Article
Biotechnology & Applied Microbiology
Surajit Bhattacharya, Hayk Barseghyan, Emmanuele C. Delot, Eric Vilain
Summary: nanotatoR, an R-based package, provides comprehensive annotation for SV classification, enabling analysts to rapidly identify potential pathogenic SVs.
Review
Microbiology
Nora Vazquez-Laslop, Cynthia M. Sharma, Alexander Mankin, Allen R. Buskirk
Summary: Small open reading frames (sORFs) are often missed by annotation engines and are difficult to characterize. Ribosome profiling can improve genome annotations and has revealed new sORFs in bacterial model organisms. Antibiotics that trap ribosomes have played a key role in this development. This article describes new methods and provides important considerations for adapting ribosome profiling to different prokaryotic species.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Plant Sciences
Noah Fahlgren, Muskan Kapoor, Galabina Yordanova, Irene Papatheodorou, Jamie Waese, Benjamin Cole, Peter Harrison, Doreen Ware, Timothy Tickle, Benedict Paten, Tony Burdett, Christine G. Elsik, Christopher K. Tuggle, Nicholas J. Provart
Summary: Building a data infrastructure for the Plant Cell Atlas using existing infrastructure and platforms will allow biologists and data scientists to gain new insights into plant biology. The development of the Human Cell Atlas and the Single Cell Expression Atlas by the European Bioinformatics Institute has laid the foundation for constructing the data infrastructure for the Plant Cell Atlas. The utilization of appropriate ontologies is crucial for describing plant single cell experiments.
Article
Biochemistry & Molecular Biology
Connor D. Harris, Ellis L. Torrance, Kasie Raymann, Louis-Marie Bobay
Summary: The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. CoreCruncher is a robust and fast program that can construct core genomes across hundreds or thousands of genomes. Compared to other tools, CoreCruncher is more conservative and less sensitive to the presence of paralogs and xenologs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Marie E. Sweet, Casper Larsen, Xihui Zhang, Michael Schlame, Bjorn P. Pedersen, David L. Stokes
Summary: KdpFABC is an oligomeric K* transport complex in prokaryotes consisting of channel-like subunit KdpA and pump-like subunit KdpB. Research shows that KdpB undergoes conformational changes during transport, while KdpA, KdpC, and KdpF remain static. The structures suggest a mechanism where ATP hydrolysis is linked to K* transfer, ultimately releasing K* to the cytoplasm through a water-filled pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Entomology
Takako Mochizuki, Mika Sakamoto, Yasuhiro Tanizawa, Hitomi Seike, Zhen Zhu, Yi Jun Zhou, Keisuke Fukumura, Shinji Nagata, Yasukazu Nakamura
Summary: We identified neuropeptides and their genomic loci in Gryllus bimaculatus, improving the draft genome annotation and facilitating research. Genome annotation is essential for supporting studies, but often lacks tissue-specific or low-expression genes. Through reference mapping, de novo transcriptome assembly, and manual curation, we annotated 41 neuropeptides in the cricket. These annotation methods can be applied to other insects and provide useful infrastructures for neuropeptide studies.
Article
Biochemical Research Methods
Andrew J. Olson, Doreen Ware
Summary: TRaCE ranks transcripts at gene loci using annotation edit distance from RNA-seq samples, elects a canonical transcript through multiple rounds of voting based on relevance criteria, and identifies common isoforms or prioritizes alternative transcripts expressed in specific contexts from the provided expression data set.
Article
Multidisciplinary Sciences
Evangelia Vayena, Anush Chiappino-Pepe, Homa MohammadiPeyhani, Yannick Francioli, Noushin Hadadi, Meric Ataman, Jasmin Hafner, Stavros Pavlou, Vassily Hatzimanikatis
Summary: This study introduces a workflow called NICEgame for identifying and curating nonannotated metabolic functions in genomes. By providing alternative reaction sets and candidate genes, NICEgame can resolve gaps in metabolic models and improve genome annotation accuracy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou
Summary: The study introduces FusionGDB 2.0, a database with updated functional annotations of fusion genes, which is crucial for understanding genomic breakage context and developing therapeutic strategies. FusionGDB 2.0 provides comprehensive information on human fusion genes and their characteristics, making it a valuable resource for diverse human genomic studies.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Matthew R. Lueder, Regina Z. Cer, Miles Patrick, Logan J. Voegtly, Kyle A. Long, Gregory K. Rice, Kimberly A. Bishop-Lilly
Summary: Manual Annotation Studio (MAS) is a software tool designed to improve the efficiency of manual functional annotation for prokaryotic and viral genomes. It allows users to upload, edit, and track annotations, provides structure to projects, and reduces errors. MAS can interface with HPC clusters, support multiple users, and export data in various formats.
Article
Multidisciplinary Sciences
Ka Ming Nip, Saber Hafezqorani, Kristina K. Gagalova, Readman Chiu, Chen Yang, Rene L. Warren, Inanc Birol
Summary: Long-read sequencing technologies have greatly improved, but there is little focus on reference-free transcriptome assembly methods. In this study, the authors introduce RNA-Bloom2, a reference-free method for long-read transcriptome sequencing data. They demonstrate its competitive assembly quality compared to reference-based methods, as well as its lower memory and runtime requirements. They also showcase its application in assembling a transcriptome sample of Sitka spruce, setting the groundwork for large-scale comparative transcriptomics without readily available genome assemblies.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Carlos A. Ruiz-Perez, Roth E. Conrad, Konstantinos T. Konstantinidis
Summary: MicrobeAnnotator is a comprehensive pipeline for functional annotation of microbial genomes, combining results from multiple reference protein databases to provide functional annotations and metabolic summaries. Implemented in Python 3, it is freely available for download, demonstrating higher efficiency and accuracy compared to other tools for annotating genomes. Its output can be easily integrated into other analysis pipelines, offering a user-friendly interface for comparing and clustering genomes based on metabolic similarity.
BMC BIOINFORMATICS
(2021)
Editorial Material
Cell Biology
Annan S. I. Cook, James H. Hurley
Summary: Two papers in this issue address a longstanding challenge in autophagosome biogenesis in mammals. The first paper confirms the presence of the lipid scramblase ATG9A as an authentic component of autophagosomes using biochemistry, while the second paper demonstrates through particle tracking that the dynamics of autophagy proteins support the proposed concept.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biochemical Research Methods
Akshay Khanduja, Manish Kumar, Debasisa Mohanty
Summary: Small open reading frames (smORFs) encoding proteins less than 100 amino acids (aa) are important regulators of cellular processes. Computational identification of smORFs remains challenging. The ProsmORF-pred resource utilizes a machine learning-based method to predict smORFs in prokaryotic genomes, achieving comparable performance to other state-of-the-art approaches. It can also aid in functional annotation of predicted smORFs based on sequence similarity in ProsmORFDB.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Plant Sciences
Cheng Zou, Surya Sapkota, Rosa Figueroa-Balderas, Jeff Glaubitz, Dario Cantu, Brewster F. Kingham, Qi Sun, Lance Cadle-Davidson
Summary: Fine mapping of quantitative trait loci (QTL) is essential in modern breeding practice. This study presents a multitiered haplotypic marker system that improves fine mapping accuracy and successfully identifies a grapevine downy mildew resistance locus. The strategy combines different resolutions of genome sequencing and integrates high-density genetic information to pinpoint the genetic basis of QTLs.
Article
Biochemistry & Molecular Biology
Brayon J. Fremin, Nikos C. Kyrpides
Summary: In this study, a large-scale comparative genomics approach was used to predict 156 novel candidate structured RNAs from 36,111 CRISPR-Cas systems, some of which overlapped with coding genes. This highlights the importance of expanding the search windows in coding regions for the identification of novel structured RNAs.
Article
Microbiology
Bertrand Eardly, Wan Adnawani Meor Osman, Julie Ardley, Jaco Zandberg, Margaret Gollagher, Peter van Berkum, Patrick Elia, Dora Marinova, Rekha Seshadri, T. B. K. Reddy, Natalia Ivanova, Amrita Pati, Tanja Woyke, Nikos Kyrpides, Matthys Loedolff, Damian W. Laird, Wayne Reeve
Summary: The study identified the genome features of R. favelukesii OR191 important for symbiotic interactions with Medicago and Phaseolus vulgaris, including acid adaptation loci, Nod factor synthesis genes, and nitrogen fixation genes. These findings provide insights into the genetic basis of nodulation requirements and symbiotic effectiveness with different hosts.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Naihao Ye, Wentao Han, Andrew Toseland, Yitao Wang, Xiao Fan, Dong Xu, Cock van Oosterhout, Igor Grigoriev, Alessandro Tagliabue, Jian Zhang, Yan Zhang, Jian Ma, Huan Qiu, Youxun Li, Xiaowen Zhang, Thomas Mock
Summary: This study reveals that polar microalgae have a higher demand for zinc due to elevated cellular levels of zinc-binding proteins. Zinc plays an important role in supporting photosynthetic growth in eukaryotic polar phytoplankton, which is critical for algal colonization of low-temperature polar oceans.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Microbiology
Gina Chaput, Jacob Ford, Lani DeDiego, Achala Narayanan, Wing Yin Tam, Meghan Whalen, Marcel Huntemann, Alicia Clum, Alex Spunde, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, I-Min Chen, Dimitrios Stamatis, T. B. K. Reddy, Ronan O'Malley, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos C. Kyrpides, Tanja Woyke, Tijana Glavina del Rio, Kristen M. DeAngelis
Summary: In this study, a novel bacterium strain 159R belonging to the genus Sodalis was successfully isolated from temperate forest soil. It has the capability to depolymerize lignin and can survive in anaerobic conditions. Its application potential in lignocellulosic biofuel production is promising.
MICROBIOLOGY SPECTRUM
(2022)
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Article
Biochemistry & Molecular Biology
Supratim Mukherjee, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Jon Bertsch, Jagadish Chandrabose Sundaramurthi, Mahathi Kandimalla, Paul A. Nicolopoulos, Alessandro Favognano, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The Genomes OnLine Database (GOLD) continues to serve as a flagship genomic metadata repository, providing freely available projects and metadata for large-scale comparative genomics analysis. New features and components have been added in the latest GOLD v.9 version.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin
Summary: We developed a computational pipeline to identify viroid-like cccRNAs and found a 5-fold increase in the number of identified elements compared to previous studies. The presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems suggests that their host range is broader than currently known.
Article
Ecology
Antonio P. Camargo, Rafael S. C. de Souza, Juliana Jose, Isabel R. Gerhardt, Ricardo A. Dante, Supratim Mukherjee, Marcel Huntemann, Nikos C. Kyrpides, Marcelo F. Carazzolle, Paulo Arruda
Summary: The grassland ecosystem of Brazilian campos rupestres has low concentrations of phosphorus and nitrogen, yet supports a high plant diversity. This study explores the taxonomic profile and functional potential of microbial communities associated with two plant species of the campos rupestres. The results show that the soil and rock communities associated with these plants share a core group of efficient colonizers enriched in certain bacterial families. The microbial populations associated with plant roots have a genetic repertoire for organic compound intake, phosphorus and nitrogen turnover, highlighting their role in nutrient availability.
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan J. Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Simon Roux
Summary: Viruses play critical roles in all microbiomes and their genomic diversity and impacts on biological processes are extensively explored through metagenomics. IMG/VR is a platform providing access to a large collection of viral sequences along with functional annotation and metadata. The latest version, IMG/VR v4, contains over 15 million virus genomes and genome fragments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan J. Ritter, Cody Webb, Dongying Wu, Neha J. Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The Integrated Microbial Genomes & Microbiomes system (IMG/M) at the Department of Energy Joint Genome Institute (JGI) provides support for comparative analysis of various genomes, metagenomes, and metatranscriptomes. It includes datasets from JGI, as well as imported datasets from public sources and user-submitted datasets. In recent years, efforts have been made to improve annotation pipeline, upgrade reference database versions, and add new analysis functionalities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Yiran Liang, Thy Truong, Aubrianna J. Saxton, Hannah Boekweg, Samuel H. Payne, Pam M. Van Ry, Ryan T. Kelly
Summary: Recent advances in mass spectrometry-based single-cell proteomics have improved sensitivity, but measurement throughput is still limited. To increase throughput, we combined isobaric and isotopic labeling methods for multiplexing. By using SILAC and TMT labeling, we were able to analyze up to 28 single cells in a single LC-MS analysis. With a customized nanowell chip, sample losses were minimized. The measurement throughput could be further increased with a high-duty-cycle multicolumn LC system.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Hannah Boekweg, Samuel H. Payne
Summary: Single-cell proteomics is growing rapidly, but there is a lack of attention on algorithms for identifying and quantifying proteins. Current algorithms designed for bulk data may not hold true for single-cell data, so it is important to assess their performance and optimize them for single-cell data.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Mathematical & Computational Biology
Supratim Mukherjee, Galina Ovchinnikova, Dimitri Stamatis, Cindy Tianqing Li, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The power of next-generation sequencing has led to a massive increase in projects aiming to understand the diversity of complex microbial environments. However, the lack of standardized reporting standards for microbiome data and samples poses a challenge for follow-up studies. The Genomes OnLine Database (GOLD) has developed a standardized naming system for microbiome samples to address this issue and has continued to enrich the research community with well-curated and understandable names for metagenomes and metatranscriptomes. This naming system should be adopted as a best practice to improve the interoperability and reusability of microbiome data.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Multidisciplinary Sciences
Milene C. Vallejo, Soumyadeep Sarkar, Emily C. Elliott, Hayden R. Henry, Samantha M. Powell, Ivo Diaz Ludovico, Youngki You, Fei Huang, Samuel H. Payne, Sasanka Ramanadham, Emily K. Sims, Thomas O. Metz, Raghavendra G. Mirmira, Ernesto S. Nakayasu
Summary: Extracellular vesicles (EVs) have important roles in cell-to-cell communication and biomarker studies. In this study, a proteomics meta-analysis was performed to refine the composition of plasma EVs by separating EV proteins and contaminants into different clusters. The refined EV protein list obtained from this study provides a valuable resource for mechanistic and biomarker studies.