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Planar structures dramatically increase the surface‐area‐to‐volume ratio, which is critically important for multicellular organisms. In this study, we utilize naturally occurring phenotypic variation among three Sansivieria species (Asperagaceae) to investigate leaf margin expression patterns that are associated with mediolateral and adaxial/abaxial development. We identified differentially expressed genes (DEGs) between center and margin leaf tissues in two planar‐leaf species Sansevieria subspicata and Sansevieria trifasciata and compared these with expression patterns within the cylindrically leaved Sansevieria cylindrica. Two YABBY family genes, homologs of FILAMENTOUS FLOWER and DROOPING LEAF, are overexpressed in the center leaf tissue in the planar‐leaf species and in the tissue of the cylindrical leaves. As mesophyll structure does not indicate adaxial versus abaxial differentiation, increased leaf thickness results in more water‐storage tissue and enhances resistance to aridity. This suggests that the cylindrical‐leaf in S. cylindrica is analogous to the central leaf tissue in the planar‐leaf species. Furthermore, the congruence of the expression patterns of these YABBY genes in Sansevieria with expression patterns found in other unifacial monocot species suggests that patterns of parallel evolution may be the result of similar solutions derived from a limited developmental toolbox. [ABSTRACT FROM AUTHOR]

Loop closure detection is a crucial part of VSLAM. However, the traditional loop closure detection algorithms are difficult to adapt to complex and changeable scenes. In this paper, we fuse Gist features, semantic features and appearance features of the image to detect the loop closures quickly and accurately. Firstly, we take advantage of the fast extraction speed of the Gist feature by using it to screen the loop closure candidate frames. Then, the current frame and the candidate frame are semantically segmented to obtain the mask blocks of various types of objects, and the semantic nodes are constructed to calculate the semantic similarity between them. Next, the appearance similarity between the images is calculated according to the shape of the mask blocks. Finally, based on Gist similarity, semantic similarity and appearance similarity, the image similarity calculation model can be built as the basis for loop closure detection. Experiments are carried out on both public and self-filmed datasets. The results show that our proposed algorithm can detect the loop closure in the scene quickly and accurately when the illumination, viewpoint and object change. [ABSTRACT FROM AUTHOR]

In May 2011, officials in northern Germany reported a sudden surge in illness due to Shiga-toxigenic Escherichia coli (STEC). Symptoms of infection ranged from self-limiting episodes of diarrhea to life-threatening [...]

Abstract Background Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. Lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches. Methods A maximum likelihood analysis was done on the five sequenced corynebacterial genomes to model the rates of gene insertions/deletions at various depths of the phylogeny. Results The study shows that most of the laterally acquired genes are transient and the inferred rates of gene movement are higher on the external branches of the phylogeny and decrease as the phylogenetic depth increases. The newly acquired genes are under relaxed selection and evolve faster than their older counterparts. Analysis of some of the functionally characterised LGTs in each species has indicated that they may have a possible adaptive role. Conclusion The five Corynebacterial genomes sequenced to date have evolved by acquiring between 8 – 14% of their genomes by LGT and some of these genes may have a role in adaptation.

Analysis of genome variation provides insights into mechanisms in genome evolution. This is increasingly appreciated with the rapid growth of genomic data. Mitochondrial genomes (mitogenomes) are well known to vary substantially in many genomic aspects, such as genome size, sequence context, nucleotide base composition and substitution rate. Such substantial variation makes mitogenomes an excellent model system to study the mechanisms dictating mitogenome variation. Recent sequencing efforts have not only covered a rich number of yeast species but also generated genomes from abundant strains within the same species. The rich yeast genomic data have enabled detailed investigation from genome variation into molecular mechanisms in genome evolution. This mini-review highlights some recent progresses in yeast mitogenome studies. [ABSTRACT FROM AUTHOR]

Abstract Background Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests that transferred genes may be evolutionarily important in generating mitochondrial genetic diversity. Finally, the complex relationships within each lineage of transferred genes imply a surprisingly complicated history of these genes in Plantago subsequent to their acquisition via HGT and this history probably involves some combination of additional transfers (including intracellular transfer), gene duplication, differential loss and mutation-rate variation. Unravelling this history will probably require sequencing multiple mitochondrial and nuclear genomes from Plantago. See Commentary: http://www.biomedcentral.com/1741-7007/8/147.

Abstract Background The ancestry of mitochondria and chloroplasts traces back to separate endosymbioses of once free-living bacteria. The highly reduced genomes of these two organelles therefore contain very distant homologs that only recently have been shown to recombine inside the mitochondrial genome. Detection of gene conversion between mitochondrial and chloroplast homologs was previously impossible due to the lack of suitable computer programs. Recently, I developed a novel method and have, for the first time, discovered recurrent gene conversion between chloroplast mitochondrial genes. The method will further our understanding of plant organellar genome evolution and help identify and remove gene regions with incongruent phylogenetic signals for several genes widely used in plant systematics. Here, I implement such a method that is available in a user friendly web interface. Results OrgConv (Organellar Conversion) is a computer package developed for detection of gene conversion between mitochondrial and chloroplast homologous genes. OrgConv is available in two forms; source code can be installed and run on a Linux platform and a web interface is available on multiple operating systems. The input files of the feature program are two multiple sequence alignments from different organellar compartments in FASTA format. The program compares every examined sequence against the consensus sequence of each sequence alignment rather than exhaustively examining every possible combination. Making use of consensus sequences significantly reduces the number of comparisons and therefore reduces overall computational time, which allows for analysis of very large datasets. Most importantly, with the significantly reduced number of comparisons, the statistical power remains high in the face of correction for multiple tests. Conclusions Both the source code and the web interface of OrgConv are available for free from the OrgConv website http://www.indiana.edu/~orgconv. Although OrgConv has been developed with main focus on detection of gene conversion between mitochondrial and chloroplast genes, it may also be used for detection of gene conversion between any two distinct groups of homologous sequences.

Genome-wide nucleotide composition varies widely among species. Despite extensive research, the source of genome-wide nucleotide composition diversity remains elusive. Yeast mitochondrial genomes (mitogenomes) are highly A + T rich, and they provide a unique opportunity to study the evolution of AT-biased landscape. In this study, we sequenced ten complete mitogenomes of the Saccharomycodes ludwigii yeast with 8% G + C content, the lowest genome-wide %(G + C) in all published genomes to date. The S. ludwigii mitogenomes have high densities of short tandem repeats but severely underrepresented mononucleotide repeats. Comparative population genomics of these record-setting A + T-rich genomes shows dynamic indel mutations and strong mutation bias toward A/T. Indel mutations play a greater role in genomic variation among very closely related strains than nucleotide substitutions. Indels have resulted in presence–absence polymorphism of tRNAArg (ACG) among S. ludwigii mitogenomes. Interestingly, these mitogenomes have undergone recombination, a genetic process that can increase G + C content by GC-biased gene conversion. Finally, the expected equilibrium G + C content under mutation pressure alone is higher than observed G + C content, suggesting existence of mechanisms other than AT-biased mutation operating to increase A/T. Together, our findings shed new lights on mechanisms driving extremely AT-rich genomes. [ABSTRACT FROM AUTHOR]

Summary: Mitochondrial recombination in yeast is well recognized, yet the underlying genetic mechanisms are not well understood. Recent progress has suggested that mobile introns in mitochondrial genomes (mitogenomes) can facilitate the recombination of their corresponding intron‐containing genes through a mechanism known as intron homing. As many mitochondrial genes lack introns, there is a critical need to determine the extent of recombination and underlying mechanism of intron‐lacking genes. This study leverages yeast mitogenomes to address these questions. In Saccharomyces cerevisiae, the 3′‐end sequences of at least three intron‐lacking mitochondrial genes exhibit elevated nucleotide diversity and recombination hotspots. Each of these 3′‐end sequences is immediately adjacent to or even fused as overlapping genes with a stand‐alone endonuclease. Our findings suggest that SAEs are responsible for recombination and elevated diversity of adjacent intron‐lacking genes. SAEs were also evident to drive recombination of intron‐lacking genes in Lachancea kluyveri, a yeast species that diverged from S. cerevisiae more than 100 million years ago. These results suggest SAEs as a common driver in recombination of intron‐lacking genes during mitogenome evolution. We postulate that the linkage between intron‐lacking gene and its adjacent endonuclease gene is the result of co‐evolution. [ABSTRACT FROM AUTHOR]

The study of genetic and phenotypic variation is fundamental for understanding the dynamics of bacterial genome evolution and untangling the evolution and epidemiology of bacterial pathogens. Neisseria meningitidis (Nm) is among the most intriguing bacterial pathogens in genomic studies due to its dynamic population structure and complex forms of pathogenicity. Extensive genomic variation within identical clonal complexes (CCs) in Nm has been recently reported and suggested to be the result of homologous recombination, but the extent to which recombination contributes to genomic variation within identical CCs has remained unclear. In this study, we sequenced two Nm strains of identical serogroup (C) and multi-locus sequence type (ST60), and conducted a systematic analysis with an additional 34 Nm genomes. Our results revealed that all gene content variation between the two ST60 genomes was introduced by homologous recombination at the conserved flanking genes, and 94.25% or more of sequence divergence was caused by homologous recombination. Recombination was found in genes associated with virulence factors, antigenic outer membrane proteins, and vaccine targets, suggesting an important role of homologous recombination in rapidly altering the pathogenicity and antigenicity of Nm. Recombination was also evident in genes of the restriction and modification systems, which may undermine barriers to DNA exchange. In conclusion, homologous recombination can drive both gene content variation and sequence divergence in Nm. These findings shed new light on the understanding of the rapid pathoadaptive evolution of Nm and other recombinogenic bacterial pathogens. [ABSTRACT FROM PUBLISHER]

Due to divergence, genetic variation is generally believed to be high among distantly related strains, low among closely related ones and little or none within the same classified clonal groups. Several recent genome-wide studies, however, revealed that significant genetic variation resides in a considerable number of genes among strains with identical MLST (Multilocus sequence typing) types and much of the variation was introduced by homologous recombination. Recognizing and understanding genomic variation within clonal bacterial groups could shed new light on the evolutionary path of infectious agents and the emergence of particularly pathogenic or virulent variants. This commentary presents our recent contributions to this line of work. [ABSTRACT FROM AUTHOR]

We analyzed travel-associated clinical isolates of Escherichia coli O104:H4, including 1 from the 2011 German outbreak and 1 from a patient who returned from the Philippines in 2010, by genome sequencing and optical mapping. Despite extensive genomic similarity between these strains, key differences included the distribution of toxin and antimicrobial drug-resistance determinants. [ABSTRACT FROM AUTHOR]

Abstract: The evolution of influenza viruses is remarkably dynamic. Influenza viruses evolve rapidly in sequence and undergo frequent reassortment of different gene segments. Homologous recombination, although commonly seen as an important component of dynamic genome evolution in many other organisms, is believed to be rare in influenza. In this study, 256 gene segments from 32 influenza A genomes were examined for homologous recombination, three recombinant H1N1 strains were detected and they most likely resulted from one recombination event between two closely rated parental sequences. These findings suggest that homologous recombination in influenza viruses tends to take place between strains sharing high sequence similarity. The three recombinant strains were isolated at different time periods and they form a clade, indicating that recombinant strains could circulate. In addition, the simulation results showed that many recombinant sequences might not be detectable by currently existing recombinant detection programs when the parental sequences are of high sequence similarity. Finally, possible ways were discussed to improve the accuracy of the detection for recombinant sequences in influenza. [Copyright &y& Elsevier]

Meningococcal disease is a widely distributed complex disease affecting all age categories. It can cause severe meningitis and septicemia, especially in unvaccinated infants and young children. The causative agent, Neisseria meningitidis (Nm), can be phenotypically and genetically differentiated into serogroups and sequence types (STs) and has a highly dynamic population structure. To obtain a deeper understanding of the epidemiology of Nm, we sequenced seven Nm genomes. Large-scale genomic analysis was conducted with these 7 Nm genomes, 27 additional Nm genomes from GenBank, and 4 other Neisseria genomes. We observed extensive homologous recombination in all gene functional categories among different Nm genomes. Homologous recombination is so frequent that it has resulted in numerous chimeric open reading frames, including genes in the capsule biosynthesis cluster and loci targeted by commercial vaccines. Our results reveal that, despite widespread use, evolutionary relationships inferred from the standard seven-gene multilocus sequence typing (MLST) method could not predict virulence gene content or strain phenotype. In fact, up to 28% of the virulence-associated genes could differ between strains of identical STs. Consistent with previous studies, we found that allelic recombination is also associated with alterations in antibiotic susceptibility. Overall, these findings emphasize the extensive genomic plasticity of Nm and the limitations of standard molecular methods to quantify this genotypic and phenotypic diversity. [ABSTRACT FROM AUTHOR]

Abstract: Methods for assessing gene presence and absence have been widely used to study bacterial genome evolution. A recent report by Zhaxybayeva et al. [Zhaxybayeva, O., Nesbo, C. L., and Doolittle, W. F., 2007. Systematic overestimation of gene gain through false diagnosis of gene absence. Genome. Biol. 8, 402] suggests that false diagnosis of gene absence or the presence of undetected truncated genes leads to a systematic overestimation of gene gain. Here (1) we argue that these annotation errors can cause more complicated effects and are not necessarily systematic, (2) we argue that current annotations (supplemented with BLAST searches) are the best way to consistently score gene presence/absence and (3) that genome wide estimates of gene gain/loss are not strongly affected by small differences in gene annotations but that the number of related gene families is strongly affected. We have estimated the rates of gene insertions/deletions using a variety of cutoff thresholds and match lengths as a way in which to alter the recognition of genes and gene fragments. The results reveal that different cutoffs for match length only cause a small variation of the estimated insertion/deletion rates. The rates of gene insertions/deletions on recent branches remain relatively high regardless of the thresholds for match length. Lastly (4), the dynamic process of gene truncation needs to be further considered in genome comparison studies. The data presented suggest that gene truncation tends to take place preferentially in recently transferred genes, which supports a fast turnover of recent laterally transferred genes. The presence of truncated genes or false diagnosis of gene absence therefore does not significantly affect the estimation of gene insertions/deletions rates, but there are several other factors that bias the results toward an under-estimation of the rate of gene insertion/deletion. All of these factors need to be considered. [Copyright &y& Elsevier]

Urban agricultural soils can be an important reservoir of antibiotic resistance, and have great food safety and public health indications. This study investigated antibiotic-resistant bacteria and antibiotic resistance genes in urban agricultural soils using phenotypic and metagenomic tools. In total, 207 soil bacteria were recovered from 41 soil samples collected from an urban agricultural garden in Detroit, MI, USA. The most prevalent antibiotic resistance phenotype demonstrated by Gram-negative bacteria was resistance to ampicillin (94.2%), followed by chloramphenicol (80.0%), cefoxitin (79.5%), gentamicin (78.4%) and ceftriaxone (71.1%). All Gram-positive bacteria were resistant to gentamicin, kanamycin and penicillin. Genes encoding resistance to quinolones, β-lactams and tetracyclines were the most prevalent and abundant in the soil. qepA and tetA , both encoding efflux pumps, predominated in the quinolone and tetracycline resistance genes tested, respectively. Positive correlation ( P <0.05) was identified among groups of antibiotic resistance genes, and between antibiotic resistance genes and metal resistance genes. The data demonstrated a diverse population of antibiotic resistance in urban agricultural soils. Phenotypic determination together with soil metagenomics proved to be a valuable tool to study the nature and extent of antibiotic resistance in the environment. [ABSTRACT FROM AUTHOR]