Article
Biochemical Research Methods
Sylwester Swat, Artur Laskowski, Jan Badura, Wojciech Frohmberg, Pawel Wojciechowski, Aleksandra Swiercz, Marta Kasprzak, Jacek Blazewicz
Summary: This study proposes a new genome-scale de novo assembler, ALGA, based on the overlap graph approach, which can generate more accurate contigs in a short amount of time. ALGA outperforms nine state-of-the-art assemblers in terms of overall quality of genome reconstruction, achieving a good balance between genome coverage, accuracy, and length of resulting sequences.
Article
Multidisciplinary Sciences
Johnathan Wong, Lauren Coombe, Vladimir Nikolic, Emily Zhang, Ka Ming Nip, Puneet Sidhu, Rene L. Warren, Inanc Birol
Summary: Current state-of-the-art de novo long read genome assemblers often require excessive RAM. Our work introduces GoldRush, a new algorithm with linear time complexity that achieves efficient genome assembly using a dynamic data structure. We tested GoldRush on different datasets and demonstrated its scalability and effectiveness in producing high-quality assembly scaffolds within a day.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Catarina Ines Mendes, Pedro Vila-Cerqueira, Yair Motro, Jacob Moran-Gilad, Joao Andre Carrico, Mario Ramirez
Summary: The study developed a flexible platform, LMAS, for evaluating the performance of de novo assemblers in metagenomic analysis. The k-mer De Bruijn graph assemblers outperformed other approaches but had higher computational cost. Metagenomic specific assemblers did not consistently outperform other genomic assemblers in metagenomic samples. Therefore, caution should be exercised when using certain assemblers for complex samples.
Article
Multidisciplinary Sciences
Mohamed Awad, Xiangchao Gan
Summary: This paper introduces GALA, a computational framework for chromosome-based sequencing data separation and gap-free de novo assembly. It allows integration of different data sources and addresses the challenge of achieving gap-free chromosome-scale assemblies using current workflows for long-read platforms. The method is demonstrated through the assembly of various genomes.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Lifu Song, Feng Geng, Zi-Yi Gong, Xin Chen, Jijun Tang, Chunye Gong, Libang Zhou, Rui Xia, Ming-Zhe Han, Jing-Yi Xu, Bing-Zhi Li, Ying-Jin Yuan
Summary: The study introduces a novel DNA strand assembly algorithm, DBGPS, that utilizes de Bruijn graph and greedy path search to tackle errors commonly encountered in DNA data storage. DBGPS demonstrates significant advantages in handling DNA breaks, rearrangements, and indels, and its robustness is demonstrated through various tests.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ting-Ting Li, Tian Xia, Jia-Qi Wu, Hao Hong, Zhao-Lin Sun, Ming Wang, Fang-Rong Ding, Jing Wang, Shuai Jiang, Jin Li, Jie Pan, Guang Yang, Jian-Nan Feng, Yun-Ping Dai, Xue-Min Zhang, Tao Zhou, Tao Li
Summary: This study reports the de novo assembly of a cattle genome and provides a detailed annotation of the immunogenomic loci. The immunogenomic regions, including immunoglobulin (IG) loci, T-cell receptor (TR) loci, and the major histocompatibility complex (MHC) locus, are seamlessly assembled and precisely annotated. The characterization of immune genes in cattle reveals their diversity and the MHC gene structures are also revealed with properly phased haplotypes.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Maria Gladysheva-Azgari, Kristina Petrova, Svetlana Tsygankova, Irina Mitrofanova, Anatoliy Smykov, Eugenia Boulygina, Natalia Slobodova, Sergey Rastorguev, Fedor Sharko
Summary: This paper presents the assembly of the P. persica cv. 'Sovetskiy' genome using a hybrid assembly approach with Oxford Nanopore long reads and Illumina short reads. The unique cultivars from the Nikitsky Botanical Garden are essential for a more comprehensive assessment of the peach genome in Crimea and southern Russia.
Article
Microbiology
Daria Shafranskaya, Varsha Kale, Rob Finn, Alla L. Lapidus, Anton Korobeynikov, Andrey D. Prjibelski
Summary: While metagenome sequencing provides insights on microbial communities, metatranscriptome analysis is useful for studying functional activity. However, the complexity, dynamic range, and lack of computational methods for assembling metatranscriptomes pose challenges. This study presents MetaGT, a pipeline that combines metatranscriptomic and metagenomic data to improve assembly coverage and completeness. Results show significant improvement compared to existing methods. The pipeline, implemented in NextFlow, is available athttps://github.com/ablab/metaGT.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Shuangying Jiang, Yuanwei Tang, Liang Xiang, Xinlu Zhu, Zelin Cai, Ling Li, Yingxi Chen, Peishuang Chen, Yuge Feng, Xin Lin, Guoqiang Li, Jafar Sharif, Junbiao Dai
Summary: Synthetic genomics has opened new avenues for the functional study of viral and microbial genomes, as well as providing a method for constructing larger genomes of higher organisms. The study introduces an efficient pipeline for constructing large DNA fragments and describes a scar-free engineering method for assembling sequences. This method offers a standard framework for producing long DNA molecules crucial for synthetic genomics and metabolic engineering.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Multidisciplinary Sciences
Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong Won Kim, Yibing Zeng, Christine H. O'Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia Krasileva, John L. Portwood, Ethalinda K. S. Cannon, Carson M. Andorf, Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan Gent, Candice N. Hirsch, Doreen Ware, R. Kelly Dawe
Summary: The study reports de novo genome assemblies, transcriptomes, annotations, and methylomes for 26 maize inbreds, with over 103,000 pangenes identified. It shows that the ancient tetraploid character of maize continues to degrade by fractionation, and reveals variation in DNA methylation levels across genotypes.
Article
Biochemical Research Methods
Jia-Yuan Zhang, Hannah Roberts, David S. C. Flores, Antony J. Cutler, Andrew C. Brown, Justin P. Whalley, Olga Mielczarek, David Buck, Helen Lockstone, Barbara Xella, Karen Oliver, Craig Corton, Emma Betteridge, Rachael Bashford-Rogers, Julian C. Knight, John A. Todd, Gavin Band
Summary: The human immune system relies on a vast array of antibodies and protein receptors to recognize pathogens, making analysis of gene families complex due to their intricate patterns of similarities and differences. By applying various sequencing methods and reconstructing immune-associated gene sequences, accurate assemblies were generated from a single individual's DNA, revealing structural differences and gene copy number variations. In-depth study of these variations may lead to a better understanding of the impact of genetic variation on human diseases.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Pietro Libro, Andrea Chiocchio, Erika De Rysky, Jessica Di Martino, Roberta Bisconti, Tiziana Castrignano, Daniele Canestrelli
Summary: Dispersal is a crucial process in ecology and evolutionary biology, which shapes biodiversity patterns. Individual attitudes to disperse vary within populations and individual personality plays a key role in shaping these attitudes. In this study, we generated and annotated the first de novo transcriptome of head tissues from Salamandra salamandra individuals with distinct behavioral profiles. The resulting transcriptome provides a reliable reference for comparative gene expression studies and whole transcriptome and proteome studies in amphibians.
Article
Agronomy
Tae-Heon Kim, Young-Mi Yoon, Jin-Cheon Park, Jong-Ho Park, Kyong-Ho Kim, Yang-Kil Kim, Jae-Han Son, Tae-Il Park
Summary: This study used transcriptome sequencing to investigate the seedling stage of oat and developed 30 dCAPS markers, which are important for oat genetic analysis, cultivar identification, and breeders' rights protection.
Article
Biochemistry & Molecular Biology
Ligang Ma, Chengming Dong, Chi Song, Xiaolan Wang, Xiaoke Zheng, Yan Niu, Shilin Chen, Weisheng Feng
Summary: Rehmannia glutinosa is a medicinal plant with important pharmaceutical properties in traditional Chinese medicine. A reference genome has been reported using Nanopore technology, Illumina and Hi-C sequencing, revealing insights into the molecular biology and evolution of R. glutinosa. The genome assembly has facilitated the discovery and development of pharmacological compounds.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li
Summary: hifiasm is a novel assembler that utilizes long high-fidelity sequence reads to accurately represent haplotype information, outperforming existing tools in haplotype-resolved assembly on various datasets, including a hexaploid genome dataset.
Article
Food Science & Technology
Madhushri S. Varunjikar, Carlos Moreno-Ibarguen, Juan S. Andrade-Martinez, Hui-Shan Tung, Ikram Belghit, Magnus Palmblad, Pal A. Olsvik, Alejandro Reyes, Josef D. Rasinger, Kai K. Lie
Summary: The study shows that both DNA and protein-based approaches can efficiently tackle current challenges in feed and food authentication analyses.
Article
Biochemistry & Molecular Biology
Andre Luiz de Oliveira, Jessica Mitchell, Peter Girguis, Monika Bright
Summary: The study presents the high-quality draft genome of the giant tubeworm Riftia pachyptila, revealing signs of reductive evolution and evolutionary adaptations to the vent environment and endosymbiosis. The conservation of developmental gene repertoire in the gutless tubeworm and the role of innate immune system in establishing symbiosis are highlighted. The research bridges four decades of physiological research in Riftia and sheds new light on development, whole organism functions, and evolution in the giant tubeworm.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Allan C. de Azevedo-Martins, Kary Ocana, Wanderley de Souza, Ana Tereza Ribeiro de Vasconcelos, Marta M. G. Teixeira, Erney P. Camargo, Joao M. P. Alves, Maria Cristina M. Motta
Summary: The symbiotic relationship between trypanosomatids and bacteria involves extensive metabolic exchanges, with the bacteria providing essential metabolic pathways for the protozoan. An in-silico study found that most genes involved in glycerophospholipid production are only present in the Symbiont Harboring Trypanosomatids (SHTs) and not in the bacteria. The bacterium has specific sequences and genes related to phosphatidylglycerol and phosphatidic acid production, which likely enhance SHT phosphatidic acid production. Phylogenetic analysis suggests that enzymes involved in the glycerophospholipid pathway have eukaryotic characteristics, indicating no gene transfers from the bacterium to the SHT nucleus. Overall, the data indicate that the symbiont plays a limited role in glycerophospholipid production, acquiring most of these molecules from the SHT.
Review
Microbiology
Juan Sebastian Andrade-Martinez, Laura Carolina Camelo Valera, Luis Alberto Chica Cardenas, Laura Forero-Junco, Gamaliel Lopez-Leal, J. Leonardo Moreno-Gallego, Guillermo Rangel-Pineros, Alejandro Reyes
Summary: Over a century of bacteriophage research has uncovered fundamental aspects of their biology, ecology, and evolution. The introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on ecological and physiological processes. The availability of computational tools has greatly contributed to our knowledge of phage diversity and ecology, but the ongoing surge in software programs makes it challenging to keep up with them.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Thays Bueno, Patricia P. Fontes, Valeria Y. Abe, Alice Satiko Utiyama, Renato L. Senra, Liliane S. Oliveira, Adriana Brombini dos Santos, Everton G. Capote Ferreira, Luana M. Darben, Aluizio Borem de Oliveira, Ricardo Abdelnoor, Steven A. Whitham, Luciano G. Fietto, Francismar C. Marcelino-Guimaraes
Summary: This study investigates the pathogenic mechanisms of Asian soybean rust, focusing on the interaction between the effector protein Phapa7431740 and a soybean protein Gm beta GLU. The results show that Phapa-7431740 suppresses host immune response and interacts with Gm beta GLU. The findings suggest that Phapa-7431740 may inhibit immune response by interfering with the activity of glucan endo-1,3-beta-glucosidase.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Daniel Ferreira de Lima Neto, Vagner Fonseca, Ronaldo Jesus, Leonardo Hermes Dutra, Layssa Miranda de Oliveria Portela, Carla Freitas, Eduardo Fillizola, Breno Soares, Andre Luiz de Abreu, Sandeep Twiari, Vasco Azevedo, Aristoteles Goes-Neto, Arnaldo Correia de Medeiros, Norberto Peporine Lopes, Paolo Marinho de Andrade Zanotto, Rodrigo Bentes Kato
Summary: This study used the structure of SARS-CoV-2 spike protein to examine the impact of mutations on the protein's stability and interaction with ACE-2 receptor. Molecular dynamics simulations and protein-protein docking experiments revealed that the mutations affected the stability of the protein and improved its interaction with ACE-2 receptor, particularly in the Gamma variant.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Andre Luiz De Oliveira, Abhishek Srivastava, Salvador Espada-Hinojosa, Monika Bright
Summary: This study presents the closed chromosomal sequence of the endosymbiont Endoriftia using single-molecule real-time sequencing. The genome of Endoriftia is smaller than expected and shows versatility in sulfur metabolism. The presence of rRNA operons, CRISPR regions, and different secretion systems suggests lineage-specific adaptations. The study also highlights the importance of molecular memory-based immunity against phages in Endoriftia.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Virology
Liliane S. S. Oliveira, Alejandro Reyes, Bas E. E. Dutilh, Arthur Gruber
Summary: The study developed protocols for the rational design of profile HMMs, which can automatically identify informative sequence motifs and construct profile HMMs. These methods were applied to detect and classify different viral groups and related transposable elements.
Article
Microbiology
Alejandro Castellanos, Leda Restrepo, Leandro Bajana, Irma Betancourt, Bonny Bayot, Alejandro Reyes
Summary: AHPND is a disease causing significant losses in the shrimp farming industry, with global losses exceeding $2.6 billion. The most common etiological agent is V. parahaemolyticus strains carrying the PirAB(vp) toxin. By analyzing South American AHPND-causing V. parahaemolyticus isolates at the genomic level, it was found that they have high similarity but do not cluster with other Mexican strains, suggesting different genetic backgrounds and possible acquisition of the pVA1-type plasmid through horizontal gene transfer at different times.
MICROBIOLOGY SPECTRUM
(2023)
Article
Infectious Diseases
Alioune Gaye, Cheikh Fall, Oumar Faye, Myrielle Dupont-Rouzeyrol, El Hadji Ndiaye, Diawo Diallo, Paolo Marinho de Andrade Zanotto, Ibrahima Dia, Scott C. Weaver, Mawlouth Diallo
Summary: This study assessed the susceptibility of A. aegypti and C. quinquefasciatus to ZIKV strains from Senegal, Brazil, and New Caledonia, and found that the Senegalese strain had a significantly higher infection rate compared to the Brazilian and New Caledonian strains. No infection was recorded for C. quinquefasciatus.
TROPICAL MEDICINE AND INFECTIOUS DISEASE
(2023)
Letter
Biotechnology & Applied Microbiology
Evelien M. M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cedric Lood, Elliot J. J. Lefkowitz, Matthew B. B. Sullivan, Robert A. A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. E. Dutilh
NATURE BIOTECHNOLOGY
(2023)
Correction
Biotechnology & Applied Microbiology
Evelien M. M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cedric Lood, Elliot J. Lefkowitz, Matthew B. B. Sullivan, Robert A. A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. E. Dutilh
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina Sakharova, Manja Marz, Alejandro Reyes Munoz, Martin Hoelzer, Robert D. Finn
Summary: VIRify is a computational pipeline that accurately characterizes the functional and taxonomic aspects of viral communities based on sequencing data. It utilizes viral profile hidden Markov models to identify and classify viral contigs, providing taxonomic classifications at different ranks.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Microbiology
Kelly Yovani Olivos Caicedo, Francelys V. Fernandez-Materan, Alvaro G. Hernandez, Steven L. Daniel, Joao M. P. Alves, Jason M. Ridlon
Summary: Clostridium scindens strain VPI12708 is used as a model organism to study bile acid 7a-dehydroxylating pathways. The closed circular genome of C. scindens VPI12708, with 3,983,052 bp and 47.59% G + C, was obtained by PacBio sequencing. A total of 3,707 coding DNA sequences are predicted in the genome.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biochemistry & Molecular Biology
Salvador Espada-Hinojosa, Clarissa Karthauser, Abhishek Srivastava, Lukas Schuster, Teresa Winter, Andre Luiz de Oliveira, Frederik Schulz, Matthias Horn, Stefan Sievert, Monika Bright
Summary: This study reveals the impact of strict host dependence on genome evolution and host adaptation of a bacterial ectosymbiont. Thiobius has a smaller genome, reduced metabolic capabilities, and fewer functional traits compared to its free-living relative ODIII6. The differences in functional capabilities at the gene, metabolic pathway, and trait levels between Thiobius and ODIII6 illustrate adaptations to different environmental conditions.
MOLECULAR ECOLOGY RESOURCES
(2023)