Transcriptional Profiling of a Yeast Colony Provides New Insight into the Heterogeneity of Multicellular Fungal Communities

Fruit development proceeds from cell division to expansion, maturation, and ripening. Expansion is critical for size, yield, and quality; however, this period of development has received little attention. We used 454-pyrosequencing to develop a cucumber (Cucumis sativus) fruit transcriptome, identify highly expressed transcripts, and characterize key functions during exponential fruit growth. The resulting 187,406 expressed sequence tags (ESTs) were assembled into 13,878 contigs. Quantitative real-time polymerase chain reaction (qRT-PCR) verification of differentially expressed genes from fruit of different ages, and high correlation in transcript frequency between replicates, indicated that number of reads/contig reflects transcript abundance. Putative homologs were identified in Arabidopsis thaliana for 89% of the contigs represented by at least 10 ESTs; another 4% had homologs in other species. The remainder had homologs only in cucurbit species. The most highly expressed contigs were strongly enriched for growth (aquaporins, vacuolar ATPase, phloem proteins, tubulins, actins, cell wall-associated, and hormone-related), lipid, latex, and defense-related homologs. These results provide a resource for gene expression analysis in cucumber, profile gene expression in rapidly growing fruit, and shed insight into an important, but poorly characterized, developmental stage influencing fruit yield and quality.

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Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts

Journal of Fungi ◽

10.3390/jof6040273 ◽

2020 ◽

Vol 6 (4) ◽

pp. 273

Author(s):

Stephen A. James ◽

Sarah Phillips ◽

Andrea Telatin ◽

David Baker ◽

Rebecca Ansorge ◽

...

Keyword(s):

Preterm Infant ◽

Premature Infants ◽

Human Microbiome ◽

Single Species ◽

Fungal Communities ◽

Distinctive Features ◽

Fundamental Part ◽

Health And Development ◽

Abundant Genus ◽

Insight Into

Fungi and the mycobiome are a fundamental part of the human microbiome that contributes to human health and development. Despite this, relatively little is known about the mycobiome of the preterm infant gut. Here, we have characterised faecal fungal communities present in 11 premature infants born with differing degrees of prematurity and mapped how the mycobiome develops during early infancy. Using an ITS1 sequencing-based approach, the preterm infant gut mycobiome was found to be often dominated by a single species, typically a yeast. Candida was the most abundant genus, with the pathobionts C.albicans and C.parapsilosis highly prevalent and persistent in these infants. Gestational maturity at birth affected the distribution and abundance of these Candida, with hospital-associated C.parapsilosis more prevalent and abundant in infants born at less than 31 weeks. Fungal diversity was lowest at 6 months, but increased with age and change of diet, with food-associated Saccharomycescerevisiae most abundant in infants post weaning. This study provides a first insight into the fungal communities present within the preterm infant gut, identifying distinctive features including the prominence of pathobiont species, and the influence age and environmental factors play in shaping the development of the mycobiome.

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Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months

International Journal of Microbiology ◽

10.1155/2017/9547063 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 5

Author(s):

Floor Hugenholtz ◽

Jarmo Ritari ◽

Lotta Nylund ◽

Mark Davids ◽

Reetta Satokari ◽

...

Keyword(s):

Gut Microbiota ◽

Transcriptional Profiling ◽

Lactobacillus Rhamnosus ◽

Rna Seq ◽

Faecal Samples ◽

Carbohydrate Fermentation ◽

Stool Samples ◽

The Impact ◽

Increased Activity ◽

Insight Into

Newborns are rapidly colonized by microbes and their intestinal tracts contain highly dynamic and rapidly developing microbial communities in the first months of life. In this study, we describe the feasibility of isolating mRNA from rapidly processed faecal samples and applying deep RNA-Seq analysis to provide insight into the active contributors of the microbial community in early life. Specific attention is given to the impact of removing rRNA from the mRNA on the phylogenetic and transcriptional profiling and its analysis depth. A breastfed baby was followed in the first six months of life during adaptation to solid food, dairy products, and formula. It was found that, in the weaning period, the total transcriptional activity of Actinobacteria, mainly represented by Bifidobacterium, decreased while that of Firmicutes increased over time. Moreover, Firmicutes and Actinobacteria, including the canonical Bifidobacteria as well as Collinsella, were found to be important contributors to carbohydrate fermentation and vitamin biosynthesis in the infant intestine. Finally, the expression of Lactobacillus rhamnosus-like genes was detected, likely following transfer from the mother who consumed L. rhamnosus GG. The study indicates that metatranscriptome analysis of the infant gut microbiota is feasible on infant stool samples and can be used to provide insight into the core activities of the developing community.

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Arbuscular mycorrhizal fungal succession in a long-lived perennial

Botany ◽

10.1139/cjb-2013-0185 ◽

2014 ◽

Vol 92 (4) ◽

pp. 313-320 ◽

Cited By ~ 16

Author(s):

Miranda M. Hart ◽

Monika Gorzelak ◽

Diane Ragone ◽

Susan J. Murch

Keyword(s):

High Throughput Sequencing ◽

Selective Pressure ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Fungal Communities ◽

Artocarpus Altilis ◽

Host Identity ◽

Arbuscular Mycorrhizal Fungal ◽

Insight Into

It is difficult to understand why arbuscular mycorrhizal (AM) fungal communities change over time. The role of host identity confounds our understanding of successional changes in AM fungal communities because hosts exert strong selective pressure on their root-associated microbes. In this study we looked at the AM fungi associated with a long-lived perennial breadfruit (Artocarpus altilis (Parkinson) Fosberg) to see how AM communities change over the life span of a single, long-lived host. Using 454 high-throughput sequencing, we found evidence that older trees had more AM fungal taxa than younger trees and were associated with different AM fungal communities, but these differences were not apparent early in the life cycle. Older trees were dominated by species of Rhizophagus, whereas younger trees and genets were dominated by species of Glomus. Some taxa were only detected in older trees (e.g., Funneliformis) or genets (e.g., Racocetra and Scutellospora), indicating that certain AM fungal taxa may serve as “indicators” of the successional age of the fungal community. These results provide important information about a poorly studied system and give insight into how AM communities change over longer time scales.

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Insight into Genes Regulating Postharvest Aflatoxin Contamination of Tetraploid Peanut from Transcriptional Profiling

Genetics ◽

10.1534/genetics.118.300478 ◽

2018 ◽

Vol 209 (1) ◽

pp. 143-156 ◽

Cited By ~ 13

Author(s):

Walid Korani ◽

Ye Chu ◽

C. Corley Holbrook ◽

Peggy Ozias-Akins

Keyword(s):

Transcriptional Profiling ◽

Aflatoxin Contamination ◽

Insight Into

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Characterization of the Habitat- and Season-Independent Increase in Fungal Biomass Induced by the Invasive Giant Goldenrod and Its Impact on the Fungivorous Nematode Community

Microorganisms ◽

10.3390/microorganisms9020437 ◽

2021 ◽

Vol 9 (2) ◽

pp. 437

Author(s):

Paula Harkes ◽

Lisa J. M. van Heumen ◽

Sven J. J. van den Elsen ◽

Paul J. W. Mooijman ◽

Mariëtte T. W. Vervoort ◽

...

Keyword(s):

Fungal Community ◽

Fungal Biomass ◽

Invasive Plant ◽

Nematode Community ◽

Fungal Communities ◽

Obvious Effect ◽

Fungal Assemblages ◽

Potential Impact ◽

Insight Into

Outside its native range, the invasive plant species giant goldenrod (Solidago gigantea) has been shown to increase belowground fungal biomass. This non-obvious effect is poorly characterized; we don’t know whether it is plant developmental stage-dependent, which fractions of the fungal community are affected, and whether it is reflected in the next trophic level. To address these questions, fungal assemblages in soil samples collected from invaded and uninvaded plots in two soil types were compared. Although using ergosterol as a marker for fungal biomass demonstrated a significant increase in fungal biomass, specific quantitative PCR (qPCR) assays did not point at a quantitative shift. MiSeq-based characterization of the belowground effects of giant goldenrod revealed a local increase of mainly Cladosporiaceae and Glomeraceae. This asymmetric boost in the fungal community was reflected in a specific shift in the fungivorous nematode community. Our findings provide insight into the potential impact of invasive plants on local fungal communities.

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Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Nature Communications ◽

10.1038/s41467-020-18923-6 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Therese Mitros ◽

Adam M. Session ◽

Brandon T. James ◽

Guohong Albert Wu ◽

Mohammad B. Belaffif ◽

...

Keyword(s):

Comparative Genomics ◽

Transcriptional Profiling ◽

Nutrient Recycling ◽

Biomass Accumulation ◽

Asymmetric Distribution ◽

Bioenergy Crop ◽

Biomass Crop ◽

Growing Seasons ◽

Rhizome Development ◽

Insight Into

Abstract Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

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Agarwood wound locations provide insight into the association between fungal diversity and volatile compounds in Aquilaria sinensis

Royal Society Open Science ◽

10.1098/rsos.190211 ◽

2019 ◽

Vol 6 (7) ◽

pp. 190211 ◽

Cited By ~ 1

Author(s):

Juan Liu ◽

Xiang Zhang ◽

Jian Yang ◽

Junhui Zhou ◽

Yuan Yuan ◽

...

Keyword(s):

Fungal Diversity ◽

Chemical Properties ◽

Fungal Species ◽

Fungal Communities ◽

Strongly Correlated ◽

Resolution Time ◽

Aquilaria Sinensis ◽

Flight Mass Spectrometry ◽

Insight Into ◽

Wound Tissue

The aim of the present study was to investigate the effect of wound location on the fungal communities and volatile distribution of agarwood in Aquilaria sinensis . Two-dimensional gas chromatography with high-resolution time-of-flight mass spectrometry revealed 60 compounds from the NIST library, including 25 sesquiterpenes, seven monoterpenes, two diterpenes, nine aromatics, nine alkanes and eight others. Of five agarwood types, Types IV and II contained the greatest number and concentration of sesquiterpenes, respectively. The fungal communities of the agarwood were dominated by the phylum Ascomycota and were significantly affected by the type of wound tissue. Community richness indices (observed species, Chao1, PD whole tree, ACE indices) indicated that Types I and IV harboured the most and least species-rich fungal communities, and the fungal communities of Types V, I, III and IV/II were dominated by Lasiodiplodia , Hydnellum , Phaeoisaria and Ophiocordyceps species, respectively. Correlations between fungal species and agarwood components revealed that the chemical properties of A. sinensis were associated with fungal diversity. More specifically, the dominant fungal genera of Types V, I and III ( Lasiodiplodia , Hydnellum and Phaeoisaria , respectively) were strongly correlated with specific terpenoid compounds. The finding that wound location affects the fungal communities and volatile distribution of agarwood provides insight into the formation of distinct agarwood types.

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Transcriptional profiling of sequentially generated septal neuron fates

10.1101/2021.06.29.450296 ◽

2021 ◽

Author(s):

Corey C Harwell ◽

Miguel Turrero García ◽

Sarah K Stegmann ◽

Tiara Lacey ◽

Christopher M Reid ◽

...

Keyword(s):

Transcriptional Profiling ◽

Neural Progenitors ◽

Proliferative Capacity ◽

Proliferative Zone ◽

Single Cell Rna Sequencing ◽

Septal Nuclei ◽

Neuronal Types ◽

Septal Neurons ◽

Innate Behaviors ◽

Insight Into

The septum is a ventral forebrain structure known to regulate innate behaviors. During embryonic development, septal neurons are produced in multiple proliferative areas from neural progenitors following transcriptional programs that are still largely unknown. Here, we use a combination of single cell RNA sequencing, histology and genetic models to address how septal neuron diversity is established during neurogenesis. We find that the transcriptional profiles of septal progenitors change along neurogenesis, coinciding with the generation of distinct neuron types. We characterize the septal eminence, a spatially distinct and transient proliferative zone composed of progenitors with distinctive molecular profiles, proliferative capacity and fate potential compared to the rostral septal progenitor zone. We show that Nkx2.1-expressing septal eminence progenitors give rise to neurons belonging to at least three morphological classes, born in temporal cohorts that are distributed across different septal nuclei in a sequential fountain-like pattern. Our study provides insight into the molecular programs that control the sequential production of different neuronal types in the septum, a structure with important roles in regulating mood and motivation.

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Single-Cell Transcriptional Profiling of the Adult Corticospinal Tract Reveals Forelimb and Hindlimb Molecular Specialization

10.1101/2021.06.02.446653 ◽

2021 ◽

Author(s):

Noa Golan ◽

Sierra Dawn Kauer ◽

Daniel Benjamin Ehrlich ◽

Neal Ravindra ◽

David van Dijk ◽

...

Keyword(s):

Single Cell ◽

Corticospinal Tract ◽

Transcriptional Profiling ◽

Axon Growth ◽

Retrograde Tracing ◽

Motor Deficits ◽

Molecular Heterogeneity ◽

Cord Injury ◽

Cns Trauma ◽

Insight Into

The corticospinal tract (CST) is refractory to repair after CNS trauma, resulting in chronic debilitating functional motor deficits after spinal cord injury. While novel pro-axon growth activators have stimulated plasticity and regeneration of corticospinal neurons (CSNs) after injury, robust functional recovery remains elusive. These repair strategies are sub-optimal in part due to underexplored molecular heterogeneity within the developing and adult CST. In this study, we combine retrograde CST tracing with single-cell RNA sequencing to build a comprehensive atlas of CSN subtypes. By comparing CSNs to non-spinally projecting neurons in layer Vb, we identify pan-CSN markers including Wnt7b. By leveraging retrograde tracing, we are able to compare forelimb and hindlimb projecting CSNs, identifying subtype-specific markers, including Cacng7 and Slc16a2 respectively. These markers are expressed in embryonic and neonatal CSNs and can be used to study early postnatal patterning of the CST. Our results provide molecular insight into the differences between anatomically distinct CSN subtypes and provide a resource for future screening and exploitation of these subtypes to repair the damaged CST after injury and disease.

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