Article
Plant Sciences
Ana Vucurovic, Denis Kutnjak, Natasa Mehle, Ivana Stankovic, Anja Pecman, Aleksandra Bulajic, Branka Krstic, Maja Ravnikar
Summary: This study identified four new viruses in Serbia using high-throughput sequencing, including devastating viruses to tomatoes. The successful application of post hoc HTS testing encourages the use of this technology in research and diagnostic laboratories to discover new viruses.
Article
Plant Sciences
Zhengmei Yang, Tingting Dong, Xibin Dai, Yiliang Wei, Yujie Fang, Lei Zhang, Mingku Zhu, Ghazala Nawaz, Qinghe Cao, Tao Xu
Summary: This study identified and compared miRNAs in sweetpotato cultivars with different salt sensitivity, and found differentially expressed miRNAs and salt-responsive miRNAs. The target genes of these miRNAs were mainly transcription factors and proteins related to metabolism and stress response. These findings contribute to understanding the regulatory pattern of miRNAs in different sweetpotato genotypes and provide references for improving the agronomic traits of sweetpotato through miRNA manipulation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Virology
Hang Yin, Zheng Dong, Xulong Wang, Shuhao Lu, Fei Xia, Annihaer Abuduwaili, Yang Bi, Yongqiang Li
Summary: Various viruses infecting marigold plants were identified, including marigold mosaic virus and marigold cryptic virus, through deep sequencing. Genetic and phylogenetic analysis revealed the relationships between these viruses and other known viruses, enriching our understanding of viral infections in marigolds.
Article
Gastroenterology & Hepatology
Liuyang Zhao, Yu Shi, Harry Cheuk-Hay Lau, Weixin Liu, Guangwen Luo, Guoping Wang, Changan Liu, Yasi Pan, Qiming Zhou, Yanqiang Ding, Joseph Jao-Yiu Sung, Jun Yu
Summary: Through ultra-deep metagenomic sequencing, we discovered 1058 novel human gut viruses, including some viral genomes longer than the largest bacteriophage found in humans. Our study also demonstrated that a biomarker panel of 14 novel viruses can differentiate patients with colorectal cancer from controls in a training cohort.
Review
Microbiology
Amy H. Fitzpatrick, Agnieszka Rupnik, Helen O'Shea, Fiona Crispie, Sinead Keaveney, Paul Cotter
Summary: This review assesses and recommends approaches for targeted and agnostic High Throughput Sequencing of RNA viruses, highlighting the challenges and biases that method choice can impart to sequencing results. Methodology choices from RNA extraction to library preparation have a significant impact on the detection or characterization of RNA viruses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tao Zhou, Shidong Zhou, Yong Chen, Jun Wang, Ruina Zhang, Huan Xiang, Zihao Xia, Mengnan An, Xiuxiang Zhao, Yuanhua Wu
Summary: This study identified major plant viruses affecting cigar and flue-cured tobacco in Sichuan through deep sequencing and molecular techniques, and developed a fast detection method for these viruses.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Plant Sciences
Anning Jia, Chenge Yan, Hang Yin, Rui Sun, Fei Xia, Lan Gao, Yongjiang Zhang, Yongqiang Li
Summary: High-throughput sequencing and bioinformatic analysis revealed mixed viral infections in symptomatic tree peony plants, including three newly identified viruses. These viruses show phylogenetic relationships with existing viruses like citrus leaf blotch virus but exhibit significant differences.
Article
Biochemistry & Molecular Biology
Cristian Morales, Raul Arias-Carrasco, Vinicius Maracaja-Coutinho, Pamela Seron, Fernando Lanas, Luis A. Salazar, Nicolas Saavedra
Summary: This study aimed to identify differences in bacterial small RNAs between hypercholesterolemic and normocholesterolemic individuals at the gut level. Most of the small RNAs were of bacterial origin and had a higher number of readings in normocholesterolemic participants. Small RNA ID 2909606 associated with Coprococcus eutactus and small RNA ID 2149569 from the species Blautia wexlerae were upregulated in hypercholesterolemic subjects, and other bacterial and archaeal small RNAs interacting with the LDL receptor were identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Bramwel W. Wanjala, Elijah M. Ateka, Douglas W. Miano, Segundo Fuentes, Ana Perez, Jan W. Low, Jan F. Kreuze
Summary: A simple and rapid LAMP assay was developed for the detection of sweet potato viruses with 100% diagnostic sensitivity in laboratory validation. Customized for field testing, the results of on-site LAMP testing were comparable to PCR and RT-PCR confirmatory tests.
JOURNAL OF VIROLOGICAL METHODS
(2021)
Article
Oncology
Yan Kong, Huanhuan Hu, Yangyang Shan, Zhen Zhou, Ke Zen, Yulu Sun, Rong Yang, Zheng Fu, Xi Chen
Summary: This study identified the lineage of 3'-terminal 2'-O-methyl plant miRNAs using oxidative deep sequencing and compared different methods for quantifying this RNA modification. The results showed that stem-loop RT-qPCR was the only suitable approach for quantifying 3'-terminal 2'-O-methyl miRNAs in plants and human tissues.
FRONTIERS OF MEDICINE
(2022)
Article
Plant Sciences
Leonardo Velasco, Carlos V. Padilla
Summary: Biological indexing is the primary method for certifying propagative grapevines, with HTS proposed as an alternative. Research findings indicate that HTS is more effective than biological indexing in terms of identifying viruses, saving time, and reducing costs.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Virology
Lizheng Guan, Gongxun Zhong, Shufang Fan, Erin M. Plisch, Robert Presler, Chunyang Gu, Lavanya Babujee, David Pattinson, Hang Le Khanh Nguyen, Vu Mai Phuong Hoang, Mai Quynh Le, Harm van Bakel, Gabriele Neumann, Yoshihiro Kawaoka
Summary: Surveillance in Vietnam's northern live poultry markets identified 27 highly pathogenic avian influenza H5N1 and H5N6 viruses from 2016 to 2017, belonging to 3 different clades. Sequencing and phylogenetic analysis revealed reassortment with low pathogenic avian influenza viruses and identified minor viral subpopulations encoding variants that may affect pathogenicity and antiviral drug sensitivity. Mice infected with clade 2.3.2.1c viruses rapidly lost weight and died, while those infected with clade 2.3.4.4f or 2.3.4.4g experienced non-lethal infections.
Article
Microbiology
Anja Pecman, Ian Adams, Ion Gutierrez-Aguirre, Adrian Fox, Neil Boonham, Maja Ravnikar, Denis Kutnjak
Summary: Nanopore sequencing, as a novel high-throughput sequencing technology, shows similar performance to Illumina sequencing in the detection of plant viruses and viroids, while offering the advantages of faster and more affordable diagnostics.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Heinner Guio, Victor Aliaga-Tobar, Marco Galarza, Oscar Pellon-Cardenas, Silvia Capristano, Henry L. Gomez, Mivael Olivera, Cesar Sanchez, Vinicius Maracaja-Coutinho
Summary: Tuberculosis is a fatal infectious disease with a third of the global population infected. Cured tuberculosis patients are at a higher risk for developing pulmonary adenocarcinoma. Analysis of small RNAs extracted from blood samples of Peruvian patients revealed 24 perturbed microRNAs that may serve as potential biomarker candidates for the Peruvian population.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Chenge Yan, Hang Yin, Yongjiang Zhang, Zhengguang Ren, Jinzhong Wang, Yongqiang Li
Summary: Two new viruses infecting jujube plants were identified, and mixed infections of JYMaV and JaBV were common in jujube in Beijing.
INTERNATIONAL MICROBIOLOGY
(2023)
Article
Plant Sciences
Monica A. Kehoe, Craig Webster, Cuiping Wang, Roger A. C. Jones, Brenda A. Coutts
Summary: Cucumber green mottle mosaic virus (CGMMV) was detected in watermelon crops in Australia for the first time, and further investigations revealed its presence in cucumber, rockmelon, honeydew melon, and watermelon crops. Genetic analysis showed limited diversity of CGMMV within Australia, suggesting a recent single incursion.
AUSTRALASIAN PLANT PATHOLOGY
(2022)
Review
Public, Environmental & Occupational Health
Abdul Walusansa, Savina Asiimwe, Jesca L. Nakavuma, Jamilu E. Ssenku, Esther Katuura, Hussein M. Kafeero, Dickson Aruhomukama, Alice Nabatanzi, Godwin Anywar, Arthur K. Tugume, Esezah K. Kakudidi
Summary: Antimicrobial resistance in pathogenic bacteria isolated from herbal medicine in Africa has been found to be high, with prevalent resistance to conventional drugs. This study highlights the urgent need for further research and collaborative quality control mechanisms in the herbal medicine industry in Africa.
ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL
(2022)
Article
Computer Science, Software Engineering
Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru Tomescu, Veli Makinen
Summary: This paper investigates the problem of matching a string in a labeled graph. Previous research has shown that it is difficult to solve this problem in strongly sub-quadratic time unless the Orthogonal Vectors Hypothesis is false. However, there are graph classes, such as Wheeler graphs, that can be easily indexed. This paper proposes a method to alleviate the construction bottleneck of Wheeler graphs by studying graphs induced from multiple sequence alignments. The paper introduces the concept of elastic founder graphs and proves that even such induced graphs are hard to index. It also presents two subclasses, repeat-free and semi-repeat-free graphs, that are easy to index.
Article
Forestry
Eeva Terhonen, Muhammad Kashif, Tuula Piri, Matti Haapanen, Jarkko Hantula
Summary: The most destructive root rot pathogen of Norway spruce is Heterobasidion parviporum, and it has been found that trees with allele PaLAR3B have higher resistance against this pathogen. In a study testing the resistance of trees with homo- or heterozygous PaLAR3B allele, it was found that the genotype did not significantly affect the infection rate, and neither did the distance from the inoculated stump or the tree diameter.
Article
Virology
Roger A. C. Jones, Ines Vazquez-Iglesias, Sam McGreig, Adrian Fox, Adrian J. Gibbs
Summary: High Plains wheat mosaic virus (HPWMoV) is a serious disease affecting wheat in major wheat-growing regions worldwide. This study reports the complete or partial genomic sequences of five HPWMoV isolates from Australian wheat samples. Phylogenetic analysis revealed the presence of two lineages, L1 and L2, with L1 containing isolates from the North American Great Plains Region and L2 consisting of isolates from Australia and the Great Plains Region. Recombination in the nucleocapsid gene was unexpectedly observed in a quarter of the L2B isolates. The study also identified similarities between HPWMoV and other emaraviruses in certain genomic segments.
Article
Computer Science, Theory & Methods
Massimo Equi, Veli Makinen, Alexandru I. Tomescu, Roberto Grossi
Summary: Exact string matching in labeled graphs is a fundamental problem that is at the core of various applications in computational biology, graph databases, and heterogeneous networks. We provide a conditional lower bound that proves the hardness of achieving efficient exact string matching algorithms in graphs, unless certain computational assumptions are false. Our results hold even for restricted cases, such as undirected graphs and directed acyclic graphs, making the lower bound stricter than previous bounds derived from regular expression matching. Additionally, our findings suggest that exact and approximate matching have the same level of difficulty in graphs under certain assumptions, while in strings, they have different time complexities.
ACM TRANSACTIONS ON ALGORITHMS
(2023)
Article
Virology
Serife Topkaya, Ali Celik, Adyatma Irawan Santosa, Roger A. C. Jones
Summary: In 2020, 264 potato field samples were collected from Bolu, Afyon, Kayseri, and Nigde provinces in Turkey. Potato virus S (PVS) was detected in 35 samples using RT-PCR tests. Phylogenetic analysis revealed that the PVS isolates in Turkey belonged to three phylogroups (PVSI, PVSII, and PVSIII), with considerable genetic variation within PVSI and PVSII. PVSII, which spreads easily and causes more severe symptoms, poses a biosecurity threat to countries without it.
Review
Plant Sciences
Arthur K. Tugume, Deusdedith R. Mbanzibwa, Titus Alicai, Christopher A. Omongo, M. N. Maruthi
Summary: Viruses have the ability to colonize new hosts and niches due to their genetic and evolutionary plasticity. Changes in viral or environmental factors can determine the epidemiological status of a virus, as seen in the case of sweet potato mild mottle virus (SPMMV). SPMMV remains endemic in eastern Africa and causes significant losses, but its global occurrence is limited. Despite its importance, there are research gaps surrounding SPMMV that hinder virus disease management in sweet potato.
PHYTOBIOMES JOURNAL
(2023)
Review
Plant Sciences
Jerome Kubiriba, Rockefeller Erima, Arthur K. Tugume, William Tinzaara, Wilberforce K. Tushemereirwe
Summary: BXW is a destructive disease caused by Xanthomonas vasicola pv. musacearum (Xvm), which infects all banana varieties in East and Central Africa. Previous control methods based on Moko disease symptoms were unsuccessful, leading to the spread of BXW in six countries and threatening the banana industry. However, effective control practices based on epidemiological information have successfully controlled BXW.
PHYTOBIOMES JOURNAL
(2023)
Article
Biochemical Research Methods
Jun Ma, Manuel Caceres, Leena Salmela, Veli Makinen, Alexandru Tomescu
Summary: GraphChainer is a new algorithm that can co-linearly chain a set of seeds in a string labeled acyclic graph. Compared to GraphAligner, GraphChainer aligns 12-17% more reads and 21-28% more total read length on real and simulated PacBio CLR reads.
Article
Biochemistry & Molecular Biology
Cyprian Osinde, Islam S. Sobhy, David Wari, Son Truong Dinh, Yuko Hojo, Dandy A. Osibe, Tomonori Shinya, Arthur K. Tugume, Anthony M. Nsubuga, Ivan Galis
Summary: This paper examines how genetically related plants determine their species identity within the ecological space through their volatile toolboxes. The study focuses on rice, a representative C3 plant, and sorghum, a representative C4 plant, comparing their constitutive and stress-induced headspace volatile organic compounds (VOCs). Despite emitting similar types of VOCs, sorghum showed lower abundance of certain mono- and sesquiterpenes compared to rice, indicating potential divergence in dispersal mechanisms. Additionally, the variation in VOCs among different sorghum cultivars suggests their potential use in enhancing resistance against herbivores.
PLANT SIGNALING & BEHAVIOR
(2023)
Article
Plant Sciences
John Fosu-Nyarko, Ian P. Adams, Michael G. K. Jones, Adrian Fox, Roger A. C. Jones
Summary: This study compared the complete genomic sequences of five historical Western Australian isolates of subterranean clover mottle virus (SCMoV) from 1989-2000, as well as an infectious clone of its 1989 isolate. Sanger Sequencing (SS) and High Throughput Sequencing (HTS) were used to obtain these genomes. The results showed that the sequences obtained from four isolates differed by only 18-59 nucleotides, which could be attributed to different sequencing methods, the time each isolate was host passaged, or a combination of both factors. Additionally, the study revealed that the ORF1 gene region was the most variable, and the phylogenetic tree constructed with ORF1 sequences showed grouping of isolates based on the severity of symptoms in subterranean clover, indicating a possible role of the ORF1-encoded P1 protein in symptom determination. Furthermore, the presence of a satellite RNA was found in all SCMoV genomes obtained by HTS but not in those derived by SS.
JOURNAL OF PLANT PATHOLOGY
(2022)
Article
Biochemical Research Methods
Abubakar S. Mustafa, Jamilu E. Ssenku, Paul Ssemanda, Saidi Ntambi, Savithramma P. Dinesh-Kumar, Arthur K. Tugume
Summary: Various methods exist for callose quantification, but many have limitations and technical difficulties. This study introduces a Sandwich Enzyme-Linked Immunosorbent Assay (S-ELISA) method for callose quantification, which successfully quantified callose levels in different tissues of banana plants inoculated with Xcm bacteria. The method demonstrates advantages in terms of specificity, reproducibility, and high throughput capabilities.
METHODS AND PROTOCOLS
(2022)
Article
Plant Sciences
Roger A. C. Jones, Aimee R. Fowkes, Sam McGreig, Adrian Fox, Ian P. Adams
Summary: Although the beet ringspot virus (BRSV) was found in the pollen of potato flowers, there is no evidence of its transmission through true seeds.
JOURNAL OF PLANT PATHOLOGY
(2022)
Article
Horticulture
Allan Waniale, Settumba B. Mukasa, Arthur K. Tugume, Jerome Kubiriba, Wilberforce K. Tushemereirwe, Robooni Tumuhimbise
Summary: This study investigated the pollen tube growth, position of fertilized ovule development, and seed set in banana genotypes. The results showed that pollen tubes can reach different parts of the ovary, fertilized ovule development occurs along the entire length of the fruit but is biased towards the distal end in some genotypes, and there are differences in ovule fertilization rates between hands.
