Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers.

The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers.

Systematic review on raphide morphotype calcium oxalate crystals in angiosperms.

Calcium oxalate (CaOx) crystals are biominerals present in a wide variety of plants. Formation of these crystals is a biomineralization process occurring in vacuoles within specialized cells called crystal idioblasts. This process is dependent on two key components: deprotonated oxalic acid, and calcium ions (Ca2+), and can result in multiple crystal morphologies. Raphides are needle-like CaOx crystals found in various plant organs and tissues. Though their function is highly debated, they can potentially store calcium, sequester heavy metals, protect against herbivory and possibly programmed cell death. The last review of the taxonomic and anatomical distribution of raphides across the plant kingdom dates back to 1980, in a review by Franceschi and Horner, prompting an updated systematic review of raphides in plants. We conduct a broad literature search to record plant taxa and tissue locations containing raphides. We provide an overview of raphide-forming plant taxa, discussing phylogenetic distribution of raphides at the order level, and report on the specific locations of raphides within plants. Our review reveals raphide occurrence has been studied in 33 orders, 76 families and 1305 species, with raphides presence confirmed in 24 orders, 46 families and 797 species. These taxa represented less than 1 % of known species per family. Leaves are the most prominent raphide-containing primary location in all three major angiosperm clades investigated: Eudicots, Magnoliids, and Monocots. Roots are least reported to contain raphides. The collation of such information lays the groundwork to unveil the genetic origin and evolution of raphides in plants, and highlights targets for future studies of the presence and role of plant raphides.

Dynamic plastid and mitochondrial genomes in Chaetopeltidales (Chlorophyceae) and characterization of a new chlorophyte taxon.

PREMISE: Chaetopeltidales is a poorly characterized order in the Chlorophyceae, with only two plastid and no mitochondrial genomes published. Here we describe a new taxon in Chaetopeltidales, Gormaniella terricola gen. et sp. nov. and characterize both of its organellar genomes. METHODS: Gormaniella terricola was inadvertently isolated from a surface-sterilized hornwort thallus. Light microscopy was used to characterize its vegetative morphology. Organellar genomes were assembled, annotated, and analyzed using a variety of software packages. RESULTS: The mitochondrial genome (66,927 bp) represents the first complete mitochondrial genome published for Chaetopeltidales. The chloroplast genome, measuring 428,981 bp, is one of the largest plastid genomes published to date and shares this large size and an incredible number of short, dispersed repeats with the other sequenced chloroplast genomes in Chaetopeltidales. Despite these shared features, the chloroplast genomes of Chaetopeltidales appear to be highly rearranged when compared to one another, with numerous inversions, translocations, and duplications, suggesting a particularly dynamic chloroplast genome. Both the chloroplast and mitochondrial genomes of G. terricola contain a number of mobile group I and group II introns, which appear to have invaded separately. Three of the introns within the mitochondrial genome encode homing endonucleases that are phylogenetically nested within those found in fungi, rather than algae, suggesting a possible case of horizontal gene transfer. CONCLUSIONS: These results help to shed light on a poorly understood group of algae and their unusual organellar genomes, raising additional questions about the unique patterns of genome evolution within Chaetopeltidales.

A platform for oncogenomic reporting and interpretation.

Manual interpretation of variants remains rate limiting in precision oncology. The increasing scale and complexity of molecular data generated from comprehensive sequencing of cancer samples requires advanced interpretative platforms as precision oncology expands beyond individual patients to entire populations. To address this unmet need, we introduce a Platform for Oncogenomic Reporting and Interpretation (PORI), comprising an analytic framework that facilitates the interpretation and reporting of somatic variants in cancer. PORI integrates reporting and graph knowledge base tools combined with support for manual curation at the reporting stage. PORI represents an open-source platform alternative to commercial reporting solutions suitable for comprehensive genomic data sets in precision oncology. We demonstrate the utility of PORI by matching 9,961 pan-cancer genome atlas tumours to the graph knowledge base, calculating therapeutically informative alterations, and making available reports describing select individual samples.

Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae.

Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. Although extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis and Microchloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis strains C73 and C141 (60 Mb) and Vischeria strain C74 (106 Mb), which are the sister groups to Nannochloropsis and Microchloropsis in the order Eustigmatales. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis and Microchloropsis, long interspersed nuclear element repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and nonmevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis and Microchloropsis that have only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis and Microchloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.

The diversity and community structure of symbiotic cyanobacteria in hornworts inferred from long-read amplicon sequencing.

PREMISE: Nitrogen-fixing endosymbioses with cyanobacteria have evolved independently in five very different plant lineages. Expanding knowledge of these symbioses promises to improve the understanding of symbiosis evolution and broaden the toolkit for agricultural engineering to reduce artificial fertilizer use. Here we focused on hornworts, a bryophyte lineage in which all members host cyanobacteria, and investigated factors shaping the diversity of their cyanobiont communities. METHODS: We sampled hornworts and adjacent soils in upstate New York throughout the hornwort growing season. We included all three sympatric hornwort species in the area, allowing us to directly compare partner selectivity. To profile cyanobacteria communities, we established a metabarcoding protocol targeting rbcL-X with PacBio long reads. RESULTS: The hornwort cyanobionts detected were phylogenetically diverse, including clades that do not contain other known plant symbionts. We found significant overlap between hornwort cyanobionts and soil cyanobacteria, a pattern not previously reported in other plant-cyanobacteria symbioses. Cyanobiont communities differed between host plants only centimeters apart, but we did not detect an effect of sampling time or host species on the cyanobacterial community structure. CONCLUSIONS: This study expands the phylogenetic diversity of known symbiotic cyanobacteria. Our analyses suggest that hornwort cyanobionts have a tight connection to the soil background, and we found no evidence that time within growing season, host species, or distance at the scale of meters strongly govern cyanobacteria community assembly. This study provides a critical foundation for further study of the ecology, evolution, and interaction dynamics of plant-cyanobacteria symbiosis.

A novel thylakoid-less isolate fills a billion-year gap in the evolution of Cyanobacteria.

Cyanobacteria have played pivotal roles in Earth's geological history, especially during the rise of atmospheric oxygen. However, our ability to infer the early transitions in Cyanobacteria evolution has been limited by their extremely lopsided tree of life-the vast majority of extant diversity belongs to Phycobacteria (or "crown Cyanobacteria"), while its sister lineage, Gloeobacteria, is depauperate and contains only two closely related species of Gloeobacter and a metagenome-assembled genome. Here, we describe a new cultured member of Gloeobacteria, Anthocerotibacter panamensis, isolated from a tropical hornwort. Anthocerotibacter diverged from Gloeobacter over 1.4 Ga ago and has low 16S rDNA identities with environmental samples. Our ultrastructural, physiological, and genomic analyses revealed that this species possesses a unique combination of traits that are exclusively shared with either Gloeobacteria or Phycobacteria. For example, similar to Gloeobacter, it lacks thylakoids and circadian clock genes, but the carotenoid biosynthesis pathway is typical of Phycobacteria. Furthermore, Anthocerotibacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria. Despite this, Anthocerotibacter is capable of oxygenic photosynthesis under a wide range of light intensities, albeit with much less efficiency. Given its key phylogenetic position, distinct trait combination, and availability as a culture, Anthocerotibacter opens a new window to further illuminate the dawn of oxygenic photosynthesis.

Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase.

Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant-microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation.

A novel experimental system using the liverwort Marchantia polymorpha and its fungal endophytes reveals diverse and context-dependent effects.

Fungal symbioses are ubiquitous in plants, but their effects have mostly been studied in seed plants. This study aimed to assess the diversity of fungal endophyte effects in a bryophyte and identify factors contributing to the variability of outcomes in these interactions. Fungal endophyte cultures and axenic liverwort clones were isolated from wild populations of the liverwort, Marchantia polymorpha. These collections were combined in a gnotobiotic system to test the effects of fungal isolates on the growth rates of hosts under laboratory conditions. Under the experimental conditions, fungi isolated from M. polymorpha ranged from aggressively pathogenic to strongly growth-promoting, but the majority of isolates caused no detectable change in host growth. Growth promotion by selected fungi depended on nutrient concentrations and was inhibited by coinoculation with multiple fungi. The M. polymorpha endophyte system expands the resources for this model liverwort. The experiments presented here demonstrate a wealth of diversity in fungal interactions even in a host reported to lack standard mycorrhizal symbiosis. In addition, they show that some known pathogens of vascular plants live in M. polymorpha and can confer benefits to this nonvascular host. This highlights the importance of studying endophyte effects across the plant tree of life.