Topic 122

honeybee clean article apis raw reads fungal chalkbrood ascosphaera nosema ceranae quality spores larvae c_lio_lithe respectively widespread subspecies value c_lio_lithis cdna bee mrnas act2 act1 acck2 acck1 yielded obtained transcriptome beekeeping c_li aam infects dataset cerana total transcripts followed mecylia microsporidiosis resource sequencing industry ranged parasite seriously kb aas redundant nanopore read n50 library length workers productivity mycelium colony datao_lithe totally additionally purified q12 q6 midguts un promethion introns abundant bp contributes exons better mapped polyadenylation eastern valuable pathogen gc subreads circrnas removed infected datao_licurrent construction 10 generation spore accessible guts molecular 727 distribution datao_lithis reported platform q30 data amck2

12 items. Top items listed below.

Nanopore long-read transcriptome data of fungal pathogen of chalkbrood disease, Ascosphaera apis 122 25 9

Strand-specific cDNA library-based RNA sequencing dataset of un-infected and Ascosphaera apis-infected larval guts of Apis cerana cerana 122 25

Whole transcriptome data of uninfected and Nosema ceranae-infected midguts of eastern honeybee workers 122 25

Long-read transcriptome data of bee fungal parasite, Nosema ceranae 122 25 15 4

A full-length transcriptome dataset of normal and Nosema ceranae-challenged midgut tissues of eastern honeybee workers 122 25

Genome-wide bisulfite sequencing data of normal and Ascosphaera apis-infected larval guts of eastern honeybee 122

PacBio SMRT-based full-length transcriptome data of Ascosphaera apis mycelium and spore 122 25

Nanopore-based long-read transcriptome data of Nosema ceranae-infected and un-infected western honeybee workers' midguts 122 25

Whole genome bisulfite sequencing dataset of mycelium and spore of chalkbrood disease pathogen Ascosphaera apis 122 25 15

MeRIP-seq and RNA-seq data of mycelium and spore of Ascosphaera apis, a widespread bee fungal pathogen 122 15

Comprehensive transcriptome data of normal and Ascosphaera apis-infected western honeybee larval guts 122

Pacific Biosciences long reads-based genome sequencing data from a widespread bee fungal parasite, Nosema ceranae 122 25

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis 25 4

Queen pheromone modulates the expression of epigenetic modifier genes in the brain of honey bee workers

A comparative transcriptional landscape of two castor cultivars obtained by single-molecule sequencing comparative analysis 25 9

LIQA: Long-read Isoform Quantification and Analysis 25 13 4

High accuracy DNA sequencing on a small, scalable platform via electrical detection of single base incorporations 25 4

Long-read shotgun metagenome sequencing using PromethION uncovers novel bacteriophages, their abundance, and interaction with host bacterial immunity in the oral microbiota 25 12 5 4

Short and Long-read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and its Host 25 4

Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex 9

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacbio Sequel II system and ultralong reads of Oxford Nanopore 25 4

De novo genome assembly and transcriptome analysis for the drought and salt resistant Solanum sitiens 25 9 4

Targeted Transcriptome Analysis using Synthetic Long Read Sequencing Uncovers Isoform Reprograming in the Progression of Colon Cancer 25 9 4

Virus infections in Varroa destructor-resistant honeybees 5

A short read de novo transcriptome construction pipeline optimized by long reads reveals novel developmentally regulated gene isoforms and disease targets in hundreds of eye samples 25 9 4

Whole genome sequencing of cell-free DNA yields genome-wide read distribution patterns to track tissue of origin in cancer patients 97 9 4

Novel reference transcriptomes for the sponges Carteriospongia foliascens and Cliona orientalis and associated algal symbiont Gerakladium endoclionum 25 5

Assessment of mapping strategies for determining the 5'-end of mRNAs and long-noncoding RNAs with short read sequences 25 9 4

The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range 21 5

Long-Read cDNA Sequencing Enables a 'Gene-Like' Transcript Annotation of Arabidopsis Transposable Elements 81 25 9 4

Transposable element expression at unique loci in single cells with CELLO-seq 81 9 4

Highly Multiplexed Single-Cell Full-Length cDNA Sequencing of human immune cells with 10X Genomics and R2C2 25 4

Transcriptomic and epigenomic dynamics of honey bees in response to lethal IAPV viral infection 41 9

Identification and characterization of long noncoding RNAs and their association with acquisition of blood meal in Culex quinquefasciatus 48 9

CONSENT: Scalable long read self-correction and assembly polishing with multiple sequence alignment 25 13 4

GALA: gap-free chromosome-scale assembly with long reads 25 4

High-quality de novo genome assembly of Kappaphycus alvarezii based on both PacBio and HiSeq sequencing 25 5 4

Stage-Specific Long Non-coding RNAs in Cryptosporidium parvum as Revealed by Stranded RNA-Seq 49 9

Whole Genome Sequences of Aedes aegypti (Linn.) Field Isolates from Southern India 48 25 9 5 4

Chromosome-scale genome assembly of Fusarium oxysporum strain Fo47, a fungal endophyte and biocontrol agent 25 5

Long-read genome sequencing for the diagnosis of neurodevelopmental disorders 25 4

QAlign: Aligning nanopore reads accurately using current-level modeling 25 13 4

SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi Associated Microorganisms 121 4

Origin of imported SARS-CoV-2 strains in The Gambia identified from Whole Genome Sequences. 37 1

A chromosome-scale genome assembly for the Fusarium oxysporum strain Fo5176 to establish a model Arabidopsis-fungal pathosystem 25 12 9 4

Long-read Assays Shed New Light on the Transcriptome Complexity of a Viral Pathogen and on Virus-Host Interaction 25 9 4

A multi-platform reference for somatic structural variation detection 25 4

Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol 25 4

mRNA and Small RNA-seq Reveal Insights into Immune Regulation in Apis cerana after Chinese Sacbrood Virus Infection 41 9 3

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification 25 4

First complete genome sequences of Streptococcus pyogenes NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies 25 12 5

NanoReviser: An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm 13 4

Novel rRNA-depletion methods for total RNA sequencing and ribosome profiling developed for avian species 125 49 4

Genome-wide identification of Aedes albopictus long noncoding RNAs and their association with dengue and zika virus infection 48 41 9

Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru 13 4

Profiling of Human Gut Virome with Oxford Nanopore Technology 25 4

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora 25 5 4

A workflow for accurate metabarcoding using nanopore MinION sequencing 125 25 4

Time-course Profiling of Bovine Herpesvirus Type 1 and Host Cell Transcriptomes using Multiplatform Sequencing 25 9 4

Comparison of long read sequencing technologies in resolving bacteria and fly genomes 25 4

Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains 25 5

Can colony size of honeybees (Apis mellifera) be used as predictor for colony losses due to Varroa destructor during winter? 84 5

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16s rDNA amplicon sequencing 125 29 25 15 5 4

Genomic region associated with pod color variation in pea (Pisum sativum) 25 9 5 4

Duplications drive diversity in Bordetella pertussis on an underestimated scale. 25 9 5 4

Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines 25 4

Identification of silkworm hemocyte subsets and analysis of their response to BmNPV infection based on single-cell RNA sequencing 120 9

Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding 7 1

Improving the chromosome-level genome assembly of the Siamese fighting fish (Betta splendens) in a university Master's course. 25 4

Genome-wide identification of long non-coding RNAs in the gravid ectoparasite Varroa destructor 9

Complete and validated genomes from a metagenome 25 4

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies 25 4

Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus 25 9 4

Integrate Heterogeneous NGS and TGS Data to Boost Genome-free Transcriptome Research 25 4

Nanopore direct RNA sequencing detects differential expression between human cell populations 25 9 4

Refinement of Genome assemblies of Pigeonpea (Cajanus cajan) 25 4

nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class Classification 13 4

Nanopore sequencing reveals full-length Tropomyosin 1 isoforms and their regulation by RNA binding proteins during rat heart development 49 9 3


De novo assembly of trachidermus fasciatus genome by nanopore sequencing 25 5 4

A bacterial symbiont protects honey bees from fungal disease 114 12 5

Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing 35 1

Artificial diets modulate infection rates of Nosema ceranae in bumblebees 194 30

A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina 25 5

Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss 25 9

Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture 121 5

Single cell transcriptome sequencing on the Nanopore platform with ScNapBar 25 4

Transcriptome analysis of resistant and susceptible pepper (Capsicum annuum L.) in response to Xanthomonas campestris pv. Vesicatoria 120 9

GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation 134 49 9

CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages 62 4

Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra 25 5 4

Long-read error correction: a survey and qualitative comparison 25 4

Long-reads assembly of the Brassica napus reference genome, Darmor-bzh 25 4

Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0) 9 4

A transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure 25 5 4

Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms 25 9 4

A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data 25 4

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts 120 9 3

Chromosome-level genome assembly of the African pike, Hepsetus odoe 25 5

AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data 13 4