keyword
https://read.qxmd.com/read/38537141/first-record-of-diplodia-gallae-causing-branch-cankers-on-declining-scarlet-oak-quercus-coccinea-in-virginia
#1
JOURNAL ARTICLE
Devin Bily, Tashi Gyatso, Matt Wolanski, Amanda Conrad, Connor Goolsby, Lori A Chamberlin, Katlin M DeWitt
Members of Botryosphaeria s.l. have an extensive history as cankering pathogens of stressed and declining oak trees in the eastern United States (Ferreira et al. 2021). The host range, distribution, and virulence among two closely related species, Diplodia corticola and D. gallae, remains unclear (Brazee et al. 2023). On 15 August 2023, a survey was conducted at a declining natural hardwood site in Shenandoah County, Virginia (GPS coordinates 38.922089, -78.606125). One mature Quercus coccinea tree that displayed scorched leaf margins and branch dieback was felled and a cankered branch from the crown was sampled (Fig...
March 27, 2024: Plant Disease
https://read.qxmd.com/read/38536889/multilocus-sequence-typing-and-antibiotic-resistance-of-aeromonas-isolated-from-freshwater-fish-in-hebei-province
#2
JOURNAL ARTICLE
Zixiao Yu, Yunseok Oh, Songmi Kim, Kyudong Han, Kornsorn Srikulnath, Qingyang Li, Ji-Seok Jang, Ho-Seong Lee
Aeromonas spp. are the opportunistic pathogens that infect both aquatic and terrestrial homeotherms. They were commonly present in aquatic environments, including effluent, tap water, marine, river, and lake, where they are often isolated from aquatic animals, including fish, molluscs, and crustaceans. The Aeromonas infections can cause sepsis, ulcer, and other symptoms, resulting in the death of massive aquatic animals. Therefore, the prevention and control of Aeromonas is of great significance for the healthy development of aquaculture...
2024: PloS One
https://read.qxmd.com/read/38531918/the-complete-mitochondrial-genome-of-leucoptera-coffeella-lepidoptera-lyonetiidae-and-phylogenetic-relationships-within-the-yponomeutoidea-superfamily
#3
JOURNAL ARTICLE
Mateus Pereira Dos Santos, Ana Paula Zotta Mota, Roberto Coiti Togawa, Natalia Florencio Martins, Eliza Fabricio de Melo Bellard do Nascimento, Vivian Santos Lucena, Maria Aparecida Castellani, Erika Valéria Saliba Albuquerque, Frédérique Hilliou
The coffee leaf miner (Leucoptera coffeella) is one of the major pests of coffee crops in the neotropical regions, and causes major economic losses. Few molecular data are available to identify this pest and advances in the knowledge of the genome of L. coffeella will contribute to improving pest identification and also clarify taxonomy of this microlepidoptera. L. coffeella DNA was extracted and sequenced using PacBio HiFi technology. Here we report the complete L. coffeella circular mitochondrial genome (16,407 bp) assembled using Aladin software...
March 26, 2024: Scientific Reports
https://read.qxmd.com/read/38529929/auto-phylo-v2-and-auto-phylo-pipeliner-building-advanced-flexible-and-reusable-pipelines-for-phylogenetic-inferences-estimation-of-variability-levels-and-identification-of-positively-selected-amino-acid-sites
#4
JOURNAL ARTICLE
Hugo López-Fernández, Miguel Pinto, Cristina P Vieira, Pedro Duque, Miguel Reboiro-Jato, Jorge Vieira
The vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprecedented insight into the evolution of genes and gene families, and thus on biological issues. Here, new modules for gene annotation, further BLAST search algorithms, further multiple sequence alignment methods, the adding of reference sequences, further tree rooting methods, the estimation of rates of synonymous and nonsynonymous substitutions, and the identification of positively selected amino acid sites, have been added to auto-phylo (version 2), a recently developed software to address biological problems using phylogenetic inferences...
March 27, 2024: Journal of Integrative Bioinformatics
https://read.qxmd.com/read/38525230/phylogenetic-analysis-of-the-trypanosomatid-parasite-lotmaria-passim-in-honey-bees-apis-mellifera-in-poland
#5
JOURNAL ARTICLE
Maria Iller, Karolina Lipczyńska-Ilczuk, Rajmund Sokół, Grzegorz Borsuk, Agata Bancerz-Kisiel
INTRODUCTION: Lotmaria passim ( L. passim ) is a single-celled flagellate which colonises the bee gastrointestinal tract and is highly prevalent in honey bees. This parasite is associated with colony losses. Honey bee ( Apis mellifera ) colonies were sampled from five apiaries in the north-eastern part of Poland for the phylogenetic analysis of L. passim . MATERIAL AND METHODS: Each apiary consisted of approximately 60 bee colonies, of which 20 were randomly selected...
March 2024: Journal of Veterinary Research
https://read.qxmd.com/read/38514421/alerax-a-tool-for-gene-and-species-tree-co-estimation-and-reconciliation-under-a-probabilistic-model-of-gene-duplication-transfer-and-loss
#6
JOURNAL ARTICLE
Benoit Morel, Tom A Williams, Alexandros Stamatakis, Gergely J Szöllősi
MOTIVATION: Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree...
March 21, 2024: Bioinformatics
https://read.qxmd.com/read/38509222/technology-enabled-great-leap-in-deciphering-plant-genomes
#7
REVIEW
Lingjuan Xie, Xiaojiao Gong, Kun Yang, Yujie Huang, Shiyu Zhang, Leti Shen, Yanqing Sun, Dongya Wu, Chuyu Ye, Qian-Hao Zhu, Longjiang Fan
Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades...
March 20, 2024: Nature Plants
https://read.qxmd.com/read/38507308/datelife-leveraging-databases-and-analytical-tools-to-reveal-the-dated-tree-of-life
#8
JOURNAL ARTICLE
Luna L Sánchez Reyes, Emily Jane McTavish, Brian O'Meara
Chronograms -phylogenies with branch lengths proportional to time- represent key data on timing of evolutionary events for the study of natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www ...
March 20, 2024: Systematic Biology
https://read.qxmd.com/read/38499971/-epicoccum-sorghinum-causing-leaf-spot-on-polygonatum-cyrtonema-in-china
#9
JOURNAL ARTICLE
Juan Zou, Huan Yao, Tingting Lei, Zi-Yi Chen, Xian-Ying Su, Shenggui Liu
Polygonatum cyrtonema Hua (family Asparagaceae) is a traditional Chinese medicinal plant that is widely cultivated in various parts of China, including Hunan Province. In summer 2022, a leaf spot disease was observed in 10% of the P. cyrtonema plants (Huang jing) in 18 hectares of this crop in the Hongjiang District (27°18'4″N, 110°11'1″E) of Hunan Province. The initial symptoms of the disease were brown spots on young leaves, and adjacent tissues gradually changed from green to yellow...
March 18, 2024: Plant Disease
https://read.qxmd.com/read/38493292/the-rise-of-taxon-specific-epitope-predictors
#10
JOURNAL ARTICLE
Felipe Campelo, Francisco P Lobo
Computational predictors of immunogenic peptides, or epitopes, are traditionally built based on data from a broad range of pathogens without consideration for taxonomic information. While this approach may be reasonable if one aims to develop one-size-fits-all models, it may be counterproductive if the proteins for which the model is expected to generalize are known to come from a specific subset of phylogenetically related pathogens. There is mounting evidence that, for these cases, taxon-specific models can outperform generalist ones, even when trained with substantially smaller amounts of data...
January 22, 2024: Briefings in Bioinformatics
https://read.qxmd.com/read/38493130/infrared-a-declarative-tree-decomposition-powered-framework-for-bioinformatics
#11
JOURNAL ARTICLE
Hua-Ting Yao, Bertrand Marchand, Sarah J Berkemer, Yann Ponty, Sebastian Will
MOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations. METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a generalization of constraint networks...
March 16, 2024: Algorithms for Molecular Biology: AMB
https://read.qxmd.com/read/38491928/evolution-of-wing-shape-in-geometrid-moths-phylogenetic-effects-dominate-over-ecology
#12
JOURNAL ARTICLE
Kadri Ude, Erki Õunap, Ants Kaasik, Robert B Davis, Juhan Javoiš, Vineesh Nedumpally, Stenio I A Foerster, Toomas Tammaru
Locomotory performance is an important determinant of fitness in most animals, including flying insects. Strong selective pressures on wing morphology are therefore expected. Previous studies on wing shape in Lepidoptera have found some support for hypotheses relating wing shape to environment-specific selective pressures on aerodynamic performance. Here, we present a phylogenetic comparative study on wing shape in the lepidopteran family Geometridae, covering 374 species of the northern European fauna. We focused on eleven wing traits including aspect ratio, wing roundness, and the pointedness of the apex, as well as the ratio of forewing and hindwing areas...
March 16, 2024: Journal of Evolutionary Biology
https://read.qxmd.com/read/38470530/application-of-nested-qpcr-high-resolution-melting-hrm-technology-on-strongyloides-stercoralis-isolates-from-iran
#13
JOURNAL ARTICLE
Zohreh Fakhrieh-Kashan, Reza Fotouhi-Ardakani, Farzaneh Zahabiun, Meysam Sharifdini, Eshrat Beigom Kia
PURPOSE: Strongyloides stercoralis is a parasite with special characteristics presenting it as a unique nematode. Iran is an endemic area for S. stercoralis. In this study, nested-qPCR-high resolution melting (HRM) technology was applied on some human isolates of S. stercoralis from this country by focusing on evolutionary genetics analysis. METHODS: Twelve human isolates of S. stercoralis were collected from four endemic provinces of Iran. Genomic DNA was extracted from a single filariform larva for every isolate...
March 12, 2024: Acta Parasitologica
https://read.qxmd.com/read/38468816/genotypic-diversity-and-epidemiology-of-trichomonas-gallinae-in-columbidae-insights-from-a-comprehensive-analysis
#14
JOURNAL ARTICLE
Yu Liu, Haiming Cai, Dingai Wang, Shenquan Liao, Nanshan Qi, Juan Li, Zhuanqiang Yan, Hanqin Shen, Siyun Fang, Minna Lv, Xuhui Lin, Yongle Song, Junjing Hu, Yibin Zhu, Xiangjie Chen, Lijun Yin, Jianfei Zhang, Yaqiong Guo, Mingfei Sun
Trichomonas gallinae is a protozoa that parasitizes the upper gastrointestinal and respiratory tracts of various animals and birds, including Columbidae, Passeriformes, and Falconiformes. Polymerase chain reaction-based T. gallinae ITS1/5.8S/ITS2 gene typing yields inconsistent results owing to methodological differences. To standardize the statistical analysis of T. gallinae genotype distributions, this study employed MEGA-X software with the Tamamura 3-parameter (T92) + G model in the neighbor-joining method, with 2,000 bootstrap replicates, to calculate a systematic evolutionary tree...
April 2024: International Journal for Parasitology. Parasites and Wildlife
https://read.qxmd.com/read/38468746/scrub-typhus-an-underestimated-infectious-disease-attributable-to-community-acquired-acute-kidney-injury
#15
JOURNAL ARTICLE
Arpita Paul, Vaishali Sarma, Parasmita Das Choudhury, Gayatri Pegu, Kishore Sarma, Anisha Sarma, Lahari Saikia
UNLABELLED: Acute Kidney Injury (AKI) associated with Scrub typhus is an emerging health problem which is more common in the tropics including India. This study intended to find out the occurrence of Scrub typhus among the Community Acquired Acute Kidney Injury patients in a tertiary care hospital in Assam, North East India. AKI patients with acute febrile illness admitted to Gauhati Medical College and Hospital, Guwahati, Assam were included in the study and demographic characteristics along with clinical features were recorded...
March 2024: Indian Journal of Microbiology
https://read.qxmd.com/read/38468136/fruit-anthracnose-on-cavendish-bananas-caused-by-colletotrichum-fructicola-in-guangxi-china
#16
JOURNAL ARTICLE
Weiyu Zheng, Zhihe Yu, SuiPing Huang, Lihua Tang, Xiaolin Chen, Tangxun Guo, Qili Li, Tom Hsiang, Yun Wang
Cavendish banana (Musa spp. AAA group) is one of the main fruit crops worldwide. It is widely planted in Guangdong, Hainan, Guangxi, Fujian and Yunnan provinces in southern China. In November 2020, banana fruits with anthracnose symptoms were collected from Dayu Town (N 23.17°, E 109.80°), Guigang City, and Chengjun Town (N 22.60°, E 110.00°), Yulin City, Guangxi Province, China, where the disease was found on about 70% of the banana plants, and on individual fruit, up to 10% of the surface was covered with symptoms...
March 11, 2024: Plant Disease
https://read.qxmd.com/read/38461372/alterations-of-lacrimal-sac-microbiota-in-failed-dacryocystorhinostomy-the-lacriome-paper-6
#17
JOURNAL ARTICLE
Mohammad Javed Ali
PURPOSE: To study the metagenomics of the microbes isolated from the lacrimal sac in patients with failed dacryocystorhinostomy (DCR). METHODS: A prospective study was performed on 10 consecutive patients with failed DCR. Lacrimal sac samples were obtained for metagenomic analysis during the revision endoscopic DCR. The samples were collected intraoperatively after a full-length lacrimal sac marsupialization and immediately transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the IlluminaTM platform following DNA extraction and library preparation...
March 9, 2024: Seminars in Ophthalmology
https://read.qxmd.com/read/38448390/first-report-of-anthracnose-caused-by-colletotrichum-grevilleae-on-apple-in-korea
#18
JOURNAL ARTICLE
Young-Ju Nam, Seung-Yeol Lee, Weon-Dae Cho, Hee-Young Jung
In October 2022, typical symptoms of anthracnose were observed on apple (Malus ⅹ domestica cv. Fuji) fruits collected from Pocheon in Gyeonggi province, South Korea (N37.98074°, E127.33995°). In the surveyed orchard, the incidence rate of apple anthracnose was less than 1%. The initial symptoms were brown-to-dark brown lesions, and with disease progression, they enlarged and the pulp became soft, forming a brown band. In total 29 apple fruits were collected, and the causal agent was isolated by removing the peel, and the diseased tissues were directly transferred onto potato dextrose agar (PDA), followed by incubation for 7 days at 25°C...
March 6, 2024: Plant Disease
https://read.qxmd.com/read/38436865/genetic-diversity-of-leishmania-major-isolated-from-different-dermal-lesions-using-its2-region
#19
JOURNAL ARTICLE
Ruaa M Khazal, Mohammed H Flaih, Manar K Kadhim, Khwam R Hussein
BACKGROUND AND OBJECTIVE: Cutaneous leishmaniasis (CL) is still considered to be an uncontrolled endemic disease that spreads in many countries. The current study aimed to determine intra-species relationships of L. major using ITS2 sequencing. METHODS: The study was conducted from the beginning of March to the end of November 2022. All medical information regarding CL was collected from patients of Thi-Qar province who attended the Dermatology Department of Al-Hussein Teaching Hospital in Nasiriyah city...
March 4, 2024: Acta Parasitologica
https://read.qxmd.com/read/38422439/first-report-of-green-mould-on-leaf-of-phaseolus-vulgaris-caused-by-cladosporium-tenuissimum-in-liaoning-china
#20
JOURNAL ARTICLE
Xiaomei Gao, Xiaohe Yang, Yang Li, Miao Yu, Jing Ao, Xiaohui Liu, Yulu Sun, Liqun Song, Fei Chen, Lingling Guo
Phaseolus vulgaris Linn. is a widely cultivated vegetable throughout the world. From spring 2019 to 2022, green mould symptoms were observed on leaves of P. vulgaris in the greenhouse in Liaoning, China, with disease incidence of 8-75% (plants) and 6-23% (leaves). Symptoms appeared as chlorotic lesions covered with dark green mould. The infections started at the apex or margin of the leaves and then spread inward with a characteristic "V" shape. Lesions exhibited curly morphology. 15 leaf samples with typical symptoms were collected from 5 different greenhouses...
February 29, 2024: Plant Disease
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