Blattabacterium Genome: Structure, Function, and Evolution

Blattabacterium, an obligate bacterial endosymbiont, functions as a mechanism of nitrogen recycling and nutrient synthesis within the Order Blattaria (cockroaches). Through genome annotation and the application of bioinformatics, the function of Blattabacterium within the cockroach Nauphoeta cinerea was described. Results of analyses indicate that the Blattabacterium genome, comprised of ~620,000 base pairs and ~620 individual genes, is drastically reduced when compared Flavobacterium, Blattabacterium’s closest free-living relative. However, the Blattabacterium genome retained functionality vital to host survival and fecundity and functions as a source of additional nutrient biosynthesis within its host. Like other intracellular endosymbionts, the Blattabacterium genome has a G+C content of ~27%. Synteny within the Blattabacterium genome is well conserved. In addition, results of genetic drift analyses indicate that Blattabacterium is experiencing elevated rates of functional genome evolution, when compared to free-living bacterial relatives, resulting from the unique evolutionary constraints of an intracellular lifestyle

Random Genetic Drift and Selective Pressures Shaping the Blattabacterium Genome

Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium – providing nutritional augmentation to its host in the form of amino acid synthesis – displays radical genome alterations when compared to its most recent free-living relative Flavobacterium. To date, eight Blattabacterium genomes have been published, affording an unparalleled opportunity to examine the direction and magnitude of selective forces acting upon this group of symbionts. Here, we find that the Blattabacterium genome is experiencing a 10-fold increase in selection rate compared to Flavobacteria. Additionally, the proportion of selection events is largely negative in direction, with only a handful of loci exhibiting signatures of positive selection. These findings suggest that the Blattabacterium genome will continue to erode, potentially resulting in an endosymbiont with an even further reduced genome, as seen in other insect groups such as Hemiptera

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on ∼1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genetic basis of behavior in Temnothorax ants

The transition to parasitism is a drastic lifestyle shift, characterized by rapid changes in gene structure, function, and expression. Combined with the co-evolutionary arms races common to parasite-host systems, recently-evolved or evolutionarily-'young' parasitic species represent an ideal system for elucidating the molecular underpinnings of parasite- and host-specific behavioral phenotypes. The repeated evolution of social parasitism and slavery among Temnothorax ants allows us to examine the molecular patterns characterizing the raiding phenotypes of slavemaking species within this taxon, as well as reciprocal host defensive phenotypes against their slavemakers. Previous studies of Temnothorax provide behavioral and chemical evidence for reciprocal adaptations between parasite and host, as well as diverging raiding strategies between slavemakers. Utilizing transcriptomics, gene expression, and selection analyses, we reveal that the slavemaker raiding phenotype and host response to these attacks are characterized largely by species-specific molecular patterns. Moreover, only a small number of genes share expression or selection patterns between slavemaking species. A number of candidate genes for slavemaker raiding behavior were identified, including Tyrpsin-7, Trypsin Inhibitor, and painless. Experimental down-regulation of Trypsin Inhibitor via RNAi resulted in an altered slave raiding pattern, shedding some light onto the role that single genes can play within complex behavioral phenotypes. Finally, an additional transcriptomic experiment investigated the molecular similarity between the externally-analogous slavemaker raiding recruitment and host tandem-running behavior of Temnothorax ants. We detected a number of genes differentially expressed in the brains of scouting and tandem-running individuals that are known to be involved in learning and memory formation in other insects. As such, our findings here reinforce previous conclusions: that molecular-specificity underlies externally similar behaviors. Taken together, the findings presented here suggest that Temnothorax slavemakers and hosts are on species-specific rather than convergent evolutionary trajectories, and that the evolution of social parasitism even among closely-related species may be reached in diverse ways.Der Übergang zu einer parasitären Überlebensstrategie stellt eine drastische Veränderung der Lebensbedingungen dar und wird von Änderungen in der Struktur, Funktion und Expression von Genen in kürzester Zeit begleitet. In Kombination mit dem koevolutionären Wettrüsten, welches gewöhnlich zwischen Parasit und Wirt stattfindet, stellen - aus evolutionärer Perspektive - relativ junge Wirt-Parasit-Systeme ein hervorragendes Modell dar, um die oft komplexen molekularen Grundlagen von spezifischen Verhaltensphänotypen der Parasiten und Wirte zu verstehen. In Ameisenspezies des Genus Temnothorax ist sozialer Parasitismus mehrfach entstanden, was eine ideale Situation darstellt, um die molekularen Muster der Raubzug-Phänotypen der sklavenhaltenden Spezies sowie die Verteidigungsmuster der jeweiligen Wirte in dieser Speziesgruppe zu untersuchen. Bisherige Studien zu Temnothorax konnten zeigen, dass es wechselseitige chemische- und Verhaltensanpassungen in sowohl Parasiten als auch Wirten in diesem System gibt, sowie deutliche Unteschiede in den Raubzugstrategien der Sklavenhalter. Unter Verwendung von Transkriptoms-, Genexpressions- und Selektionsanalysen präsentieren wir hier Belege für Spezies-spezifische molukulare Muster als Grundlage für die verschiedenen Raubzug-Phänotypen der Sklavenhalter und Verteidigungsstrategien der Wirte. Dementsprechend finden sich nur wenige Gene, deren Expressions- und Selektionsmuster in den sklavenhaltenden Spezies identisch sind. Wir konnten mehrere Kandidatengene, die für das Raubzugverhalten mitverantwortlich sind, identifizieren; unter anderem Tyrpsin-7, Trypsin Inhibitor, und painless. Experimentelles Herunterregulieren des Trypsin Inhbitor Gens mittels RNAi brauchte ein verändertes Raubzugverhalten hervor, was auf Schlüsselrollen einzelner Gene in komplexen Verhaltensphänotypen hinweist. Eine weitere Transkriptomanalyse untersuchte mögliche Analogien in den molekularen Grundlagen für ähnliche Verhaltensmuster in Sklavenhaltern und Wirten, nämlich des Rekrutierens von Mitgliedern eines Raubzugs durch Skalvenhalter-Kundschafter, und dem Tandemlauf zu möglichen Neststätten oder Nahrungsquellen in den Wirten. Diese Untersuchungen weisen in jeder Spezies unterschiedliche, differenziell expremierte Gene im Gehirn von Raubzug-Kundschaftern und Wirt-Tandemläufern auf, welche in vergangen Stuiden mit Lernen und Gedächtnisbildung in Verbindung gebracht wurden. Diese Ergebnisse sind im Einklang unserer vorherigen Schlussfolgerungen, dass oberflächlich ähnlichen Verhaltensmustern unterschiedliche und Spezies-spezifische molekulare Muster zu Grunde liegen können. Die hier präsentierten Ergebnisse zeigen zusammenfassend, dass Sklavenhalter und Wirte im Genus Temnothorax nicht auf konvergenten, sondern Spezies-spezifischen Evolutionspfaden sind, und dass die Evolution von sozialem Parastismus auch in eng verwandten Spezies auf unabhängige und unterschiedliche Weise erfolgen kann

Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes

The transition to parasitism is a drastic shift in lifestyle, involving rapid changes in gene structure, function, and expression. After the establishment of antagonistic relationships, parasites and hosts co-evolve through reciprocal adaptations, often resulting in evolutionary arms-races. Repeated evolution of social parasitism and slavery among Temnothorax ants allows us to examine those gene expression patterns that characterize slavemaker raiding and reciprocal host defensive phenotypes. Previous behavioural studies have established that raiding strategies between Temnothorax slavemakers diverge, while host defense portfolios shift similarly under parasite pressure. We are the first to confirm this at the molecular level, revealing that slavemaking species exhibit a wider variety of genes with species-specific patterns of expression within their raiding phenotypes, whereas expression similarity is commonly found during the non-raiding phenotype. Host species response to slavemaker aggression, however, is indicated by strong changes in the expression of a relatively few number genes. Additionally, the expression of individual genes such as Acyl-CoA-Delta(11) desaturase and Trypsin-7 is strongly associated with the raiding phenotype of all three slavemaking species. Here, we provide novel insight into the gene expression patterns associated with raiding and nest defense behavior in Temnothorax ants, suggesting lineage-specific evolutionary patterns among both slavemakers and hosts

Complete genome sequence of the endosymbiont Blattabacterium from the cockroach Nauphoeta cinerea (Blattodea: Blaberidae)

AbstractAll cockroaches, with the exception of one cave-dwelling genus, harbor endosymbiotic bacteria, Blattabacterium. After much confusion concerning their function, recent genomic studies indicate that Blattabacterium synthesize amino acids, vitamins, and other compounds. However, the Blattabacterium genomes sequenced so far suggest that the endosymbionts are variable in their genome size, gene composition, and compounds they synthesize. Therefore, there is a need for sequencing additional Blattabacterium genomes to fully comprehend their evolution. Here, we report the complete genome sequence of Blattabacterium (BNCIN) harbored by the host Nauphoeta cinerea (Blaberidae). The BNCIN genome is 622,952bp long and consists of 581 protein coding regions and 627 genes of putative function. The genome of BNCIN is comparable, with a few structural and functional differences, to the genomes of the other sequenced Blattabacterium. The endosymbiont is involved in complete or partial synthesis of 15 amino acids

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This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": DESeq2 analysis of T. americanus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSE

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This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": Homologue analysis between T. americanus and T. longispinosus, Transcriptomes constructed using Trinity, DEGs obtained by using DESeq2, Orthogroups created using Orthofinder