CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Genomic mechanisms for cold tolerance and production of exopolysaccharides in the Arctic cyanobacterium Phormidesmis priestleyi BC1401

BACKGROUND

Cyanobacteria are major primary producers in extreme cold ecosystems. Many lineages of cyanobacteria thrive in these harsh environments, but it is not fully understood how they survive in these conditions and whether they have evolved specific mechanisms of cold adaptation. Phormidesmis priestleyi is a cyanobacterium found throughout the cold biosphere (Arctic, Antarctic and alpine habitats). Genome sequencing of P. priestleyi BC1401, an isolate from a cryoconite hole on the Greenland Ice Sheet, has allowed for the examination of genes involved in cold shock response and production of extracellular polymeric substances (EPS). EPSs likely enable cyanobacteria to buffer the effects of extreme cold and by identifying mechanisms for EPS production in P. priestleyi BC1401 this study lays the way for investigating transcription and regulation of EPS production in an ecologically important cold tolerant cyanobacterium.

RESULTS

We sequenced the draft genome of P. priestleyi BC1401 and implemented a new de Bruijn graph visualisation approach combined with BLAST analysis to separate cyanobacterial contigs from a simple metagenome generated from non-axenic cultures. Comparison of known cold adaptation genes in P. priestleyi BC1401 with three relatives from other environments revealed no clear differences between lineages. Genes involved in EPS biosynthesis were identified from the Wzy- and ABC-dependent pathways. The numbers of genes involved in cell wall and membrane biogenesis in P. priestleyi BC1401 were typical relative to the genome size. A gene cluster implicated in biofilm formation was found homologous to the Wps system, although the intracellular signalling pathways by which this could be regulated remain unclear.

CONCLUSIONS

Results show that the genomic characteristics and complement of known cold shock genes in P. priestleyi BC1401 are comparable to related lineages from a wide variety of habitats, although as yet uncharacterised cold shock genes in this organism may still exist. EPS production by P. priestleyi BC1401 likely contributes to its ability to survive efficiently in cold environments, yet this mechanism is widely distributed throughout the cyanobacterial phylum. Discovering how these EPS related mechanisms are regulated may help explain why P. priestleyi BC1401 is so successful in cold environments where related lineages are not.

Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata

We announce a draft genome sequence of a Proteus mirabilis strain derived from Lucilia sericata salivary glands. This strain is demonstrated to attract and induce oviposition by L. sericata, a common blow fly important to medicine, agriculture, and forensics. The genome sequence will help dissect interkingdom communication between the species.

Complete genome sequence of Streptococcus agalactiae strain GBS85147 serotype of type Ia isolated from human oropharynx

Streptococcus agalactiae, also referred to as Group B Streptococcus, is a frequent resident of the rectovaginal tract in humans, and a major cause of neonatal infection. The pathogen can also infect adults with underlying disease, particularly the elderly and immunocompromised ones. In addition, S. agalactiae is a known fish pathogen, which compromises food safety and represents a zoonotic hazard. This study provides valuable structural, functional and evolutionary genomic information of a human S. agalactiae serotype Ia (ST-103) GBS85147 strain isolated from the oropharynx of an adult patient from Rio de Janeiro, thereby representing the first human isolate in Brazil. We used the Ion Torrent PGM platform with the 200 bp fragment library sequencing kit. The sequencing generated 578,082,183 bp, distributed among 2,973,022 reads, resulting in an approximately 246-fold mean coverage depth and was assembled using the Mira Assembler v3.9.18. The S. agalactiae strain GBS85147 comprises of a circular chromosome with a final genome length of 1,996,151 bp containing 1,915 protein-coding genes, 18 rRNA, 63 tRNA, 2 pseudogenes and a G + C content of 35.48 %.

Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology

A wide variety of genome sequencing platforms have emerged in the recent past. High-throughput platforms like Illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. To reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. The contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using a combination of the two approaches. While the reference-based approach appears to mask strain-specific information, scaffolding based on paired-end information suffers when repetitive elements longer than the size of the sequencing reads are present in the genome. Sequencing technologies that produce long reads can solve the problems associated with repetitive elements but are not necessarily easily available to researchers. The most common high-throughput technology currently used is the Illumina short read platform. To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.

Genome Sequences of 12 Spore-Forming Bacillus Species, Comprising Bacillus coagulans, Bacillus licheniformis, Bacillus amyloliquefaciens, Bacillus sporothermodurans, and Bacillus vallismortis, Isolated from Foods

Here, we report the draft genomes of twelve isolates of five different Bacillus species, all spore-forming, Gram-positive bacteria.

Draft Genome Sequences of Seven Thermophilic Spore-Forming Bacteria Isolated from Foods That Produce Highly Heat-Resistant Spores, Comprising Geobacillus spp., Caldibacillus debilis, and Anoxybacillus flavithermus

Here, we report the draft genomes of five strains of Geobacillus spp., one Caldibacillus debilis strain, and one draft genome of Anoxybacillus flavithermus, all thermophilic spore-forming Gram-positive bacteria.

Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002

Background

Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements.

Results

In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions.

Conclusion

In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2673-7) contains supplementary material, which is available to authorized users.

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics of appearance or responsiveness to medical treatments. Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. However, the public reference genome was derived with the DNA from multiple individuals. As a result of this, the reference genome is incomplete and may misrepresent the sequence variants of the general population. The more reliable solution is to compare sequences of diseased tissue with its own genome sequence derived from tissue in a normal state. As the price to sequence the human genome has dropped dramatically to around $1000, it shows a promising future of documenting the personal genome for every individual. However, de novo assembly of individual genomes at an affordable cost is still challenging. Thus, till now, only a few human genomes have been fully assembled. In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging "third generation sequencing" technologies. We present the currently available de novo assembly and post-assembly software packages for human genome assembly and their requirements for computational infrastructures. We recommend that a combined hybrid assembly with long and short reads would be a promising way to generate good quality human genome assemblies and specify parameters for the quality assessment of assembly outcomes. We provide a perspective view of the benefit of using personal genomes as references and suggestions for obtaining a quality personal genome. Finally, we discuss the usage of the personal genome in aiding vaccine design and development, monitoring host immune-response, tailoring drug therapy and detecting tumors. We believe the precision medicine would largely benefit from bioinformatics solutions, particularly for personal genome assembly.

Complete genome sequences of Francisella noatunensis subsp. orientalis strains FNO12, FNO24 and FNO190: a fish pathogen with genomic clonal behavior

The genus Francisella is composed of Gram-negative, pleomorphic, strictly aerobic and non-motile bacteria, which are capable of infecting a variety of terrestrial and aquatic animals, among which Francisella noatunensis subsp. orientalis stands out as the causative agent of pyogranulomatous and granulomatous infections in fish. Accordingly, F. noatunensis subsp. orientalis is responsible for high mortality rates in freshwater fish, especially Nile Tilapia. In the current study, we present the genome sequences of F. noatunensis subsp. orientalis strains FNO12, FNO24 and FNO190. The genomes include one circular chromosome of 1,859,720 bp, consisting of 32 % GC content, 1538 coded proteins and 363 pseudogenes for FNO12; one circular chromosome of 1,862,322 bp, consisting of 32 % GC content, 1537 coded proteins and 365 pseudogenes for FNO24; and one circular chromosome of 1,859,595 bp, consisting of 32 % GC content, 1539 coded proteins and 362 pseudogenes for FNO190. All genomes have similar genetic content, implicating a clonal-like behavior for this species.

The genome anatomy of Corynebacterium pseudotuberculosis VD57 a highly virulent strain causing Caseous lymphadenitis

Corynebacterium pseudotuberculosis strain VD57 (Cp_VD57), a highly virulent, nonmotile, non-sporulating, and a mesophilic bacterium, was isolated from a goat’s granulomatous lesion in the municipality of Juazeiro, Bahia State, Brazil. Here, we describe a set of features of the strain, together with the details of its complete genome sequence and annotation. The genome comprises of a 2.5 Mbp long, single circular genome with 2,101 protein-coding genes, 12 rRNA, 49 tRNA and 47 pseudogenes and a G + C content of 52.85 %. Genetic variation was detected in Cp_VD57 using C. pseudotuberculosis strain 1002 as reference, wherein small genomic insertions and deletions were identified. The comparative analysis of the genome sequence provides means to better understand the host pathogen interactions of this strain and can also help us to understand the molecular and genetic basis of virulence of this bacterium.

Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits

Acidovorax citrulli is a seedborne bacterium that causes bacterial fruit blotch of cucurbit plants including watermelon and melon. A. citrulli strains can be divided into two major groups based on DNA fingerprint analyses and biochemical properties. Group I strains have been generally isolated from non-watermelon cucurbits, while group II strains are closely associated with watermelon. In the present study, we report the genome sequence of M6, a group I model A. citrulli strain, isolated from melon. We used comparative genome analysis to investigate differences between the genome of strain M6 and the genome of the group II model strain AAC00-1. The draft genome sequence of A. citrulli M6 harbors 139 contigs, with an overall approximate size of 4.85 Mb. The genome of M6 is ∼500 Kb shorter than that of strain AAC00-1. Comparative analysis revealed that this size difference is mainly explained by eight fragments, ranging from ∼35-120 Kb and distributed throughout the AAC00-1 genome, which are absent in the M6 genome. In agreement with this finding, while AAC00-1 was found to possess 532 open reading frames (ORFs) that are absent in strain M6, only 123 ORFs in M6 were absent in AAC00-1. Most of these M6 ORFs are hypothetical proteins and most of them were also detected in two group I strains that were recently sequenced, tw6 and pslb65. Further analyses by PCR assays and coverage analyses with other A. citrulli strains support the notion that some of these fragments or significant portions of them are discriminative between groups I and II strains of A. citrulli. Moreover, GC content, effective number of codon values and cluster of orthologs' analyses indicate that these fragments were introduced into group II strains by horizontal gene transfer events. Our study reports the genome sequence of a model group I strain of A. citrulli, one of the most important pathogens of cucurbits. It also provides the first comprehensive comparison at the genomic level between the two major groups of strains of this pathogen.

Complete genome sequence of Peptoclostridium difficile strain Z31

BACKGROUND

Peptoclostridium (Clostridium) difficile is a spore-forming bacterium responsible for nosocomial infections in humans. It is recognized as an important agent of diarrhea and colitis in several animal species and a possible zoonotic agent. Despite the known importance of P. difficile infection in humans and animals, no vaccine or other effective measure to control the disease is commercially available. A possible alternative treatment for P. difficile infection is the use of a nontoxigenic strain of P. difficile as a competitive exclusion agent. However, a thorough knowledge of this strain is necessary for this purpose. We selected P. difficile Z31, a nontoxigenic strain (PCR ribotype 009), for investigation because it prevents P. difficile infection in a hamster model.

RESULTS

The genome sequence of P. difficile Z31 is a circular chromosome of 4298,263 bp, with a 29.21 % GC content, encoding 4128 proteins, and containing 78 pseudogenes. This strain belongs to ST 3, clade 1, and has five phage regions in its genome. Genes responsible for resistance to tetracycline and erythromycin were detected and more importantly, Z31 also contains genes that promote spore production and stability, cell attachment, intestinal adherence, and biofilm formation.

CONCLUSION

In this study, we present the first complete genome sequence of nontoxigenic P. difficile strain Z31. When the Z31 genome was compared with those of other isolates available in GenBank, including a draft genome of a nontoxigenic strain, several unique regions were evident. Z31 contains no toxin genes, but encodes several non-toxin virulence factors, which may favor host colonization.

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus

Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its microbiota. Our data suggest the presence of a sponge-specific lineage of Pseudovibrio. The reduction in genome size and the loss of some systems potentially used to successfully enter the host, leads to the hypothesis that P. axinellae strain AD2 may be a lineage that presents an ancient association with the host and that may be vertically transmitted to the progeny.

Draft Genome Sequence of "Halomonas chromatireducens" Strain AGD 8-3, a Haloalkaliphilic Chromate- and Selenite-Reducing Gammaproteobacterium

Here, we report the complete genome sequence (3.97 Mb) of "Halomonas chromatireducens" AGD 8-3, a denitrifying bacterium capable of chromate and selenite reduction under extreme haloalkaline conditions. This strain was isolated from soda solonchak soils of the Kulunda steppe, Russian Federation.

Draft Genome Sequences of 10 Bacillus subtilis Strains That Form Spores with High or Low Heat Resistance

Here, we report the draft genome sequences of 10 isolates of Bacillus subtilis, a spore forming Gram-positive bacterium. The strains were selected from food products and produced spores with either high or low heat resistance.

Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome

Sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and contain metabolic versatility that enables reduction of a wide range of electron acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and nitrite. Here we describe the assembly of a Sulfurospirillum genome obtained from the metagenome of an electrosynthetic microbiome. The ubiquity and persistence of this organism in microbial electrosynthesis systems suggest it plays an important role in reactor stability and performance. Understanding why this organism is present and elucidating its genetic repertoire provide a genomic and ecological foundation for future studies where Sulfurospirillum are found, especially in electrode-associated communities. Metabolic comparisons and in-depth analysis of unique genes revealed potential ecological niche-specific capabilities within the Sulfurospirillum genus. The functional similarities common to all genomes, i.e., core genome, and unique gene clusters found only in a single genome were identified. Based upon 16S rRNA gene phylogenetic analysis and average nucleotide identity, the Sulfurospirillum draft genome was found to be most closely related to Sulfurospirillum cavolei. Characterization of the draft genome described herein provides pathway-specific details of the metabolic significance of the newly described Sulfurospirillum cavolei MES and, importantly, yields insight to the ecology of the genus as a whole. Comparison of eleven sequenced Sulfurospirillum genomes revealed a total of 6246 gene clusters in the pan-genome. Of the total gene clusters, 18.5% were shared among all eleven genomes and 50% were unique to a single genome. While most Sulfurospirillum spp. reduce nitrate to ammonium, five of the eleven Sulfurospirillum strains encode for a nitrous oxide reductase (nos) cluster with an atypical nitrous-oxide reductase, suggesting a utility for this genus in reduction of the nitrous oxide, and as a potential sink for this potent greenhouse gas.

Draft Genome Sequence of Acinetobacter baumannii IITR88, a Bacterium Degrading Indoles and Other Aromatic Compounds

Here, we report the 4.16-Mb draft genome sequence of an indole-degrading bacterium, Acinetobacter baumannii IITR88, isolated from the Bhagirathi river in India. A total of 4,069 coding regions (CDSs), 3 rRNAs, and 52 tRNAs were predicted. Genes for the degradation of indoles, phenylacetaldehyde, anthranilate, and several other aromatic compounds were present.

Genome Sequence of a Gram-Positive Diazotroph, Paenibacillus durus Type Strain ATCC 35681

Here, we report the complete genome sequence of Paenibacillus durus type strain ATCC 35681, which can fix atmospheric nitrogen even in the presence of nitrate.

Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1

We present the complete genome sequence of Corynebacterium pseudotuberculosis strain N1. The sequencing was performed with the Ion Torrent Personal Genome Machine system. The genome is a circular chromosome with 2,337,845 bp, a G+C content of 52.85%, and a total of 2,045 coding sequences, 12 rRNAs, 49 tRNAs, and 58 pseudogenes.

Whole-Genome Sequence of Francisella noatunensis subsp. orientalis Strain FNO01 Isolated from Diseased Nile Tilapia in Brazil

This paper describes the complete genome sequence of Francisella noatunensis subsp. orientalis strain FNO01, which was isolated during the first outbreak of francisellosis in cultured Nile tilapia in Brazil. The genome is composed of a circular chromosome with 1,859,830 bp and a G+C content of ~32%.

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida

BACKGROUND

Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date.

RESULTS

We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy.

CONCLUSION

Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.

The Complete Sequence and Comparative Analysis of a Multidrug-Resistance and Virulence Multireplicon IncFII Plasmid pEC302/04 from an Extraintestinal Pathogenic Escherichia coli EC302/04 Indicate Extensive Diversity of IncFII Plasmids

Extraintestinal pathogenic Escherichia coli (ExPEC) that causes extraintestinal infections often harbor plasmids encoding fitness traits such as resistance and virulence determinants that are of clinical importance. We determined the complete nucleotide sequence of plasmid pEC302/04 from a multidrug-resistant E. coli EC302/04 which was isolated from the tracheal aspirate of a patient in Malaysia. In addition, we also performed comparative sequence analyses of 18 related IncFIIA plasmids to determine the phylogenetic relationship and diversity of these plasmids. The 140,232 bp pEC302/04 is a multireplicon plasmid that bears three replication systems (FII, FIA, and FIB) with subtype of F2:A1:B1. The plasmid is self-transmissible with a complete transfer region. pEC302/04 also carries antibiotic resistance genes such as bla_TEM−1 and a class I integron containing sul1, cml and aadA resistance genes, conferring multidrug resistance (MDR) to its host, E. coli EC302/04. Besides, two iron acquisition systems (SitABCD and IutA-IucABCD) which are the conserved virulence determinants of ExPEC-colicin V or B and M (ColV/ColBM)-producing plasmids were identified in pEC302/04. Multiple toxin-antitoxin (TA)-based addiction systems (i.e., PemI/PemK, VagC/VagD, CcdA/CcdB, and Hok/Sok) and a plasmid partitioning system, ParAB, and PsiAB, which are important for plasmid maintenance were also found. Comparative plasmid analysis revealed only one conserved gene, the repA1 as the core genome, showing that there is an extensive diversity among the IncFIIA plasmids. The phylogenetic relationship of 18 IncF plasmids based on the core regions revealed that ColV/ColBM-plasmids and non-ColV/ColBM plasmids were separated into two distinct groups. These plasmids, which carry highly diverse genetic contents, are also mosaic in nature. The atypical combination of genetic materials, i.e., the MDR- and ColV/ColBM-plasmid-virulence encoding regions in a single ExPEC plasmid is rare but of clinical importance. Such phenomenon is bothersome when the plasmids are transmissible, facilitating the spread of virulence and resistance plasmids among pathogenic bacteria. Notably, certain TA systems are more commonly found in particular ExPEC plasmid types, indicating the possible relationships between certain TA systems and ExPEC pathogenesis.

Investigation of a suspected nosocomial transmission of blaKPC3-mediated carbapenem-resistant Klebsiella pneumoniae by whole genome sequencing

Whole genome sequencing (WGS) was compared to pulse-field gel electrophoresis (PFGE) of XbaI-digested genomic DNA, as methods by which to evaluate a potential transmission of carbapenem-resistant Klebsiella pneumoniae between 2 hospital inpatients. PFGE result demonstrated only 1-band difference between the isolates, suggesting probable relatedness. In contrast, while WGS data demonstrated the same sequence type and very similar chromosomal sequences, over 20 single nucleotide variants were identified between the isolates, bringing into question whether there was a transmission event. WGS also identified an additional plasmid, with an XbaI restriction site in the isolates of the second patient that was not identified by PFGE. While WGS provided additional information that was not available by PFGE, in this study, neither method could definitively conclude the relatedness between the isolates.

Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout

Background

The genus Weissella belongs to the lactic acid bacteria and includes 18 currently identified species, predominantly isolated from fermented food but rarely from cases of bacteremia in animals. Recently, a new species, designated Weissella ceti, has been correlated with hemorrhagic illness in farm-raised rainbow trout in China, Brazil, and the USA, with high transmission and mortality rates during outbreaks. Although W. ceti is an important emerging veterinary pathogen, little is known about its genomic features or virulence mechanisms. To better understand these and to characterize the species, we have previously sequenced the genomes of W. ceti strains WS08, WS74, and WS105, isolated from different rainbow trout farms in Brazil and displaying different pulsed-field gel electrophoresis patterns. Here, we present a comparative analysis of the three previously sequenced genomes of W. ceti strains from Brazil along with W. ceti NC36 from the USA and those of other Weissella species.

Results

Phylogenomic and orthology-based analyses both showed a high-similarity in the genetic structure of these W. ceti strains. This structure is corroborated by the highly syntenic order of their genes and the neutral evolution inferred from Tajima’s D. A whole-genome multilocus sequence typing analysis distinguished strains WS08 and NC36 from strains WS74 and WS105. We predicted 10 putative genomic islands (GEI), among which PAIs 3a and 3b are phage sequences that occur only in WS105 and WS74, respectively, whereas PAI 1 is species specific.

Conclusions

We identified several genes putatively involved in the basic processes of bacterial physiology and pathogenesis, including survival in aquatic environment, adherence in the host, spread inside the host, resistance to immune-system-mediated stresses, and antibiotic resistance. These data provide new insights in the molecular epidemiology and host adaptation for this emerging pathogen in aquaculture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2324-4) contains supplementary material, which is available to authorized users.

Draft Genome Sequences of Edwardsiella ictaluri Strains LADL11-100 and LADL11-194 Isolated from Zebrafish Danio rerio

Here, we report the draft genome sequences of Edwardsiella ictaluri strains LADL11-100 and LADL11-194, two isolates from natural outbreaks of edwardsiellosis in the zebrafish Danio rerio, as well as the sequences of the plasmids carried by the zebrafish strain of E. ictaluri.

Draft Genome Sequence of the Dimorphic Yeast Yarrowia lipolytica Strain W29

Here, we present the draft genome sequence of the dimorphic ascomycete yeast Yarrowia lipolytica strain W29 (ATCC 20460). Y. lipolytica is a commonly employed model for the industrial production of lipases, small molecules, and more recently for its ability to accumulate lipids.

High-Quality Draft Genome Sequence of Bacillus amyloliquefaciens Strain 629, an Endophyte from Theobroma cacao

Bacillus amyloliquefaciens strain 629 is an endophyte isolated from Theobroma cacao L. Here, we report the draft genome sequence (3.9 Mb) of B. amyloliquefaciens strain 629 containing 16 contigs (3,903,367 bp), 3,912 coding sequences, and an average 46.5% G+C content.

Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure

It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34-41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a comparative genomic approach to 1) confirm that the two species are distinct at the genomic level; 2) determine which gene groups have diverged the most and the least between species; 3) show that their overall genomic structures are similar, as predicted by the viability of hybrids, and identify genomic regions that instead are incongruent; and 4) test the previously formulated hypothesis that genes involved in pathogenicity may be less divergent between the two species than genes involved in saprobic decay and sporulation. Results based on the sequencing of three genomes per species identified a high level of interspecific similarity, but clearly confirmed the status of the two as distinct taxa. Genes involved in pathogenicity were more conserved between species than genes involved in saprobic growth and sporulation, corroborating at the genomic level that invasiveness may be determined by the two latter traits, as documented by field and inoculation studies. Additionally, the majority of genes under positive selection and the majority of genes bearing interspecific structural variations were involved either in transcriptional or in mitochondrial functions. This study provides genomic-level evidence that invasiveness of pathogenic microbes can be attained without the high levels of pathogenicity presumed to exist for pathogens challenging naïve hosts.

Complete Genome Sequence of Xanthomonas arboricola pv. juglandis 417, a Copper-Resistant Strain Isolated from Juglans regia L

Here, we report the complete genome sequence of Xanthomonas arboricola pv. juglandis 417, a copper-resistant strain isolated from a blighted walnut fruit (Juglans regia L. cv. Chandler). The genome consists of a single chromosome (5,218 kb).

Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients

The genetic disorder cystic fibrosis is a life-limiting condition affecting ∼70,000 people worldwide. Targeted, early, treatment of the dominant infecting species, Pseudomonas aeruginosa, has improved patient outcomes; however, there is concern that other species are now stepping in to take its place. In addition, the necessarily long-term antibiotic therapy received by these patients may be providing a suitable environment for the emergence of antibiotic resistance. To investigate these issues, we employed whole-genome sequencing of 28 non-Pseudomonas bacterial strains isolated from three paediatric patients. We did not find any trend of increasing antibiotic resistance (either by mutation or lateral gene transfer) in these isolates in comparison with other examples of the same species. In addition, each isolate contained a virulence gene repertoire that was similar to other examples of the relevant species. These results support the impaired clearance of the CF lung not demanding extensive virulence for survival in this habitat. By analysing serial isolates of the same species we uncovered several examples of strain persistence. The same strain of Staphylococcus aureus persisted for nearly a year, despite administration of antibiotics to which it was shown to be sensitive. This is consistent with previous studies showing antibiotic therapy to be inadequate in cystic fibrosis patients, which may also explain the lack of increasing antibiotic resistance over time. Serial isolates of two naturally multi-drug resistant organisms, Achromobacter xylosoxidans and Stenotrophomonas maltophilia, revealed that while all S. maltophilia strains were unique, A. xylosoxidans persisted for nearly five years, making this a species of particular concern. The data generated by this study will assist in developing an understanding of the non-Pseudomonas species associated with cystic fibrosis.

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF). Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in bacterial pangenomes.

The influence of transcriptional regulatory networks on the evolution of bacterial pangenomes has not yet been elucidated, even though the role of transcriptional regulation is widely recognized. Using the model symbiont Sinorhizobium meliloti we have predicted the regulatory targets of 41 transcription factors in 51 strains and 5 other rhizobial species, showing a correlation between regulon diversity and pangenome evolution, through upstream sequence diversity and accessory genome composition. We have also shown that genes not wired to the regulatory network are more likely to belong to the accessory genome, thus suggesting that inclusion in the regulatory circuits may be an indicator of gene conservation. We have also highlighted a series of transcription factors that preferentially regulate genes belonging to one of the three replicons of this species, indicating the presence of replicon-specific regulatory modules, with peculiar functional signatures. At the same time the chromid shares a significant part of the regulatory network with the chromosome, indicating an additional way by which this replicon integrates itself in the pangenome.

An efficient algorithm for the contig ordering problem under algebraic rearrangement distance

Assembling a genome from short reads currently obtained by next-generation sequencing techniques often results in a collection of contigs, whose relative position and orientation along the genome being sequenced are unknown. Given two sets of contigs, the contig ordering problem is to order and orient the contigs in each set such that the genome rearrangement distance between the resulting sets of ordered and oriented contigs is minimized. In this article, we utilize the permutation groups in algebra to propose a near-linear time algorithm for solving the contig ordering problem under algebraic rearrangement distance, where the algebraic rearrangement distance between two sets of ordered and oriented contigs is the minimum weight of applicable rearrangement operations required to transform one set into the other.

Draft Genome Sequences of Five Clinical Methicillin-Resistant Staphylococcus aureus Isolates and a Methicillin-Resistant Staphylococcus epidermidis Isolate

We report the complete draft genome sequences of five individually isolated strains of methicillin-resistant Staphylococcus aureus (MRSA) and a Staphylococcus epidermidis strain. These clinically important isolates have staphylococcal cassette chromosome mec type A, while Panton-Valentine leukocidin (PVL) toxin coding genes were present in MRSA isolates only.

Draft Genome Sequence of a Novel Nicotine-Degrading Bacterium, Pseudomonas plecoglossicida TND35

Pseudomonas plecoglossicida TND35 is a potent nicotine-degrading bacterium. The draft genome sequence of strain TND35 contains 6,209,227 bp, 5,511 coding genes, and a G+C content of 62.3%. It encompasses genes related to catabolism of nicotine, N-heterocyclic aromatic compounds, heavy metal degradation, and butanol biosynthesis.

Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 12C

We present here the complete genome sequence of Corynebacterium pseudotuberculosis strain 12C, isolated from a sheep abscess in the Brazil. The sequencing was performed with the Ion Torrent Personal Genome Machine (PGM) system, a fragment library, and a coverage of ~48-fold. The genome presented is a circular chromosome with 2,337,451 bp in length, 2,119 coding sequences, 12 rRNAs, 49 tRNAs, and a G+C content of 52.83%.

MapRepeat: an approach for effective assembly of repetitive regions in prokaryotic genomes

The newest technologies for DNA sequencing have led to the determination of the primary structure of the genomes of organisms, mainly prokaryotes, with high efficiency and at lower costs. However, the presence of regions with repetitive sequences, in addition to the short reads produced by the Next-Generation Sequencing (NGS) platforms, created a lot of difficulty in reconstructing the original genome in silico. Thus, even today, genome assembly continues to be one of the major challenges in bioinformatics specifically when repetitive sequences are considered. In this paper, we present an approach to assemble repetitive regions in prokaryotic genomes. Our methodology enables (i) the identification of these regions through visual tools, (ii) the characterization of sequences on the extremities of gaps and (iii) the extraction of consensus sequences based on mapping of raw data to a reference genome. We also present a case study on the assembly of regions that encode ribosomal RNAs (rRNA) in the genome of Corynebacterium ulcerans FRC11, in order to show the efficiency of the strategies presented here. The proposed methods and tools will help in finishing genome assemblies, besides reducing the running time and associated costs.

AVAILABILITY

All scripts are available at http://github.com/dcbmariano/maprepeat.

Pan-Genome Analysis of Brazilian Lineage A Amoebal Mimiviruses

Since the recent discovery of Samba virus, the first representative of the family Mimiviridae from Brazil, prospecting for mimiviruses has been conducted in different environmental conditions in Brazil. Recently, we isolated using Acanthamoeba sp. three new mimiviruses, all of lineage A of amoebal mimiviruses: Kroon virus from urban lake water; Amazonia virus from the Brazilian Amazon river; and Oyster virus from farmed oysters. The aims of this work were to sequence and analyze the genome of these new Brazilian mimiviruses (mimi-BR) and update the analysis of the Samba virus genome. The genomes of Samba virus, Amazonia virus and Oyster virus were 97%–99% similar, whereas Kroon virus had a low similarity (90%–91%) with other mimi-BR. A total of 3877 proteins encoded by mimi-BR were grouped into 974 orthologous clusters. In addition, we identified three new ORFans in the Kroon virus genome. Additional work is needed to expand our knowledge of the diversity of mimiviruses from Brazil, including if and why among amoebal mimiviruses those of lineage A predominate in the Brazilian environment.

Mapping contigs using CONTIGuator

Obtaining bacterial genomic sequences has become a routine task in today's biology. The emergence of the comparative genomics approach has led to an increasing number of bacterial species having more than one strain sequenced, thus facilitating the annotation process. On the other hand, many genomic sequences are now left in the "draft" status, as a series of contigs, mainly for the labor-intensive finishing task. As a result, many genomic analyses are incomplete (e.g., in their annotation) or impossible to be performed (e.g., structural genomics analysis). Many approaches have been recently developed to facilitate the finishing process or at least to produce higher quality scaffolds; taking advantage of the comparative genomics paradigm, closely related genomes are used to align the contigs and determine their relative orientation, thus facilitating the finishing process, but also producing higher quality scaffolds. In this chapter we present the use of the CONTIGuator algorithm, which aligns the contigs from a draft genome to a closely related closed genome and resolves their relative orientation based on this alignment, producing a scaffold and a series of PCR primer pairs for the finishing process. The CONTIGuator algorithm is also capable of handling multipartite genomes (i.e., genomes having chromosomes and other plasmids), univocally mapping contigs to the most similar replicon. The program also produces a series of contig maps that allow to perform structural genomics analysis on the draft genome. The functionalities of the web interface, as well as the command line version, are presented.

Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes

The marine bacterium Alteromonas macleodii is a copiotrophic r-strategist, but little is known about its potential to degrade polysaccharides. Here, we studied the degradation of alginate and other algal polysaccharides by A. macleodii strain 83-1 in comparison to other A. macleodii strains. Cell densities of strain 83-1 with alginate as sole carbon source were comparable to those with glucose, but the exponential phase was delayed. The genome of 83-1 was found to harbour an alginolytic system comprising five alginate lyases, whose expression was induced by alginate. The alginolytic system contains additional CAZymes, including two TonB-dependent receptors, and is part of a 24 kb genomic island unique to the A. macleodii 'surface clade' ecotype. In contrast, strains of the 'deep clade' ecotype contain only a single alginate lyase in a separate 7 kb island. This difference was reflected in an eightfold greater efficiency of surface clade strains to grow on alginate. Strain 83-1 furthermore hydrolysed laminarin, pullulan and xylan, and corresponding polysaccharide utilization loci were detected in the genome. Alteromonas macleodii alginate lyases were predominantly detected in Atlantic Ocean metagenomes. The demonstrated hydrolytic capacities are likely of ecological relevance and represent another level of adaptation among A. macleodii ecotypes.

Draft Genome Sequences of Five Spore-Forming Food Isolates of Bacillus pumilus

Here, we report the draft genome sequences of five food isolates of Bacillus pumilus , a spore-forming Gram-positive bacterium.

Virulence related sequences; insights provided by comparative genomics of Streptococcus uberis of differing virulence

Background

Streptococcus uberis, a Gram-positive, catalase-negative member of the family Streptococcaceae is an important environmental pathogen responsible for a significant proportion of subclinical and clinical bovine intramammary infections. Currently, the genome of only a single reference strain (0140J) has been described. Here we present a comparative analysis of complete draft genome sequences of an additional twelve S. uberis strains.

Results

Pan and core genome analysis revealed the core genome common to all strains to be 1,550 genes in 1,509 orthologous clusters, complemented by 115-246 accessory genes present in one or more S. uberis strains but absent in the reference strain 0140J. Most of the previously predicted virulent genes were present in the core genome of all 13 strains but gene gain/loss was observed between the isolates in CDS associated with clustered regularly interspaced short palindromic repeats (CRISPRs), prophage and bacteriocin production. Experimental challenge experiments confirmed strain EF20 as non-virulent; only able to infect in a transient manner that did not result in clinical mastitis. Comparison of the genome sequence of EF20 with the validated virulent strain 0140J identified genes associated with virulence, however these did not relate clearly with clinical/non-clinical status of infection.

Conclusion

The gain/loss of mobile genetic elements such as CRISPRs and prophage are a potential driving force for evolutionary change. This first “whole-genome” comparison of strains isolated from clinical vs non-clinical intramammary infections including the type virulent vs non-virulent strains did not identify simple gene gain/loss rules that readily explain, or be confidently associated with, differences in virulence. This suggests that a more complex dynamic determines infection potential and clinical outcome not simply gene content.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1512-6) contains supplementary material, which is available to authorized users.

MeDuSa: a multi-draft based scaffolder

MOTIVATION

Completing the genome sequence of an organism is an important task in comparative, functional and structural genomics. However, this remains a challenging issue from both a computational and an experimental viewpoint. Genome scaffolding (i.e. the process of ordering and orientating contigs) of de novo assemblies usually represents the first step in most genome finishing pipelines.

RESULTS

In this article we present MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries. This makes usability and running time two additional important features of our method. Moreover, benchmarks and tests on real bacterial datasets showed that MeDuSa is highly accurate and, in most cases, outperforms traditional scaffolders. The possibility to use MeDuSa on eukaryotic datasets has also been evaluated, leading to interesting results.

Genome Sequence of Corynebacterium ulcerans Strain FRC11

Here, we present the genome sequence of Corynebacterium ulcerans strain FRC11. The genome includes one circular chromosome of 2,442,826 bp (53.35% G+C content), and 2,210 genes were predicted, 2,146 of which are putative protein-coding genes, with 12 rRNAs and 51 tRNAs; 1 pseudogene was also identified.

A MAT1-2 wild-type strain from Penicillium chrysogenum: functional mating-type locus characterization, genome sequencing and mating with an industrial penicillin-producing strain

In heterothallic ascomycetes, mating is controlled by two nonallelic idiomorphs that determine the 'sex' of the corresponding strains. We recently discovered mating-type loci and a sexual life cycle in the penicillin-producing fungus, Penicillium chrysogenum. All industrial penicillin production strains worldwide are derived from a MAT1-1 isolate. No MAT1-2 strain has been investigated in detail until now. Here, we provide the first functional analysis of a MAT1-2 locus from a wild-type strain. Similar to MAT1-1, the MAT1-2 locus has functions beyond sexual development. Unlike MAT1-1, the MAT1-2 locus affects germination and surface properties of conidiospores and controls light-dependent asexual sporulation. Mating of the MAT1-2 wild type with a MAT1-1 high penicillin producer generated sexual spores. We determined the genomic sequences of parental and progeny strains using next-generation sequencing and found evidence for genome-wide recombination. SNP calling showed that derived industrial strains had an uneven distribution of point mutations compared with the wild type. We found evidence for meiotic recombination in all chromosomes. Our results point to a strategy combining the use of mating-type genes, genetics, and next-generation sequencing to optimize conventional strain improvement methods.

Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S

This genome report describes the draft genome and the physiological characteristics of Desulfitobacterium hafniense PCE-S, a Gram-positive bacterium known to dechlorinate tetrachloroethene (PCE) to dichloroethene by a PCE reductive dehalogenase. The draft genome has a size of 5,666,696 bp with a G + C content of 47.3%. The genome is very similar to the already sequenced Desulfitobacterium hafniense Y51 and the type strain DCB-2. We identified two complete reductive dehalogenase (rdh) genes in the genome of D. hafniense PCE-S, one of which encodes PceA, the PCE reductive dehalogenase, and is located on a transposon. Interestingly, this transposon structure differs from the PceA-containing transposon of D. hafniense Y51. The second rdh encodes an unknown reductive dehalogenase, highly similar to rdhA 7 found in D. hafniense DCB-2, in which the corresponding gene is disrupted. This reductive dehalogenase might be responsible for the reductive dechlorination of 2,4,5-trichlorophenol and pentachlorophenol, which is mediated by D. hafniense PCE-S in addition to the reductive dechlorination of PCE.

Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5

Lysinibacillus sphaericus CBAM5, was isolated from subsurface soil of oil well explorations in the Easter Planes of Colombia. This strain has potential in bioremediation of heavy-metal polluted environments and biological control of Culex quinquefasciatus. According to the phylogenetic analysis of 16S rRNA gene sequences, the strain CBAM5 was assigned to the Lysinibacillus sphaericus taxonomic group 1 that comprises mosquito pathogenic strains. After a combination assembly-integration, alignment and gap-filling steps, we propose a 4,610,292 bp chromosomal scaffold. The whole genome (consisting of 5,146,656 bp long, 60 contigs and 5,209 predicted-coding sequences) revealed strong functional and syntenial similarities to the L. sphaericus C3-41 genome. Mosquitocidal (Mtx), binary (Bin) toxins, cereolysin O, and heavy metal resistance clusters from nik, ars, czc, mnt, ter, cop, cad, and znu operons were identified.

Methods for assembling reads and producing contigs

Determining the genome sequence of an organism is often the first step towards its molecular characterization. Once a difficult and expensive task, nowadays it is an almost routine practice in many molecular biology labs. In this chapter we discuss in depth the various methods to assemble the short sequences (called reads) obtained from a massive sequencing system, using different software and strategies, and how to perform some fundamental quality controls on the data obtained.