002096. http://dx.doi.org/10.1371/journal.ppat.1002096.
3. Partida-Martinez LP, Hertweck C. 2005. Pathogenic fungus harbours endosymbiotic bacteria for toxin production. Nature 437:884-888. http://dx.doi.org/10.1038/nature03997.
4. Partida-Martinez LP, Groth I, Roth M, Schmitt I, Buder K, Hertweck C. 2007. Burkholderia rhizoxinica and Burkholderia endofungorum, bacterial endosymbionts of the rice pathogenic fungus Rhizopus microsporus. Int J Syst Evol Microbiol 57:2583-2590. http://dx.doi.org/10.1099/i j s. 0. 6 4 6 6 0-0.
5. Scherlach K, Partida-Martinez LP, Dahse HM, Hertweck C. 2006. Antimitotic rhizoxin derivatives from a cultured bacterial endosymbiont of the rice pathogenic fungus Rhizopus microsporus. J Am Chem Soc 128: 11529-11536. http://dx.doi.org/10.1021/ja062953o.
6. Scherlach K, Busch B, Lackner G, Paszkowski U, Hertweck C. 2012. Symbiotic cooperation in the biosynthesis of a phytotoxin. Angew Chem Int Ed Engl 51:9615-9618. http://dx.doi.org/10.1002/anie.201204540.
7. Partida-Martinez LP, Hertweck C. 2007. A gene cluster encoding rhizoxin biosynthesis in Burkholderia rhizoxina, the bacterial endosymbiont of the fungus Rhizopus microsporus. ChemBioChem 8:41-45. http://dx.doi.org/10.1002/cbic.200600393.
8. Partida-Martinez LP, Monajembashi S, Greulich KO, Hertweck C. 2007 Endosymbiont-dependent host reproduction maintains bacterialfungal mutualism. Curr Biol 17:773-777. http://dx.doi.org/10.1016/j.cub.2007.03.039.
9. Lackner G, Moebius N, Partida-Martinez LP, Boland S, Hertweck C. 2011 Evolution of an endofungal lifestyle: deductions from the Burkholderia rhizoxinica genome. BMC Genomics 12:210. http://dx.doi.org/10.1186/1471-2164-12-210.
10. Leone MR, Lackner G, Silipo A, Lanzetta R, Molinaro A, Hertweck C. 2010 An unusual galactofuranose lipopolysaccharide warrants intracellular survival of toxin-producing bacteria in their fungal host. Angew Chem Int Ed Engl 49:7476-7480. http://dx.doi.org/10.1002/anie.201003301.
11. Lackner G, Moebius N, Hertweck C. 2011. Endofungal bacterium controls its host by an hrp type III secretion system. ISME J 5:252-261. http://dx.doi.org/10.1038/ismej.2010.126.
12. Moebius N, Üzüm Z, Dijksterhuis J, Lackner G, Hertweck C. 2014. Active invasion of bacteria into living fungal cells. Elife 3:e03007. http://dx.doi.org/10.7554/eLife.03007.
13. Lackner G, Möbius N, Scherlach K, Partida-Martinez LP, Winkler R, Schmitt I, Hertweck C. 2009. Global distribution and evolution of a toxinogenic Burkholderia-Rhizopus symbiosis. Appl Environ Microbiol 75:2982-2986. http://dx.doi.org/10.1128/AEM.01765-08.
14. Liu Y, Schröder J, Schmidt B. 2013. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics 29:308-315. http://dx.doi.org/10.1093/bioinformatics/bts690.
15. Crusoe MR, Edvenson G, Fish J, Howe A, McDonald E, Nahum J, Nanlohy K, Ortiz-Zuazaga H, Pell J, Simpson J, Scott C, Srinivasan RR, Zhang Q, Brown CT. 2014. The Khmer software package: enabling efficient sequence analysis. figshare http://dx.doi.org/10.6084/m9.figshare.979190.
16. Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad SciUSA108:1513-1518. http://dx.doi.org/10.1073/pnas.1017351108.
17. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 27:18. http://dx.doi.org/10.1186/2047-217X-1-18.
18. Schmieder R, Lim YW, Edwards R. 2012. Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinformatics 28: 433-435. http://dx.doi.org/10.1093/bioinformatics/btr669.
19. Linde J, Schwartze V, Binder U, Lass-Flörl C, Voigt K, Horn F. 2014. De novo whole-genome sequence and genome annotation of Lichtheimia ramosa. Genome Announc 2:e00888-14. http://dx.doi.org/10.1128/genomeA.00888-14.
20. Linde J, Duggan S, Weber M, Horn F, Sieber P, Hellwig D, Riege K, Marz M, Martin R, Guthke R, Kurzai O. Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res [Epub ahead of print.] http://dx.doi.org/10.1093/nar/gku1357.
21. Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511-515. http://dx.doi.org/10.1038/nbt.1621.
22. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29:644-652. http://dx.doi.org/10.1038/nbt.1883.
23. Gilbert D. 2013. Gene-omes built from mRNA-seq not genome DNA: simple, quick, accurate, less cost, more complete gene sets. Indiana University, Bloomington, IN. http://arthropods.eugenes.org/EvidentialGene/about/EvigeneRNA2013poster.pdf.
24. Parra G, Bradnam K, Korf I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061-1067. http://dx.doi.org/10.1093/bioinformatics/btm071.
25. Priebe S, Kreisel C, Horn F, Guthke R, Linde J. 2014. FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics [Epub ahead of print.] http://dx.doi.org/10.1093/bioinformatics/btu627.