Article
Biochemistry & Molecular Biology
Xiaoliang He, Tianhua Lu, Xiaohui Zhou
Summary: Utilizing Single molecule real time (SMRT) sequencing technology, the high-quality genome sequence of Pectobacterium carotovorum (PC1) was obtained, revealing key pathogenic genes and regulatory systems that could be relevant to its pathogenicity and specific bactericides. This study provides a theoretical basis for further investigation into the bacterial pathogenicity of PC1 and biological specific bactericides.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biology
Carlos Farkas, Antonia Recabal, Andy Mella, Daniel Candia-Herrera, Maryori Gonzalez Olivero, Jody Jonathan Haigh, Estefania Tarifeno-Saldivia, Teresa Caprile
Summary: This study developed a genome-guided transcriptome annotation pipeline that integrates various bioinformatics approaches to accurately annotate the transcriptome and identify new genes and homologous species.
Article
Biochemical Research Methods
Le Zhang, Zichun Dai, Jun Yu, Ming Xiao
Summary: By reviewing previous studies on CpG-related genes, it is suggested that approximately half of human genes, particularly housekeeping genes, are regulated by CpG islands (CGIs). However, the specific definition of CGIs, their positioning in gene structures, and the regulatory mechanisms associated with CGIs require further explanation. Combining different analysis methods, it has been found that genes associated with high CpG density are more likely to be housekeeping genes, while the characteristics of genes with intermediate CpG density are less distinct.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Luis Pedro Coelho, Renato Alves, Alvaro Rodriguez del Rio, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquin Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjorn Nielsen, Jaime Huerta-Cepas, Peer Bork
Summary: The majority of microbial genes are specific to a single habitat, with a small fraction found in multiple habitats enriched in antibiotic-resistance genes and markers for mobile genetic elements. A small fraction of protein families contain the majority of genes, with most genetic variability observed within the families being neutral or nearly neutral.
Article
Biology
Xiaolei Liu, Yayan Feng, Xue Bai, Xuelin Wang, Rui Qin, Bin Tang, Xinxin Yu, Yong Yang, Mingyuan Liu, Fei Gao
Summary: Xiaolei Liu, Yayan Feng, et al. report an annotated draft reference genome of the non-encapsulated Trichinella pseudospiralis, and perform comparative multi-omics analyses with encapsulated T. spiralis. Overexpression of TP12446, a key excretory/secretory gene, in a mouse C2C12 skeletal muscle cell line could induce inhibition of myotube formation and differentiation. These results provide insight into the mechanism of nurse cell formation and immunoevasion, as well as the identification of potential pharmacological and diagnostic targets for trichinellosis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Plant Sciences
Seongmin Hong, Yong Pyo Lim, Suk-Yoon Kwon, Ah-Young Shin, Yong-Min Kim
Summary: In polyploids, whole genome duplication plays a significant role in genome expansion, evolution, and diversification. The flowering-time gene family, one of the largest expanded gene families in plants, has functionally diversified through evolution, providing advantages for plant adaptation and survival.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Alejandro Rubio, Juan Jimenez, Antonio J. Perez-Pulido
Summary: Bacterial genomes provide valuable data for understanding the complete set of genes of a species. By analyzing multiple bacterial strains, shared genes and strain-specific genes can be identified. However, current computational gene finders may miss some existing genes. This study estimated the selective pressure on genes in the Acinetobacter baumannii pangenome and found that most genes are under negative selection, but a subset showed values compatible with positive selection, which may be related to acquisition of new functions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Ann E. Collier, Samantha N. Piekos, Angela Liu, Jillian M. Pattison, Franco Felix, Alessandro A. Bailetti, Egor Sedov, Sadhana Gaddam, Hanson Zhen, Anthony E. Oro
Summary: This study dissects human surface ectoderm (SE) differentiation using multiomics and identifies GRHL2 as a key mediator of early SE commitment, which directs cell fate away from the neural lineage. GRHL2 and SE regulator AP2a balance cell fate decisions by facilitating or restricting binding to SE loci. Integration of regulatory sites with genomic variants associated with ectodermal dysplasias reveals 55 loci previously implicated in craniofacial disorders, including regions where disease-linked variants affect GRHL2/AP2a binding and gene transcription. These findings enhance our understanding of SE commitment and oligogenic disease pathogenesis.
Review
Biology
Mylena D. Santander, Maximiliano M. Maronna, Joseph F. Ryan, Sonia C. S. Andrade
Summary: This article reviews the current status of Medusozoa genomics, including taxonomic coverage, quality and completeness of sequencing datasets, research questions addressed with genomics, and the accessibility of data. The lack of standardization in genomic projects and reports is emphasized, and recommendations are provided to enhance future collaborative research.
Article
Biochemistry & Molecular Biology
Roman Martin, Hagen Dressler, Georges Hattab, Thomas Hackl, Matthias G. Fischer, Dominik Heider
Summary: MOSGA 2 is an accessible and easy-to-use analysis tool for eukaryotic genome annotations, developed with advanced analyses to improve annotation quality. By validating and ensuring genome data quality, integrating comparative genomics methods, and extending established applications, MOSGA 2 provides a broader genomic view and comprehensive genome analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Ecology
Stefan Kusch, Justine Larrouy, Heba M. M. Ibrahim, Shantala Mounichetty, Noemie Gasset, Olivier Navaud, Malick Mbengue, Catherine Zanchetta, Celine Lopez-Roques, Cecile Donnadieu, Laurence Godiard, Sylvain Raffaele
Summary: This article discusses the importance of the host range of parasites in assessing disease epidemic dynamics, especially the evolutionary adaptation of pathogens to new hosts. It compares the global transcriptome reprogramming of Sclerotinia sclerotiorum and S. trifoliorum on different hosts, as well as gene space conservation in the genome. The results show that there are differences in the regulation of resistance to Brassicaceae plants in S. trifoliorum, which may be related to its genetic adaptation in host range expansion.
Article
Hematology
Ricky Tirtakusuma, Katarzyna Szoltysek, Paul Milne, Vasily V. Grinev, Anetta Ptasinska, Paulynn S. Chin, Claus Meyer, Sirintra Nakjang, Jayne Y. Hehir-Kwa, Daniel Williamson, Pierre Cauchy, Peter Keane, Salam A. Assi, Minoo Ashtiani, Sophie G. Kellaway, Maria R. Imperato, Fotini Vogiatzi, Elizabeth K. Schweighart, Shan Lin, Mark Wunderlich, Janine Stutterheim, Alexander Komkov, Elena Zerkalenkova, Paul Evans, Hesta McNeill, Alex Elder, Natalia Martinez-Soria, Sarah E. Fordham, Yuzhe Shi, Lisa J. Russell, Deepali Pal, Alex Smith, Zoya Kingsbury, Jennifer Becq, Cornelia Eckert, Oskar A. Haas, Peter Carey, Simon Bailey, Roderick Skinner, Natalia Miakova, Matthew Collin, Venetia Bigley, Muzlifah Haniffa, Rolf Marschalek, Christine J. Harrison, Catherine A. Cargo, Denis Schewe, Yulia Olshanskaya, Michael J. Thirman, Peter N. Cockerill, James C. Mulloy, Helen J. Blair, Josef Vormoor, James M. Allan, Constanze Bonifer, Olaf Heidenreich, Simon Bomken
Summary: MLL/AF4 fusion gene defines a high-risk subtype of B-precursor acute lymphoblastic leukemia. Relapse can result in lineage switch to acute myeloid leukemia, which is associated with changes in chromatin accessibility and transcriptional programs. The altered expression and mutation of chromatin modifiers are recurrently associated with the relapsed myeloid phenotype, indicating disrupted epigenetic regulation drives and maintains lineage switching in MLL/AF4 leukemia.
Article
Plant Sciences
Kwanjeera Wanichthanarak, Intawat Nookaew, Phongthana Pasookhush, Thidathip Wongsurawat, Piroon Jenjaroenpun, Namkhang Leeratsuwan, Songsak Wattanachaisaereekul, Wonnop Visessanguan, Yongyut Sirivatanauksorn, Narong Nuntasaen, Chutima Kuhakarn, Vichai Reutrakul, Pravech Ajawatanawong, Sakda Khoomrung
Summary: In this study, we successfully outlined the complete chloroplast genome of Ventilago harmandiana using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the genome were confirmed with PCR amplifications and investigation of coverage depth. The phylogenetic trees reconstructed using prevalent methods were topologically similar.
Article
Multidisciplinary Sciences
Gayan Balasooriya, David L. Spector
Summary: In this study, the establishment of monoallelic gene expression in the cardiac lineage was elucidated through allele-specific single cell transcriptomic analysis. The researchers found that the regulation of monoallelically expressed autosomal genes in undifferentiated cells is dependent on the genetic background of the parental alleles, but this dependence is absent in differentiated cardiomyocytes. Additionally, epigenetic differences were observed between deterministic and random autosomal monoallelic genes, and a greater contribution of the maternal allele to cardiac tissue development and homeostasis was highlighted. These findings underscore the importance of allele-specific insights into gene regulation in development, homeostasis, and disease.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Xiaoli Xue, Wei Zhang, Anjing Fan
Summary: This paper proposes a novel strategy for identifying key proteins by constructing reliable protein-protein interaction (PPI) networks. Five Gene Ontology (GO)-based semantic similarity measurements are used to calculate the confidence scores for protein pairs, and the refined PPI networks are constructed by filtering low-confidence links. Six topology-based centrality methods are applied to test the performance of the measurements under the original and refined networks. The results show that the performance of the centrality methods is relatively better under the refined PPI networks, with Resnik using BP annotation term performing the best.
Article
Plant Sciences
Pierre Baduel, Brian Arnold, Cara M. Weisman, Ben Hunter, Kirsten Bomblies
Article
Multidisciplinary Sciences
Brian J. Arnold, Brett Lahner, Jeffrey M. DaCosta, Caroline M. Weisman, Jesse D. Hollister, David E. Salt, Kirsten Bomblies, Levi Yant
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Ecology
Patrick Monnahan, Filip Kolar, Pierre Baduel, Christian Sailer, Jordan Koch, Robert Horvath, Benjamin Laenen, Roswitha Schmickl, Pirita Paajanen, Gabriela Sramkova, Magdalena Bohutinska, Brian Arnold, Caroline M. Weisman, Karol Marhold, Tanja Slotte, Kirsten Bomblies, Levi Yant
NATURE ECOLOGY & EVOLUTION
(2019)
Review
Biochemistry & Molecular Biology
Caroline M. Weisman
Summary: This review provides an overview of the origins and molecular functions of de novo genes, and speculates on how they manage to emerge despite opposing odds.
JOURNAL OF MOLECULAR EVOLUTION
(2022)
Article
Genetics & Heredity
Daniel P. Higgins, Caroline M. Weisman, Dominique S. Lui, Frank A. D'Agostino, Amy K. Walker
Summary: Omics tools provide broad datasets for biological discovery, but the current computational tools for identifying important genes or pathways have biases towards well-described pathways, limiting their utility for poorly annotated genes. We developed WormCat, an annotation and category enrichment tool, which retains genes with no annotation information as a special UNASSIGNED category. We found that the UNASSIGNED gene category enrichment exhibits tissue-specific expression patterns and can include genes with known functions. Some of the UNASSIGNED genes have human orthologs, including those linked to human diseases. A new method called abSENSE suggests that the failure of BLAST to detect homology explains the lineage specificity of many UNASSIGNED genes, indicating a larger subset could be related to human genes. WormCat provides an annotation strategy that allows the association of UNASSIGNED genes with specific phenotypes and known pathways.
Article
Biochemistry & Molecular Biology
Caroline M. Weisman, Andrew W. Murray, Sean R. Eddy