BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan P.; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Patrick; Schuster, Stephan C.

doi:10.1093/bioinformatics/bti091

Cited by 32 publications

(27 citation statements)

References 21 publications

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“…Sequence assembly was performed by using the PHRAP assembly tool (http://www.phrap.org). The CONSED/AUTOFINISH software package 35,36 , supplemented by the in-house tool BACCardI 37 , was used for the finishing of the genome sequence.…”

Section: Methodsmentioning

confidence: 99%

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

et al. 2006

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Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.Endophytic bacteria reside within the living tissue of plants without substantively harming them. They are of high interest for agrobiotechnological applications, such as the improvement of plant growth and health, phytoremediation 1 or even as biofertilizer 2 . Supply of nitrogen derived from fixation of atmospheric N 2 by grass endophytes, such as Gluconacetobacter diazotrophicus and Azoarcus sp. strain BH72, which has been shown to occur in sugarcane 3 and Kallar grass 2 , is a process of potential agronomical and ecological importance.Although the lifestyle of these endophytes is relatively well documented, the molecular mechanisms by which they interact beneficially with plants have only been poorly elucidated. A combination of features makes Azoarcus sp. strain BH72 an excellent model grassendophyte 4 . (i) It supplies nitrogen derived from N 2 fixation to its host, Kallar grass (Leptochloa fusca (L.) Kunth); in planta it is usually not culturable, but can be detected by culture-independent methods based on nifH-encoding nitrogenase reductase, the key enzyme for N 2 fixation 2 . (ii) It colonizes nondiseased plants in remarkably high numbers: estimates range from 10 8 cells (culturable cells per gram root dry weight (RDW) of field-grown Kallar grass 5 ) to 10 10 cells (estimated on the basis of abundance of bacterial nifH-mRNA in roots) 2 . (iii) It is the only cultured grass endophyte shown by molecular methods to be the most actively N 2 -fixing bacterium of the natural population in roots 2 . (iv) It also colonizes the roots of rice, a cereal of global importance, in high numbers (10 9 cells per g RDW) in the laboratory, and spreads systemically into shoots 6 . Plant stress response is only very limited in a compatible, that is, well-colonized rice cultivar 7 . Notably, Azoarcus sp. strain BH72 is capable of endophytic N 2 -fixation inside the roots of rice 8 .For a wider application in agriculture, more knowledge is required on mechanisms o...

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Section: Methodsmentioning

confidence: 99%

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

et al. 2006

View full text Add to dashboard Cite

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“…Sequence assembly was performed by using the PHRAP assembly tool (http://www.phrap.org). The CONSED/AUTOFINISH software package 36,37 , supplemented by the in-house tool BACCardI 38 , was used for the finishing of the genome sequence.…”

Section: Methodsmentioning

confidence: 99%

“…Repetitive elements, that is, rRNA operons, were sequenced completely by primer walking on BACs and, in some cases, on shotgun clones. For assembly validation, BAC end sequences were mapped onto the genome sequence using the BACCardI tool 38 .…”

Section: Methodsmentioning

confidence: 99%

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

et al. 2006

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Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. A. borkumensis SK2 has a streamlined genome with a paucity of mobile genetic elements and energy generation–related genes, but with a plethora of genes accounting for its wide hydrocarbon substrate range and efficient oil-degradation capabilities. The genome further specifies systems for scavenging of nutrients, particularly organic and inorganic nitrogen and oligo-elements, biofilm formation at the oil-water interface, biosurfactant production and niche-specific stress responses. The unique combination of these features provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills. Supplementary information The online version of this article (doi:10.1038/nbt1232) contains supplementary material, which is available to authorized users.

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“…Sequence assembly was performed using the PHRAP assembly tool (http://www.phrap.org/). Genome finishing was accomplished using the CONSED/AUTOFINISH software package 41 , supplemented by the in-house tool BACCardI 42 . A fosmid library was constructed to perform gap closure and assembly validation by the Max Plank Institute (MPI) for Developmental Biology using the EpiFOS Fosmid Library Production Kit (Epicentre).…”

Section: Methodsmentioning

confidence: 99%

“…Repetitive elements, such as rRNA operons, were sequenced completely by primer walking on fosmid clones. To validate the assembly, we mapped fosmid end sequences onto the genome sequence by employing the BACCardI software 42 .…”

Section: Methodsmentioning

confidence: 99%

Complete genome sequence of the myxobacterium Sorangium cellulosum

et al. 2007

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The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism. Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry.Natural products and their derivatives provide the basis for medicines targeting a wide range of human diseases. The Gram-negative myxobacteria, members of the d-subgroup of proteobacteria, are an important source of novel classes of secondary metabolites 1 . Of these, the genus Sorangium is particularly valuable, as 46% of metabolites isolated from myxobacteria 1 , including the potent antitumor compound epothilone 2 , derive from this group. The majority of myxobacterial metabolites are polyketides, nonribosomal polypeptides or hybrids of the two structures, many of which are synthesized on gigantic molecular assembly lines composed of polyketide synthase (PKS) and nonribosomal polypeptide synthetase (NRPS) multienzymes 3 . Sorangium strains exhibit additional characteristic features, including 'social behavior' , cell movement by gliding, biofilm formation and morphological differentiation culminating in complex multicellular structures called fruiting bodies 4 . Three myxobacterial suborders are known 5 and the availability of the genome sequence of Myxococcus xanthus (Cystobacterineae) 6 enables comparative analysis with the Sorangium cellulosum (Sorangiineae) genome to illuminate the basis for several important behavioral and metabolic differences. These include the ability of Sorangium strains to degrade complex plant materials (Fig. 1). S. cellulosum So ce56, an obligate aerobe, was established previously as a model Sorangium strain 7 by virtue of its favorable growth characteristics and ability to differentiate reproducibly under laboratory conditions. It synthesizes the cytotoxic chivosazoles 7 and the catecholate-type siderophores myxochelins 8 . Comparison of the complete genome sequence of strain S. cellulosum

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BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

Abstract: Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

Cited by 32 publications

References 21 publications

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Complete genome sequence of the myxobacterium Sorangium cellulosum

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