EnTAP (Eukaryotic Non‐Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non‐model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein‐coding transcripts. Following filters applied through assessment of true expression and frame selection, open‐source tools are leveraged to functionally annotate the reduced set of translated proteins. Downstream features include fast similarity search across five repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology (GO) term assignment. The final annotation integrates across multiple databases and selects an optimal assignment from a combination of weighted metrics describing similarity search score, taxonomic relationship, and informativeness. Researchers have the option to include additional filters to identify and remove contaminants, identify associated pathways, and prepare the transcripts for enrichment analysis. This fully featured pipeline is easy to install, configure, and runs significantly faster than comparable annotation packages. EnTAP is optimized to generate extensive functional information for the gene space of organisms with limited or poorly characterized genomic resources.

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EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates, while focusing primarily on protein-coding transcripts. Following filters applied through assessment of true expression and frame selection, open-source tools are leveraged to functionally annotate the translated proteins. Downstream features include fast similarity search across three repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology term assignment. The final annotation integrates across multiple databases and selects an optimal assignment from a combination of weighted metrics describing similarity search score, taxonomic relationship, and informativeness. Researchers have the option to include additional filters to identify and remove contaminants, identify associated pathways, and prepare the transcripts for enrichment analysis. This fully featured pipeline is easy to install, configure, and runs significantly faster than comparable annotation packages. EnTAP is optimized to generate extensive functional information for the gene space of organisms with limited or poorly characterized genomic resources.

Background: While genome evolutionary processes of seed plants are intensively investigated, very little is known about seed-free plants in this respect. Here, we use one of the largest groups of seed-free plants, the mosses, and newly generated chromosome-scale genome assemblies to investigate three poorly known aspects of genome dynamics and their underlying processes in seed-free plants: (i) genome size variation, (ii) genomic collinearity/synteny, and (iii) gene set differentiation. Results: Comparative genomic analyses on the model moss Physcomitrium (Physcomitrella) patens and two genomes of Funaria hygrometrica reveal that, like in seed plants, genome size change (approx. 140 Mbp) is primarily due to transposable element expansion/contraction. Despite 60 million years of divergence, the genomes of P. patens and F. hygrometrica show remarkable chromosomal stability with the majority of homologous genes located in conserved collinear blocks. In addition, both genomes contain a relatively large set of lineage-specific genes with no detectible homologs in the other speciesʼ genome, suggesting a highly dynamic gene space fueled by the process of de novo gene birth and loss rather than by gene family diversification/duplication. Conclusions: These, combined with previous observations suggest that genome dynamics in mosses involves the coexistence of a collinear homologous and a highly dynamic species-specific gene sets. Besides its significance for understanding genome evolution, the presented chromosome-scale genome assemblies will provide a foundation for comparative genomic and functional studies in the Funariaceae, a family holding historical and contemporary model taxa in the evolutionary biology of mosses.

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Single cell and single nuclei RNA sequencing (scRNA-seq and snRNA-seq) have helped to identify cell type and subtypes that are present in complex tissues in both healthy samples and disease states. So far, scRNA-seq and snRNA-seq can only be performed in fresh tissues, or fresh frozen tissues. Most archived tissues are formalin-fixed, and paraffin-embedded (FFPE), making them inaccessible to the modern technology for characterization. Recently, 10x Genomics release a new reagent enabling single-cell fixed RNA characterization from fixed samples. The initial release is for fresh samples being fixed and then profiled later. However, FFPE archived tissues are not supported yet. We showed here two protocols to dissociate single cells and single nuclei from a 10-year-old FFPE human gastric tumor. We then profile them with 10x Genomics’ fixed RNA profiling kit. We further compare the data with the 10x Genomics’ Visium data obtained from the same tissues to understand the performance of these two protocols. In summary, we show that such technology will help to further characterize archived tissues that already have pathology annotation as well as clinical data and help biomarkers identification. Citation Format: Jasmine Ying-Jiun Chen, Quynh Le, Chris Kang, Roy Tam, Brian Tai, Kelly Lo, Nasim Rahmatpour, Perry Wasdin. Profiling single cell and spatial transcriptomes in FFPE archived tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 216.

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 culturable member of Gloeobacteria, Anthocerobacter panamensis, isolated from a tropical hornwort. Anthocerobacter diverged from Gloeobacter over 1.4 billion years ago and has low 16S 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, Anthocerobacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria. Despite this, Anthocerobacter 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, Anthocerobacter opens a new window to further illuminate the dawn of oxygenic photosynthesis.