Article
Biotechnology & Applied Microbiology
Danny Bergeron, Cedric Laforest, Stacey Carpentier, Annabelle Calve, Etienne Fafard-Couture, Gabrielle Deschamps-Francoeur, Michelle S. Scott
Summary: The study reveals that snoRNA copy regulation affects family sizes, genomic location of the members, and controls both member and total family abundance to meet the needs of individual tissues. Additionally, the expression variability of individual snoRNA family members is preferred over the total variability of the family, pointing towards differential regulation mechanisms exist to ensure uniformity of the total family abundance across tissues.
Article
Biotechnology & Applied Microbiology
In Seok Yang, Insu Jang, Jin Ok Yang, Jinhyuk Choi, Min-Seo Kim, Ka-Kyung Kim, Byung-Joon Seung, Jae-Ho Cheong, Jung-Hyang Sur, Hojung Nam, Byungwook Lee, Junho Kim, Sangwoo Kim
Summary: The study developed a new database, CanISO, to store a large collection of transcriptome profiles and genomic variations for domestic dogs. The results from CanISO are important for increasing understanding of the dog genome and transcriptome, as well as its functional associations with humans, particularly in cancer-related research.
Article
Plant Sciences
Pan Wang, Yi Mo, Yi Wang, Yuchong Fei, Jianting Huang, Jun Ni, Zeng-Fu Xu
Summary: This study developed the first integrated germplasm and genomic database for macadamia, which includes various genomic data and bioinformatic tools for researchers to analyze and utilize the information. The database provides abundant information on the genomic sequence of macadamia, helping scientists better conduct molecular breeding research.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Eduard Ocana-Pallares, Tom A. Williams, David Lopez-Escardo, Alicia S. Arroyo, Jananan S. Pathmanathan, Eric Bapteste, Denis Tikhonenkov, Patrick J. Keeling, Gergely J. Szollosi, Inaki Ruiz-Trillo
Summary: Animals and fungi have distinct morphologies and genetic changes. Animals gained important genes from pre-metazoan ancestors, while fungi experienced net losses in functional categories. Fungal genomes have more metabolic genes and show less divergence from the Opisthokonta ancestor compared to animals. Gene fusions are more prevalent in animals, while horizontal gene transfers are more common in fungi and protists.
Article
Biochemical Research Methods
Dorte Wittenburg, Michael Doschoris, Jan Klosa
Summary: This study constructs different groups based on dependencies between genomic regions and develops a new function package to account for the impact of family structure on genome-based evaluations. The research demonstrates that considering family structure can more accurately identify dependencies in the genome and improve the accuracy of genome-based association studies.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Shuya Ikeda, Hiromasa Ono, Tazro Ohta, Hirokazu Chiba, Yuki Naito, Yuki Moriya, Shuichi Kawashima, Yasunori Yamamoto, Shinobu Okamoto, Susumu Goto, Toshiaki Katayama
Summary: This article introduces TogoID, a service that implements ID conversion to help life science researchers seamlessly connect scattered biological data across various databases. TogoID features an intuitive interface and API access, supports multistep conversions, and provides ontology-guided interpretation of biological meanings.
Article
Biochemical Research Methods
Kristen D. Curry, Qi Wang, Michael G. Nute, Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, Tor Savidge, Sonia Villapol, Alexander Dilthey, Todd J. Treangen
Summary: 16S ribosomal RNA-based analysis is the standard method for studying microbial community composition. Full-length 16S rRNA gene sequences have the potential to provide species-level accuracy. Emu is an approach that can generate taxonomic abundance profiles from full-length 16S rRNA reads, accurately estimating microbial abundance.
Article
Genetics & Heredity
Sanjaya Gyawali, Gehendra Bhattarai, Ainong Shi, Chris Kik, Lindsey J. du Toit
Summary: Genotype-by-sequencing (GBS) was used to investigate the genetic diversity and structure between Spinacia turkestanica and cultivated spinach, S. oleracea. The study identified distinct genetic groups in both species, suggesting a clear separation in their genetic backgrounds and a role of selective sweeps during spinach domestication.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Jillian Rumore, Matthew Walker, Franco Pagotto, Jessica D. Forbes, Christy-Lynn Peterson, Andrea D. Tyler, Morag Graham, Gary Van Domselaar, Celine Nadon, Aleisha Reimer, Natalie Knox
Summary: This study evaluated the performance of a foodborne pathogen-specific reference database compared to a universal reference database, and found that using a pathogen-specific database can achieve higher classification precision in complex food matrices, with lower computational resource requirements.
Article
Biochemistry & Molecular Biology
Ying Zhang, Huaicheng Sun, Wei Zhang, Tingting Fu, Shijie Huang, Minjie Mou, Jinsong Zhang, Jianqing Gao, Yichao Ge, Qingxia Yang, Feng Zhu
Summary: This study developed the first comprehensive database of single-cell transcriptomic annotation resource (CellSTAR), providing expertly annotated reference data and thousands of marker genes for accurate cell type annotation. It is expected to attract broad research interests.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Xiaoqian Lin, Tongyuan Hu, Jianwei Chen, Hewei Liang, Jianwei Zhou, Zhinan Wu, Chen Ye, Xin Jin, Xun Xu, Wenwei Zhang, Xiaohuan Jing, Tao Yang, Jian Wang, Huanming Yang, Karsten Kristiansen, Liang Xiao, Yuanqiang Zou
Summary: The authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, which includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals. They classify 527 species from 8 phyla, including 179 previously unidentified species, and provide information on secondary metabolite biosynthetic gene clusters and gut phage-bacteria interactions.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Yheni Dwiningsih, Anuj Kumar, Julie Thomas, Charles Ruiz, Jawaher Alkahtani, Abdulrahman Al-hashimi, Andy Pereira
Summary: This study utilized a recombinant inbred line (RIL) population based on high-throughput SNP markers to identify genetic information related to rice grain characteristics and propose a strategy for improving rice quality. The results indicated that these traits were quantitatively inherited, with a total of 28 QTLs and 92 candidate genes identified.
Article
Genetics & Heredity
Paula Korkuc, Danny Arends, Katharina May, Sven Koenig, Gudrun A. Brockmann
Summary: A genome-wide association analysis of German Black Pied cattle identified SNPs affecting milk production traits, with significant effects found on chromosomes 1, 6, and 20. The study confirmed that not all detected SNPs are definitive, but the results can provide a basis for genetic improvement of DSN cattle.
FRONTIERS IN GENETICS
(2021)
Article
Microbiology
Wei Wang, Sabrina Lusvarghi, Rahul Subramanian, Nusrat J. Epsi, Richard Wang, Emilie Goguet, Anthony C. Fries, Fernando Echegaray, Russell Vassell, Si'Ana A. Coggins, Stephanie A. Richard, David A. Lindholm, Katrin Mende, Evan C. Ewers, Derek T. Larson, Rhonda E. Colombo, Christopher J. Colombo, Janet O. Joseph, Julia S. Rozman, Alfred Smith, Tahaniyat Lalani, Catherine M. Berjohn, Ryan C. Maves, Milissa U. Jones, Rupal Mody, Nikhil Huprikar, Jeffrey Livezey, David Saunders, Monique Hollis-Perry, Gregory Wang, Anuradha Ganesan, Mark P. Simons, Christopher C. Broder, David R. Tribble, Eric D. Laing, Brian K. Agan, Timothy H. Burgess, Edward Mitre, Simon D. Pollett, Leah C. Katzelnick, Carol D. Weiss
Summary: The emergence of SARS-CoV-2 variants poses challenges to vaccination strategies. A study found that mRNA COVID-19 vaccinations increased neutralization of some variants but had less effect on others. Considering antigenic differences among variants can aid in understanding the complex patterns of humoral immunity and inform the selection of future COVID-19 vaccine strains.
CELL HOST & MICROBE
(2022)
Article
Biochemical Research Methods
Grimur Hjoerleifsson Eldjarn, Andrew Ramsay, Justin J. J. van der Hooft, Katherine R. Duncan, Sylvia Soldatou, Juho Rousu, Ronan Daly, Joe Wandy, Simon Rogers
Summary: Specialised metabolites from microbial sources, particularly antibiotics, are widely used in biomedical applications. The challenge lies in establishing links between Biosynthetic Gene Clusters (BGCs) and metabolites due to the lack of detailed biosynthetic knowledge for most BGCs. The software framework NPLinker is introduced to address this challenge by combining strain correlation analysis and feature-based analysis methods for improved performance in linking genomic and metabolomic data.
PLOS COMPUTATIONAL BIOLOGY
(2021)