Article
Environmental Sciences
Vinaya Kumar Katneni, Mudagandur Shashi Shekhar, Ashok Kumar Jangam, Karthic Krishnan, Sudheesh K. Prabhudas, Nimisha Kaikkolante, Dushyant Singh Baghel, Vijayan K. Koyadan, Joykrushna Jena, Trilochan Mohapatra
Summary: The study presents a high-quality genome assembly of Penaeus indicus, meeting reference standards for contigs and scaffolds among crustacean genomes. This assembly has a high number of protein-coding genes, repeat elements, and single nucleotide polymorphisms (SNPs). It provides valuable resources for genetic improvement, evolutionary studies, and stock management in shrimp fisheries and culture.
FRONTIERS IN MARINE SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Carlos D. Ordonez, Modesto Redrejo-Rodriguez
Summary: Just like DNA polymerases (DNAPs) replicate cellular and viral genomes, a few dedicated proteins from natural origins and engineered versions are suitable for amplification of whole genomes and metagenomes (WGA). Different protocols based on various DNAPs have been developed for specific applications. Isothermal WGA using f29 DNA polymerase is widely used due to its high performance, but PCR-based methods are also available. Selection of a suitable enzyme for WGA should consider replication fidelity, processivity, thermostability, coupling replication, double helix unwinding, and maintaining replication opposite to damaged bases. This review provides an overview of the properties of DNAPs used in WGA, discusses their limitations, and suggests future research directions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Eric B. Rondeau, Kris A. Christensen, Hollie A. Johnson, Dionne Sakhrani, Carlo A. Biagi, Mike Wetklo, Cody A. Despins, Rosalind A. Leggatt, David R. Minkley, Ruth E. Withler, Terry D. Beacham, Ben F. Koop, Robert H. Devlin
Summary: Chum salmon genome was sequenced and assembled using Oxford Nanopore and Flye software. Genome assembly was characterized by resequencing 59 chum salmon from hatchery sources. Genes involved in immune system and toxin response were found to be enriched in regions collapsed due to duplicated chromosomes from ancient genome duplication.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Sureshnee Pillay, James Emmanuel San, Derek Tshiabuila, Yeshnee J. Naidoo, Yusasha Pillay, Akhil Maharaj, Ugochukwu J. Anyaneji, Eduan Wilkinson, Houriiyah Tegally, Richard Lessells, Cheryl Baxter, Tulio de Oliveira, Jennifer Giandhari
Summary: The global pandemic has increased the demand for scalable sequencing and diagnostic methods for SARS-CoV-2. However, the cost and time-consuming preparations of sequencing libraries have limited the ability to sequence the virus. This study compared different protocols and found that a modified protocol reduced the cost and preparation time without affecting the sequencing quality, providing a lower-cost and streamlined approach for SARS-CoV-2 sequencing.
Review
Biochemistry & Molecular Biology
Richard Jaeger
Summary: Modern PCR-based analytical techniques have achieved high sensitivity levels, allowing for complete forensic DNA profiles from tiny traces. However, these techniques have their limits when it comes to analyzing fingerprints or single cells. Whole genome amplification (WGA) methods have been suggested to overcome these limits, but their forensic application has faced challenges and has only recently shown potential in specific forensic applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Na Lu, Yi Qiao, Pengfei An, Jiajian Luo, Changwei Bi, Musheng Li, Zuhong Lu, Jing Tu
Summary: Multiple displacement amplification (MDA) is widely used for whole genome amplification, but the formation of chimeric sequences in MDA interferes with bioinformatics analysis. This study developed a pipeline for recognizing and restoring chimeras in long-read sequencing data, which can reduce the influence of chimeras and improve the analysis of structural variation.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Agriculture, Dairy & Animal Science
Giulietta Minozzi, Barbara Lazzari, Maria Grazia De Iorio, Cecilia Costa, Emanuele Carpana, Paola Crepaldi, Rita Rizzi, Elena Facchini, Gustavo Gandini, Alessandra Stella, Giulio Pagnacco
Summary: This study aimed to characterize the population structure of Italian honeybees, identifying the genetic originality of Sicula and limited genetic introgression in A.m. ligustica. Through whole-genome sequencing, SNP variants were detected mapping on specific chromosomes.
Article
Genetics & Heredity
Yuanchao Liu, Longhua Huang, Huiping Hu, Manjun Cai, Xiaowei Liang, Xiangmin Li, Zhi Zhang, Yizhen Xie, Chun Xiao, Shaodan Chen, Diling Chen, Tianqiao Yong, Honghui Pan, Xiong Gao, Qingping Wu
Summary: Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, exhibits diverse pharmacological activities and was widely cultivated in southwest China. The first whole-genome assembly of G. leucocontextum was successfully conducted, revealing differences in functional genes of secondary metabolites between G. leucocontextum and Ganoderma lucidum, which may contribute to their distinct biological activities.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Yuanchao Liu, Longhua Huang, Huiping Hu, Manjun Cai, Xiaowei Liang, Xiangmin Li, Zhi Zhang, Yizhen Xie, Chun Xiao, Shaodan Chen, Diling Chen, Tianqiao Yong, Honghui Pan, Xiong Gao, Qingping Wu
Summary: In this study, the first whole-genome assembly and annotation of Ganoderma leucocontextum has been completed, enriching the toolbox for biological and genetic studies on this species. Differences in functional genes related to terpenoids synthesis were found compared to Ganoderma lucidum, indicating a potential explanation for their distinct biological activities.
G3-GENES GENOMES GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Guoshun Xu, Liwen Zhang, Xiaoqing Liu, Feifei Guan, Yuquan Xu, Haitao Yue, Jin-Qun Huang, Jieyin Chen, Ningfeng Wu, Jian Tian
Summary: This study compares the application of different DNA sequencing methods in soil metagenomics research. The results show that combining long-read and short-read data can increase the length of metagenomic sequences and gene pool, and has significant advantages in studying natural product biosynthetic genes in soil microbiomes.
Article
Plant Sciences
Allison L. Graper, Andrzej K. Noyszewski, Neil O. Anderson, Alan G. Smith
Summary: Using herbarium specimens for DNA barcoding in Phalaris plants improved species identification and identified species-specific polymorphisms in ITS regions. Phalaris arundinacea showed high SNP variation, with North American populations being distinct from Eurasian types, potentially allowing for future identification of geographic origins through specific SNPs.
Article
Agronomy
Anna Marzec-Grzadziel, Anna Galazka
Summary: The isolation of new bacterial strains from the natural environment can lead to the detection of microorganisms with potential practical importance. The characterization of such microorganisms can be carried out using classical microbiological and molecular biology methods, as well as sequencing techniques. This study focused on the sequencing and analysis of the genome of Achromobacter sp. 77Bb1, a bacterium isolated from the maize crop rhizosphere. The obtained genome contained genes related to xenobiotics biodegradation and metabolisms, suggesting its potential application in natural bioremediation methods.
Article
Plant Sciences
Yahui Lei, Ling Yang, Shengchang Duan, Siqi Ning, Dawei Li, Zijun Wang, Guisheng Xiang, Ling Yang, Chunping Wang, Shiyu Zhang, Shuangyan Zhang, Shuang Ye, Ling Kui, Pratiksha Singh, Jun Sheng, Yang Dong
Summary: This study conducted population genomic analysis of tea populations in eight main tea-producing areas in Lincang, Yunnan through whole-genome resequencing, revealing the origin centers of Lincang tea and observing low genetic differentiation between geographical tea populations.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biodiversity Conservation
Shiyu Du, Jie Dong, Nerivania N. Godeiro, Jun Wu, Feng Zhang
Summary: The novel MMG pipeline integrates a faster and more accurate read mapper, as well as a seed-and-extend assembler for species-specific mitogenomes, to improve the efficiency and accuracy of mitogenome assembly in mixed-species samples.
Article
Microbiology
Tse-Yen Liu, Chao-Han Chen, Yu-Liang Yang, Isheng J. Tsai, Ying-Ning Ho, Chia-Lin Chung
Summary: The study showed that infection by Phellinus noxius significantly reduced fungal diversity in soil and plant roots, and altered the abundance and composition of certain bacterial taxa. Bacteria with antifungal activity such as Bacillus and Pseudomonas may have potential in inhibiting Phellinus noxius. Additionally, Cosmospora was found to tolerate the secretions of Phellinus noxius and utilize the conditions created by the degradation of lignin by the pathogen.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Simone Mozzachiodi, Feng-Yan Bai, Petr Baldrian, Graham Bell, Kyria Boundy-Mills, Pietro Buzzini, Neza Cadez, Francisco A. Cubillos, Sofia Dashko, Roumen Dimitrov, Kaitlin J. Fisher, Brian Gibson, Dilnora Gouliamova, Duncan Greig, Lina Heistinger, Chris Todd Hittinger, Marina Jecmenica, Vassiliki Koufopanou, Christian R. Landry, Tereza Masinova, Elena S. Naumova, Dana Opulente, Jacqueline J. Pena, Uros Petrovic, Isheng Jason Tsai, Benedetta Turchetti, Pablo Villarreal, Andrey Yurkov, Gianni Liti, Primrose Boynton
Summary: Yeasts are commonly found in temperate forests, but their niches, life cycles, and contributions to ecosystem functioning are still not well understood. They are widely distributed on various substrates in different types of temperate forests. Yeasts have close associations with soils, macroorganisms, and other habitats, playing important roles in ecosystem processes.
Article
Chemistry, Multidisciplinary
Huei-Mien Ke, Isheng Jason Tsai
Summary: This review summarizes the current understanding of fungal bioluminescence diversity, evolution, and applications. Studies from the past five years provide extensive evidence that all known bioluminescent fungal lineages share one bioluminescence pathway, which has been successfully reconstructed in multiple plant species, offering potential opportunities for sustainability.
CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY
(2022)
Article
Developmental Biology
Yun-Zhe Wu, Hang-Shiang Jiang, Hsiao-Fen Han, Po-Hsuan Li, Min R. Lu, Isheng Jason Tsai, Yi-Chun Wu
Summary: The conserved Zn-finger transcription factor BLMP-1/Blimp1 regulates the apical cell shape of epidermis in C. elegans by downregulating aECM remodeling. Loss of blmp-1 leads to upregulation of genes involved in molting, causing abnormal shape in the apical region of adult epidermal cells. This defect can be suppressed by reducing bus-8 or mlt-8 expression.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Evolutionary Biology
Chen Siang Ng, Cheng-Kuo Lai, Huei-Mien Ke, Hsin-Han Lee, Chih-Feng Chen, Pin-Chi Tang, Hsu-Chen Cheng, Meiyeh J. Lu, Wen-Hsiung Li, Isheng Jason Tsai
Summary: This study presents the first de novo assembly of the mandarin duck genome, providing insights into its evolutionary history and genetic characteristics. The findings reveal the presence of repetitive sequences and expanded gene families that are associated with olfactory perception, feather development, and branching structures.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Chia-Yu Chen, Zong-Chi Wu, Tse-Yen Liu, Shiang-Shiuan Yu, Jyh-Nong Tsai, Yu-Chang Tsai, Isheng J. Tsai, Chia-Lin Chung
Summary: The white-rot fungus Phellinus noxius can cause brown root rot disease in woody trees and shrubs as well as herbaceous plants. A survey in Taiwan revealed that Phellinus noxius was detected in seven symptomless herbaceous species. The fungus was found to infect Artemisia princeps, Oplismenus compositus, and Zoysia matrella, but not Axonopus compressus, Eremochloa ophiuroides, Ophiopogon japonicus, or Cynodon dactylon.
Article
Biochemistry & Molecular Biology
Cheng-Kuo Lai, Yi-Chien Lee, Huei-Mien Ke, Min R. Lu, Wei-An Liu, Hsin-Han Lee, Yu-Ching Liu, Toyoshi Yoshiga, Taisei Kikuchi, Peichen J. Chen, Isheng Jason Tsai
Summary: In this study, the genomes of six Aphelenchoides species, including four strains of the A. besseyi species complex, were analyzed. The systematic identification of horizontal gene transfer (HGT) genes revealed that these genes were mostly acquired from bacteria, fungi, and plants. This study provides a comprehensive understanding of HGT in nematodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Plant Sciences
Ting-Zhi Liao, Yu-Hsuan Chen, Jyh-Nong Tsai, Chieh Chao, Tzu-Pi Huang, Cheng-Fang Hong, Zong-Chi Wu, Isheng Jason Tsai, Hsin-Han Lee, Ned B. Klopfenstein, Mee-Sook Kim, Jane E. Stewart, Ndeme Atibalentja, Fred E. Brooks, Philip G. Cannon, A. Mohd Farid, Tsutomu Hattori, Hoi-Shan Kwan, Regent Yau Ching Lam, Yuko Ota, Norio Sahashi, Robert L. Schlub, Louise S. Shuey, Alvin M. C. Tang, Chia-Lin Chung
Summary: This study investigated the control efficacies and systemic activities of fungicides with different modes of action on brown root rot disease caused by Phellinus noxius. The results showed that three fungicides had high inhibitory effects on the colony growth of P. noxius, and one fungicide also showed good inhibitory effects. In addition, the experiments demonstrated that these fungicides had efficient acropetal translocation after treatment of the root organ.
Article
Ecology
Kohta Yoshida, Christian Roedelsperger, Waltraud Roeseler, Metta Riebesell, Simo Sun, Taisei Kikuchi, Ralf J. Sommer
Summary: Recent research on closely related nematode species showed that chromosome fusions have played a key role in their genomic evolution and reproductive isolation. The fusions altered recombination rates and drove the speciation process. Rating: 7/10.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Zoology
Chiho Kaneko, Akio Shinohara, Taisei Kikuchi, Asami Tokuda, Takao Irie, Kentaro Yamada, Naoaki Misawa, Ayako Yoshida
Summary: The study compared the gut microbiota of Japanese badgers and raccoon dogs and found that they had completely different gut microbiota. Badgers were dominated by the phyla Firmicutes and Proteobacteria, while raccoon dogs had abundant Firmicutes and Bacteroidota, and also exhibited richer and more diverse species. This suggests that badgers and raccoon dogs have distinct gut microbiota despite their similar diets and habitats.
Article
Biochemistry & Molecular Biology
Yi-Chien Lee, Huei-Mien Ke, Yu-Ching Liu, Hsin-Han Lee, Min-Chen Wang, Yung-Che Tseng, Taisei Kikuchi, Isheng Jason Tsai
Summary: Obtaining sufficient genetic material from limited biological sources is a major challenge in biodiversity and genome evolution studies. In this study, we successfully amplified nanograms of DNA and mRNA from individual Caenorhabditis elegans using multiple displacement amplification (MDA) and Smartseq2 techniques. We generated long-read sequences with Oxford Nanopore Technologies (ONT) and achieved high genome coverage. Through genome and transcriptome sequencing of multiple nematode species, we discovered genome diversity and phylogenetic relationships within the phylum Nematoda. This study demonstrates the robustness of MDA and ONT for studying genome diversity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yu-Chen Chen, Chia-Ying Chen, Tai-Wei Chiang, Ming-Hsien Chan, Michael Hsiao, Huei-Mien Ke, Isheng Jason Tsai, Trees-Juen Chuang
Summary: The study developed a bioinformatics pipeline, NCLscan-hybrid, to detect trans-spliced RNAs (ts-RNAs) and distinguish them from circular RNAs (circRNAs). The pipeline integrates short and long RNA-seq reads, minimizing false positives and proposing out-of-circle and rolling-circle long reads.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Marine & Freshwater Biology
Niklas Dreyer, Felipe Monteiro Gomes de Mattos, Dharmesh Jain, Chia-Ling Fong, Mattia De Vivo, Yung-Hui Victoria Wen, Yu-Hsin Huang, John Karichu Mwihaki, Hsin-Han Lee, Pei-Chen Tsai, Yao-Feng Tsao, Benny Kwok Kan Chan, Isheng Jason Tsai, Ryuji J. Machida, Tzi-Yuan Wang, John Wang
JOURNAL OF MOLLUSCAN STUDIES
(2023)