Editorial : Curriculum Applications in Microbiology: Bioinformatics in the Classroom

We would like to thank all of the authors who submitted to this special topic, committed to the furthering of academic creativity, excellence, and rigor in the challenging and virtual instructional world of SARS-CoV-2 (COVID-19). To you and all of our educators globally, you are indispensable.Non peer reviewedPublisher PD

Optical mapping as a routine tool for bacterial genome sequence finishing

Background: In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila. Results: Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished. Conclusion: Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points

Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies’ publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010’s top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century [1]. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question [1–12] in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences [13–16]. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [ www.pkal.org])

Optical mapping as a routine tool for bacterial genome sequence finishing-0

<p><b>Copyright information:</b></p><p>Taken from "Optical mapping as a routine tool for bacterial genome sequence finishing"</p><p>http://www.biomedcentral.com/1471-2164/8/321</p><p>BMC Genomics 2007;8():321-321.</p><p>Published online 14 Sep 2007</p><p>PMCID:PMC2045679.</p><p></p>ent, red regions indicate sequence that is present on at least two contigs, and yellow regions indicate inversions. Lines between maps indicate the position of identical sequences on the two maps, and can be used to visually identify misassemblies and inversions. : An early comparison of an optical map derived from digestion of the genome to the assembled contigs generated by traditional sequencing technologies. All contigs could be ordered for gap closure. In addition, the optical map indicated an overlooked misassembly. : The finishing strategy, including gap closure and misassembly resolution, was simplified using the optical map as an assembly model. The optical map derived from an digestion of the chromosome is presented as a single contig in the center. The sequenced genome contains nine contigs that have a corresponding match to the optical map. The plasmid is 158 Kb and is too small to be identified using the current optical map technology. Nonetheless, small sections of the plasmid can be identified as regions that do not have corresponding optical map locations (white in figure). : Comparison of the final assembly of the genome (bottom) to the optical map (top) for the digest. The non-aligned contig represents the plasmid, which was generated by traditional sequencing technologies. : Comparison of the finished sequence of to the optical map revealed a large inverted region of the genome. The red regions indicate regions of repeats within the genome that cannot be resolved by optical mapping. These regions were resolved using traditional sequencing methods. The sequenced genome was easily re-oriented to correct the assembly

Genome Sequence of Azotobacter vinelandii , an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes

Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. In response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. Here we report the complete genome sequence of A. vinelandii DJ, which has a single circular genome of 5,365,318 bp. In order to reconcile an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes, A. vinelandii is specialized in terms of its complement of respiratory proteins. It is able to produce alginate, a polymer that further protects the organism from excess exogenous oxygen, and it has multiple duplications of alginate modification genes, which may alter alginate composition in response to oxygen availability. The genome analysis identified the chromosomal locations of the genes coding for the three known oxygen-sensitive nitrogenases, as well as genes coding for other oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and formate dehydrogenase. These findings offer new prospects for the wider application of A. vinelandii as a host for the production and characterization of oxygen-sensitive proteins.Fil: Setubal, João C.. Virginia Polytechnic Institute; Estados UnidosFil: Dos Santos, Patricia Carolina. Wake Forest University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario; ArgentinaFil: Goldman, Barry S.. Monsanto Company; Estados UnidosFil: Ertesvag, Helga. Norwegian University of Science and Technology; NoruegaFil: Espin, Guadelupe. Universidad Nacional Autónoma de México; MéxicoFil: Rubio, Luis M.. Instituto Imdea Energia; EspañaFil: Valla, Svein. Norwegian University of Science and Technology; NoruegaFil: Almeida, Nalvo F.. Virginia Polytechnic Institute; Estados Unidos. Universidade Federal do Mato Grosso do Sul; BrasilFil: Balasubramanian, Divya. Hiram College; Estados UnidosFil: Cromes, Lindsey. Hiram College; Estados UnidosFil: Curatti, Leonardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario; Argentina. Fundación para Investigaciones Biológicas Aplicadas. Centro de Estudios de Biodiversidad y Biotecnología; ArgentinaFil: Du, Zijin. Monsanto Company; Estados UnidosFil: Godsy, Eric. Monsanto Company; Estados UnidosFil: Goodner, Brad. Hiram College; Estados UnidosFil: Hellner Burris, Kaitlyn. Hiram College; Estados UnidosFil: Hernandez, José A.. Midwestern University; Estados UnidosFil: Houmiel, Katherine. Seattle Pacific University; Estados UnidosFil: Imperial, Juan. Centro de Biotecnologia y Genomica de Plantas; EspañaFil: Kennedy, Christina. University of Arizona; Estados UnidosFil: Larson, Timothy J.. Virginia Polytechnic Institute; Estados UnidosFil: Latreille, Phil. Monsanto Company; Estados UnidosFil: Ligon, Lauren S.. Virginia Polytechnic Institute; Estados UnidosFil: Lu, Jing. Monsanto Company; Estados UnidosFil: Mærk, Mali. Norwegian University of Science and Technology; NoruegaFil: Miller, Nancy M.. Monsanto Company; Estados UnidosFil: Norton, Stacie. Monsanto Company; Estados UnidosFil: O'Carroll, Ina P.. Virginia Polytechnic Institute; Estados UnidosFil: Paulsen, Ian. Macquarie University; AustraliaFil: Raulfs, Estella C.. Virginia Polytechnic Institute; Estados UnidosFil: Roemer, Rebecca. Hiram College; Estados Unido