keyword
https://read.qxmd.com/read/38529759/what-is-new-in-fungidb-a-web-based-bioinformatics-platform-for-omics-scale-data-analysis-for-fungal-and-oomycete-species
#21
JOURNAL ARTICLE
Evelina Y Basenko, Achchuthan Shanmugasundram, Ulrike Böhme, David Starns, Paul A Wilkinson, Helen R Davison, Kathryn Crouch, Gareth Maslen, Omar S Harb, Beatrice Amos, Mary Ann McDowell, Jessica C Kissinger, David S Roos, Andrew Jones
FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e...
March 26, 2024: Genetics
https://read.qxmd.com/read/38529180/multi-omics-approaches-to-understand-pathogenicity-during-potato-early-blight-disease-caused-by-alternaria-solani
#22
JOURNAL ARTICLE
Qing Li, Yan Feng, Jianmei Li, Yang Hai, Liping Si, Chen Tan, Jing Peng, Zuo Hu, Zhou Li, Canhui Li, Dahai Hao, Wei Tang
Potato early blight (PEB), a foliar disease of potato during the growing period, caused by Alternaria sp., is common in major potato-producing areas worldwide. Effective agents to control this disease or completely resistant potato varieties are absent. Large-scale use of fungicides is limited due to possibility of increase in pathogen resistance and the requirements of ecological agriculture. In this study, we focused on the composition and infection characteristics of early blight pathogens in Yunnan Province and screened candidate pathogenesis-related pathways and genes...
2024: Frontiers in Microbiology
https://read.qxmd.com/read/38529113/the-complete-chloroplast-genome-sequence-of-myricaria-wardii-marquand-1929-tamaricaceae-a-shrub-species-endemic-to-the-tibet-plateau
#23
JOURNAL ARTICLE
Haoran Liu, Godfrey Kinyori Wagutu, Yuanyuan Chen, Xiuling Li, Xiangrong Fan
Myricaria wardii Marquand 1929, endemic to the Tibet Plateau, is a perennial shrub with important medicinal and ecological values. In this study, the complete chloroplast (cp) genome of M. wardii was assembled, and the phylogenetic tree was reconstructed to evaluate the phylogenetic location of the species. The results showed that the cp genome size of the M. wardii was 155,299 bp, which contained a pair of inverted repeat (IR) regions (26,150 bp), a large single copy (LSC) region (84,715 bp), and a small single copy (SSC) region (18,284 bp)...
2024: Mitochondrial DNA. Part B. Resources
https://read.qxmd.com/read/38529112/complete-mitochondrial-genome-of-basilepta-melanopus-lef%C3%A3-vre-1893-coleoptera-chrysomelidae-eumolpinae-a-tea-pest-from-southern-china
#24
JOURNAL ARTICLE
Yonglin Liao, Yurong Fang, Weiping Chen, Jihua Wang
The tea pest, Basilepta melanopus Lefèvre 1893 (Chrysomelidae), belongs to the subfamily Eumolpinae. In this study, the complete mitochondrial genome sequence of B. melanopus from southern China was sequenced using the next-generation sequencing technique, assembled, and annotated using bioinformatics tools. The complete mitochondrial genome was 15,905 bp in length. The overall GC content was 22.51%, in which the percentages for the bases A, T, C, and G were 41.23%, 36.26%, 8.92%, and 13.59%, respectively...
2024: Mitochondrial DNA. Part B. Resources
https://read.qxmd.com/read/38529109/the-mitochondrial-genome-of-neoperla-bimaculata-li-et%C3%A2-al-2021-plecoptera-perlidae-from-tibet-of-southwest-china-and-its-phylogenetic-analysis
#25
JOURNAL ARTICLE
Caiyue Guo, Ying Wang, Weihai Li, Jinjun Cao
The complete mitochondrial genome (mitogenome) of Neoperla bimaculata was sequenced and annotated in this study. We found that the mitogenome of N. bimaculata is 15,774 bp in length with an A + T content of 64.3%. It exhibits the classic structure of a mitogenome. Most protein-coding genes (PCGs) of the mitogenome initiate with the standard start codon ATN. Ten PCGs use the standard stop codon TAA/TAG, while the COI , COII , and ND5 genes terminate with a single T nucleotide. Phylogenetic analyses suggested that N...
2024: Mitochondrial DNA. Part B. Resources
https://read.qxmd.com/read/38528797/biodeepfuse-a-hybrid-deep-learning-approach-with-integrated-feature-extraction-techniques-for-enhanced-non-coding-rna-classification
#26
JOURNAL ARTICLE
Anderson P Avila Santos, Breno L S de Almeida, Robson P Bonidia, Peter F Stadler, Polonca Stefanic, Ines Mandic-Mulec, Ulisses Rocha, Danilo S Sanches, André C P L F de Carvalho
The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy...
January 2024: RNA Biology
https://read.qxmd.com/read/38528457/full-length-16s-rrna-gene-sequencing-by-pacbio-improves-taxonomic-resolution-in-human-microbiome-samples
#27
JOURNAL ARTICLE
Elena Buetas, Marta Jordán-López, Andrés López-Roldán, Giuseppe D'Auria, Llucia Martínez-Priego, Griselda De Marco, Miguel Carda-Diéguez, Alex Mira
BACKGROUND: Sequencing variable regions of the 16S rRNA gene (≃300 bp) with Illumina technology is commonly used to study the composition of human microbiota. Unfortunately, short reads are unable to differentiate between highly similar species. Considering that species from the same genus can be associated with health or disease it is important to identify them at the lowest possible taxonomic rank. Third-generation sequencing platforms such as PacBio SMRT, increase read lengths allowing to sequence the whole gene with the maximum taxonomic resolution...
March 25, 2024: BMC Genomics
https://read.qxmd.com/read/38528453/genome-wide-analysis-of-the-knox-gene-family-in-moso-bamboo-insights-into-their-role-in-promoting-the-rapid-shoot-growth
#28
JOURNAL ARTICLE
Yang Jiao, Jiaqi Tan, Hui Guo, Bin Huang, Yeqing Ying, Muthusamy Ramakrishnan, Zhijun Zhang
BACKGROUND: KNOTTED1-like homeobox (KNOX) genes, plant-specific homologous box transcription factors (TFs), play a central role in regulating plant growth, development, organ formation, and response to biotic and abiotic stresses. However, a comprehensive genome-wide identification of the KNOX genes in Moso bamboo (Phyllostachys edulis), the fastest growing plant, has not yet been conducted, and the specific biological functions of this family remain unknown. RESULTS: The expression profiles of 24 KNOX genes, divided into two subfamilies, were determined by integrating Moso bamboo genome and its transcriptional data...
March 25, 2024: BMC Plant Biology
https://read.qxmd.com/read/38528244/exploring-genomic-inbreeding-and-selection-signatures-in-a-commercial-brangus-herd-through-functional-annotation
#29
JOURNAL ARTICLE
Gabriel A Zayas, Eduardo E Rodriguez, Aakilah S Hernandez, Fernanda M Rezende, Raluca G Mateescu
Composite breeds, including Brangus, are widely utilized in subtropical and tropical regions to harness the advantages of both Bos t. taurus and Bos t. indicus breeds. The formation and subsequent selection of composite breeds may result in discernible signatures of selection and shifts in genomic population structure. The objectives of this study were to 1) assess genomic inbreeding, 2) identify signatures of selection, 3) assign functional roles to these signatures in a commercial Brangus herd, and 4) contrast signatures of selection between selected and non-selected cattle from the same year...
March 25, 2024: Journal of Applied Genetics
https://read.qxmd.com/read/38528107/the-complete-mitochondrial-genome-of-chibiraga-houshuaii-lepidoptera-limacodidae-and-its-phylogenetic-implications
#30
JOURNAL ARTICLE
Yanpeng Cai, Aihui Yin
Chibiraga is a mall East Asian genus in the family Limacodidae (slug-moths). The latter includes many agricultural pests. Mitochondrial genome analysis is an important tool for studying insect molecular identification and phylogenetics. However, there are very few mitogenome sequences available for Limacodidae species, and none for the genus Chibiraga at all. To explore the mitogenome features of Chibiraga and verify its phylogenetic position, the complete mitogenome of Chibiraga houshuaii was sequenced and annotated...
March 25, 2024: Scientific Reports
https://read.qxmd.com/read/38526734/multidisciplinary-methods-for-screening-toxic-proteins-from-phages-and-their-potential-molecular-targets
#31
JOURNAL ARTICLE
Xing Wan, Mikael Skurnik
This chapter presents a comprehensive methodology for the identification, characterization, and functional analyses of potentially toxic hypothetical proteins of unknown function (toxHPUFs) in phages. The methods begin with in vivo toxicity verification of toxHPUFs in bacterial hosts, utilizing conventional drop tests and following growth curves. Computational methods for structural and functional predictions of toxHPUFs are outlined, incorporating the use of tools such as Phyre2, HHpred, and AlphaFold2. To ascertain potential targets, a comparative genomic approach is described using bioinformatics toolkits for sequence alignment and functional annotation...
2024: Methods in Molecular Biology
https://read.qxmd.com/read/38526609/nephroblastoma-specific-dysregulated-gene-snhg15-with-prognostic-significance-scrna-seq-with-bulk-rna-seq-data-and-experimental-validation
#32
JOURNAL ARTICLE
Mengmeng Chang, Ding Li, Li Su, Chen Ding, Zhiyi Lu, Hongjie Gao, Fengyin Sun
Wilms tumor (WT) is the most common malignancy of the genitourinary system in children. Currently, the Integration of single-cell RNA sequencing (scRNA-Seq) and Bulk RNA sequencing (RNA-Seq) analysis of heterogeneity between different cell types in pediatric WT tissues could more accurately find prognostic markers, but this is lacking. RNA-Seq and clinical data related to WT were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Small nucleolar RNA host gene 15 (SNHG15) was identified as a risk signature from the TARGET dataset by using weighted gene co-expression network analysis, differentially expressed analysis and univariate Cox analysis...
March 25, 2024: Discover. Oncology
https://read.qxmd.com/read/38526344/a-genome-sequence-for-the-threatened-whitebark-pine
#33
JOURNAL ARTICLE
David B Neale, Aleksey V Zimin, Amy Meltzer, Akriti Bhattarai, Maurice Amee, Laura Figueroa Corona, Brian J Allen, Daniela Puiu, Jessica Wright, Amanda R De La Torre, Patrick E McGuire, Winston Timp, Steven L Salzberg, Jill L Wegrzyn
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in western contiguous US and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration...
March 25, 2024: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/38526066/genomic-analyses-of-nitrogen-utilization-efficiency-its-indicator-trait-blood-urea-nitrogen-and-the-relationship-to-classical-growth-performance-and-feed-efficiency-traits-in-a-landrace%C3%A2-%C3%A3-%C3%A2-pi%C3%A3-train-crossbred-population
#34
JOURNAL ARTICLE
Markus Schmid, Ramona Weishaar, Jana Seifert, Amélia Camarinha-Silva, Markus Rodehutscord, Jörn Bennewitz
Improving the nutrient efficiency in pork production is required to reduce the resource competition between human food and animal feed regarding diet components edible for humans and to minimize emissions relevant to climate or the environment. Thereby, protein utilization efficiency and its equivalent nitrogen utilization efficiency (NUE) play a major role. Breeding for more nitrogen (N) efficient pigs bears a promising strategy to improve such traits, however, directly phenotyping NUE based on N balance data is neither cost-efficient nor straightforward and not applicable for routine evaluations...
March 25, 2024: Journal of Animal Breeding and Genetics
https://read.qxmd.com/read/38525153/aphid-gene-expression-following-polerovirus-acquisition-is-host-species-dependent
#35
JOURNAL ARTICLE
Sudeep Pandey, Michael Catto, Phillip Roberts, Sudeep Bag, Alana L Jacobson, Rajagopalbabu Srinivasan
Upon acquisition of persistent circulative viruses such as poleroviruses, the virus particles transcytose through membrane barriers of aphids at the midgut and salivary glands via hemolymph. Such intricate interactions can influence aphid behavior and fitness and induce associated gene expression in viruliferous aphids. Differential gene expression can be evaluated by omics approaches such as transcriptomics. Previously conducted aphid transcriptome studies used only one host species as the source of virus inoculum...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38525152/the-effect-of-marker-types-and-density-on-genomic-prediction-and-gwas-of-key-performance-traits-in-tetraploid-potato
#36
JOURNAL ARTICLE
Trine Aalborg, Elsa Sverrisdóttir, Heidi Thorgaard Kristensen, Kåre Lehmann Nielsen
Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38525151/genome-wide-association-study-reveals-snp-markers-controlling-drought-tolerance-and-related-agronomic-traits-in-chickpea-across-multiple-environments
#37
JOURNAL ARTICLE
Tawffiq Istanbuli, Ahmed E Nassar, Mamdouh M Abd El-Maksoud, Sawsan Tawkaz, Alsamman M Alsamman, Aladdin Hamwieh
Chickpea, renowned for its exceptional nutritional value, stands as a crucial crop, serving as a dietary staple in various parts of the world. However, its productivity faces a significant challenge in the form of drought stress. This challenge highlights the urgent need to find genetic markers linked to drought tolerance for effective breeding programs. The primary objective of this study is to identify genetic markers associated with drought tolerance to facilitate effective breeding programs. To address this, we cultivated 185 chickpea accessions in two distinct locations in Lebanon over a two-year period, subjecting them to both irrigated and rain-fed environments...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38525148/a-chromosome-level-genome-assembly-of-solanum-chilense-a-tomato-wild-relative-associated-with-resistance-to-salinity-and-drought
#38
JOURNAL ARTICLE
Corentin Molitor, Tomasz J Kurowski, Pedro M Fidalgo de Almeida, Zoltan Kevei, Daniel J Spindlow, Steffimol R Chacko Kaitholil, Justice U Iheanyichi, H C Prasanna, Andrew J Thompson, Fady R Mohareb
INTRODUCTION: Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. METHODS: In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38525082/corrigendum-whole-genome-sequencing-annotation-and-biological-characterization-of-a-novel-siphoviridae-phage-against-multi-drug-resistant-propionibacterium-acne
#39
Danxi Liao, Jian Zhang, Ruolan Liu, Kui Chen, Yuanyuan Liu, Yuming Shao, Xi Shi, Yiming Zhang, Zichen Yang
[This corrects the article DOI: 10.3389/fmicb.2022.1065386.].
2024: Frontiers in Microbiology
https://read.qxmd.com/read/38524236/comparative-genome-wide-analysis-of-novel-streptomyces-isolates-rc1831-and-rc1832-deciphering-the-role-of-functional-carbohydrate-cazy-active-genes-including-chitinase-for-production-of-chitosan
#40
JOURNAL ARTICLE
Suchismita Nivedita, Subhransu Sekhar Behera, Himadri Tanaya Behera, Sudhansu Kumar Gouda, Ananta Narayana Panda, Lopamudra Ray
UNLABELLED: This work compares two bacterial isolates Streptomyces barkulensis RC1831 and Streptomyces chitinovorans RC1832 isolated from Chilika Lake sediments in Odisha, India, using whole-genome sequence analysis. According to the results of the genome analysis, the RC1831 genome has a chromosome with 6,383,258 bp (72.9% GC) and 6145 coding sequences and 66 RNA, while the RC1832 genome has a chromosome with 6,055,792 bp (73.1% GC) and 5824 coding sequences and 63 RNA...
April 2024: 3 Biotech
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