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

Author Correction: Cancer Testis Antigen Promotes Triple Negative Breast Cancer Metastasis and is Traceable in the Circulating Extracellular Vesicles (Scientific Reports, (2019), 9, 1, (11632), 10.1038/s41598-019-48064-w)

Triple negative breast cancer (TNBC) has poor survival, exhibits rapid metastases, lacks targeted therapies and reliable prognostic markers. Here, we examined metastasis promoting role of cancer testis antigen SPANXB1 in TNBC and its utility as a therapeutic target and prognostic biomarker. Expression pattern of SPANXB1 was determined using matched primary cancer, lymph node metastatic tissues and circulating small extracellular vesicles (sEVs). cDNA microarray analysis of TNBC cells stably integrated with a metastasis suppressor SH3GL2 identified SPANXB1 as a potential target gene. TNBC cells overexpressing SH3GL2 exhibited decreased levels of both SPANXB1 mRNA and protein. Silencing of SPANXB1 reduced migration, invasion and reactive oxygen species production of TNBC cells. SPANXB1 depletion augmented SH3GL2 expression and decreased RAC-1, FAK, A-Actinin and Vinculin expression. Phenotypic and molecular changes were reversed upon SPANXB1 re-expression. SPANXB1 overexpressing breast cancer cells with an enhanced SPANXB1:SH3GL2 ratio achieved pulmonary metastasis within 5 weeks, whereas controls cells failed to do so. Altered expression of SPANXB1 was detected in the sEVs of SPANXB1 transduced cells. Exclusive expression of SPANXB1 was traceable in circulating sEVs, which was associated with TNBC progression. SPANXB1 represents a novel and ideal therapeutic target for blocking TNBC metastases due to its unique expression pattern and may function as an EV based prognostic marker to improve TNBC survival. Uniquely restricted expression of SPANXB1 in TNBCs, makes it an ideal candidate for targeted therapeutics and prognostication

Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales

The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a non-model system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from eleven exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that while some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources

Genome evolution in monocots

Monocotyledonous plants are a well-circumscribed lineage comprising 25% of all angiosperm species, including many agriculturally and ecologically important species (e.g., grasses, gingers, palms, orchids, lilies, yams, pondweeds, seagrasses, aroids). These taxa possess nearly the full breadth of vegetative and floral morphology seen across angiosperms, dominate a variety of ecosystems, and exhibit considerable genomic complexity, including the largest genome sizes of all plants. The opportunities afforded by this wealth of variation include evaluating patterns of morphological evolution, genomic change, and geographic radiation. This same variation, however, presents unique challenges to establishing an accurate phylogenetic framework as the foundation for evolutionary analysis. This dissertation documents three vignettes in monocot evolution, each highlighting different taxonomic scales and relevant questions to the diversification and significance of both organismal (life history, biogeography, morphology) and genomic (genome size, molecular evolution) characteristics. Chapter 2 uses molecular sequence data from all three genomic partitions (nuclear and both organellar genomes) to infer evolutionary relationships in monocots. Subsequent divergence time and diversification analysis suggests that radiation of major monocot lineages was highly dependent on the origin of other plant and animal lineages. Chapter 3 evaluates a taxonomic classification system in the Tradescantia alliance (Commelinaceae, Commelinales), a group of closely related genera exhibiting kaleidoscopic variation in life history and genomic traits. The phylogeny developed for the alliance is used to re-interpret evolution of taxonomically relevant morphological characters and to test for correlations between genome size and life history/biogeography. Finally, Chapter 4 evaluates a methodological approach to genome sequencing in two lineages of monocots. Grasses (Poaceae, Poales) as a model system are used to test the efficacy of such methods. Non-model Asparagales (agave, onion, asparagus), with large genomes and a paucity of published sequence data, are used to support the ability of these genome sequencing methods to provide ample data for ecological and evolutionary studies. Each of these examples highlights the ability of monocots to serve as test cases for different types of evolutionary questions

Asparagales

Asparagale

Host identity impacts rhizosphere fungal communities associated with three alpine plant species

Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi, then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus group A and B. NONAMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats, but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared to T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity, but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum, while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF this effect was stronger for the mutualistic AMF community

The Landscape of mtDNA Modifications in Cancer: A Tale of Two Cities

Mitochondria from normal and cancerous cells represent a tale of two cities, wherein both execute similar processes but with different cellular and molecular effects. Given the number of reviews currently available which describe the functional implications of mitochondrial mutations in cancer, this article focuses on documenting current knowledge in the abundance and distribution of somatic mitochondrial mutations, followed by elucidation of processes which affect the fate of mutations in cancer cells. The conclusion includes an overview of translational implications for mtDNA mutations, as well as recommendations for future research uniting mitochondrial variants and tumorigenesis

Data from: Systematics and evolution of inflorescence structure in the Tradescantia alliance (Commelinaceae)

The Tradescantia alliance (subtribes Tradescantiinae and Thyrsantheminae of tribe Tradescantieae, family Commelinaceae) comprises a group of closely related New World genera exhibiting considerable variation in morphological, life history, and genomic traits. Despite ecological and cytogenetic significance, phylogenetic relationships among genera and species remain uncertain. In particular, variation in inflorescence morphology has confounded classification and taxonomy. The presence of self compatible and incompatible species allowed us to test the hypothesis that self compatible species will have condensed inflorescences. We inferred phylogenetic relationships using two plastid loci (rpL16, trnL-trnF) for 85 taxa in Commelinaceae, with sampling focused in the Tradescantia alliance. Constraint tests supported only subtribe Tradescantiinae, Tripogandra and Tinantia as monophyletic, with Tripogandra nested within Callisia. We estimated ancestral states for both breeding system and inflorescence condensation and tested for a correlation. Inflorescence morphology, an important character for generic identification, is more labile than previously expected, with condensed inflorescences evolving twice with three subsequent reversals. Breeding system evolution is more complex, with many more switches between self compatibility and self incompatibility and more uncertainty in ancestral state estimates. While we did not find a correlation between self compatibility and inflorescence condensation, we propose additional floral and inflorescence characteristics that may have contributed to variation in breeding system

Commelinaceae Data

Trait data compiled from primary literature regarding breeding system and inflorescence condensation for the Tradescantia allianc

12595

1259