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1. Microbiome composition and function within the Kellet’s whelk perivitelline fluid

   https://doi.org/10.1128/spectrum.03514-23  

   Daniels, Benjamin N. ; Nurge, Jenna ; De Smet, Chanel ; Sleeper, Olivia ; White, Crow ; Davidson, Jean M. ; Fidopiastis, Pat ( March 2024 , Microbiology Spectrum)

   Hom, Erik F. (Ed.)

   Microbiomes have gained significant attention in ecological research, owing to their diverse interactions and essential roles within different organismal ecosystems. Microorganisms, such as bacteria, archaea, and viruses, have profound impact on host health, influencing digestion, metabolism, immune function, tissue development, and behavior. This study investigates the microbiome diversity and function of Kellet’s whelk (Kelletia kelletii) perivitelline fluid (PVF), which sustains thousands of developingK. kelletiiembryos within a polysaccharide and protein matrix. Our core microbiome analysis reveals a diverse range of bacteria, with theRoseobactergenus being the most abundant. Additionally, genes related to host-microbe interactions, symbiosis, and quorum sensing were detected, indicating a potential symbiotic relationship between the microbiome and Kellet’s whelk embryos. Furthermore, the microbiome exhibits gene expression related to antibiotic biosynthesis, suggesting a defensive role against pathogenic bacteria and potential discovery of novel antibiotics. Overall, this study sheds light on the microbiome’s role in Kellet’s whelk development, emphasizing the significance of host-microbe interactions in vulnerable life history stages. To our knowledge, ours is the first study to use 16S sequencing coupled with RNA sequencing (RNA-seq) to profile the microbiome of an invertebrate PVF.

   This study provides novel insight to an encapsulated system with strong evidence of symbiosis between the microbial inhabitants and developing host embryos. The Kellet’s whelk perivitelline fluid (PVF) contains microbial organisms of interest that may be providing symbiotic functions and potential antimicrobial properties during this vulnerable life history stage. This study, the first to utilize a comprehensive approach to investigating Kellet’s whelk PVF microbiome, couples 16S rRNA gene long-read sequencing with RNA-seq. This research contributes to and expands our knowledge on the roles of beneficial host-associated microbes.

    

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2. Transcriptome assembly strategies for precision medicine

   https://doi.org/10.1007/s40484-017-0109-2  

   Wang, Lu ; Acharya, Lipi ; Bai, Changxin ; Zhu, Dongxiao ( December 2017 , Quantitative Biology)

   Precision medicine approach holds great promise to tailored diagnosis, treatment and prevention. Individuals can be vastly different in their genomic information and genetic mechanisms hence having unique transcriptomic signatures. The development of precision medicine has demanded moving beyond DNA sequencing (DNA‐Seq) to much more pointed RNA‐sequencing (RNA‐Seq) [Cell, 2017, 168: 584–599].

   Here we conduct a brief survey on the recent methodology development of transcriptome assembly approach using RNA‐Seq.

   Since transcriptomes in human disease are highly complex, dynamic and diverse, transcriptome assembly is playing an increasingly important role in precision medicine research to dissect the molecular mechanisms of the human diseases.

    

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3. Stage- and sex-specific transcriptome analyses reveal distinctive sensory gene expression patterns in a butterfly

   https://doi.org/10.1186/s12864-021-07819-4  

   Ernst, David A. ; Westerman, Erica L. ( August 2021 , BMC Genomics)

   Animal behavior is largely driven by the information that animals are able to extract and process from their environment. However, the function and organization of sensory systems often change throughout ontogeny, particularly in animals that undergo indirect development. As an initial step toward investigating these ontogenetic changes at the molecular level, we characterized the sensory gene repertoire and examined the expression profiles of genes linked to vision and chemosensation in two life stages of an insect that goes through metamorphosis, the butterflyBicyclus anynana.

   Using RNA-seq, we compared gene expression in the heads of late fifth instar larvae and newly eclosed adults that were reared under identical conditions. Over 50 % of all expressed genes were differentially expressed between the two developmental stages, with 4,036 genes upregulated in larval heads and 4,348 genes upregulated in adult heads. In larvae, upregulated vision-related genes were biased toward those involved with eye development, while phototransduction genes dominated the vision genes that were upregulated in adults. Moreover, the majority of the chemosensory genes we identified in theB. anynanagenome were differentially expressed between larvae and adults, several of which share homology with genes linked to pheromone detection, host plant recognition, and foraging in other species of Lepidoptera.

   These results revealed promising candidates for furthering our understanding of sensory processing and behavior in the disparate developmental stages of butterflies and other animals that undergo metamorphosis.

    

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4. Genetic and molecular landscapes of the generalist phytopathogen Botrytis cinerea

   https://doi.org/10.1111/mpp.13404  

   Singh, Ritu ; Caseys, Celine ; Kliebenstein, Daniel J. ( December 2023 , Molecular Plant Pathology)

   Botrytis cinereaPers. Fr. (teleomorph:Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants. This updated pathogen profile explores the extensive genetic diversity ofB. cinerea, highlights the progress in genome sequencing, and provides current knowledge of genetic and molecular mechanisms employed by the fungus to attack its hosts. In addition, we also discuss recent innovative strategies to combatB. cinerea.

   Kingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus:Botrytis, species:cinerea.

   B. cinereainfects almost all of the plant groups (angiosperms, gymnosperms, pteridophytes, and bryophytes). To date, 1606 plant species have been identified as hosts ofB. cinerea.

   This polyphagous necrotroph has extensive genetic diversity at all population levels shaped by climate, geography, and plant host variation.

   Genetic architecture of virulence and host specificity is polygenic using multiple weapons to target hosts, including secretory proteins, complex signal transduction pathways, metabolites, and mobile small RNA.

   Efforts to controlB. cinerea, being a high‐diversity generalist pathogen, are complicated. However, integrated disease management strategies that combine cultural practices, chemical and biological controls, and the use of appropriate crop varieties will lessen yield losses. Recently, studies conducted worldwide have explored the potential of small RNA as an efficient and environmentally friendly approach for combating grey mould. However, additional research is necessary, especially on risk assessment and regulatory frameworks, to fully harness the potential of this technology.

    

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5. Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei

   https://doi.org/10.1186/s12870-023-04281-0  

   Debernardi, Juan M. ; Burguener, German ; Bubb, Kerry ; Liu, Qiujie ; Queitsch, Christine ; Dubcovsky, Jorge ( May 2023 , BMC Plant Biology)

   The genetic information contained in the genome of an organism is organized in genes and regulatory elements that control gene expression. The genomes of multiple plants species have already been sequenced and the gene repertory have been annotated, however,cis-regulatory elements remain less characterized, limiting our understanding of genome functionality. These elements act as open platforms for recruiting both positive- and negative-acting transcription factors, and as such, chromatin accessibility is an important signature for their identification.

   In this work we developed a transgenic INTACT [isolation of nuclei tagged in specific cell types] system in tetraploid wheat for nuclei purifications. Then, we combined the INTACT system together with the assay for transposase-accessible chromatin with sequencing [ATAC-seq] to identify open chromatin regions in wheat root tip samples. Our ATAC-seq results showed a large enrichment of open chromatin regions in intergenic and promoter regions, which is expected for regulatory elements and that is similar to ATAC-seq results obtained in other plant species. In addition, root ATAC-seq peaks showed a significant overlap with a previously published ATAC-seq data from wheat leaf protoplast, indicating a high reproducibility between the two experiments and a large overlap between open chromatin regions in root and leaf tissues. Importantly, we observed overlap between ATAC-seq peaks andcis-regulatory elements that have been functionally validated in wheat, and a good correlation between normalized accessibility and gene expression levels.

   We have developed and validated an INTACT system in tetraploid wheat that allows rapid and high-quality nuclei purification from root tips. Those nuclei were successfully used to performed ATAC-seq experiments that revealed open chromatin regions in the wheat genome that will be useful to identify cis-regulatory elements. The INTACT system presented here will facilitate the development of ATAC-seq datasets in other tissues, growth stages, and under different growing conditions to generate a more complete landscape of the accessible DNA regions in the wheat genome.

    

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