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   Articles with "genome assemblies" as a keyword



Understanding bacterial pathogen diversity: A proteogenomic analysis and use of an array of genome assemblies to identify novel virulence factors of the honey bee bacterial pathogen Paenibacillus larvae

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recommendations! Published in 2024 at "PROTEOMICS"

DOI: 10.1002/pmic.202300280

Abstract: Mass spectrometry proteomics data are typically evaluated against publicly available annotated sequences, but the proteogenomics approach is a useful alternative. A single genome is commonly utilized in custom proteomic and proteogenomic data analysis. We pose… read more here.

Keywords: honey bee; analysis; bee bacterial; genome assemblies ... See more keywords

Rat Genome Assemblies, Annotation, and Variant Repository.

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recommendations! Published in 2019 at "Methods in molecular biology"

DOI: 10.1007/978-1-4939-9581-3_2

Abstract: The first and only published version of the rat reference genome sequence was RGSC3.1, accomplished by the Rat Genome Sequencing Project Consortium. Here we present the history of the community effort in the correction of… read more here.

Keywords: assemblies annotation; linkage; rat genome; rat ... See more keywords

Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

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recommendations! Published in 2024 at "Nature Communications"

DOI: 10.1038/s41467-024-44914-y

Abstract: Using long-read sequencing, we assembled and unzipped the polyploid genomes of Meloidogyne incognita, M. javanica and M. arenaria, three of the most devastating plant-parasitic nematodes. We found the canonical nematode telomeric repeat to be missing… read more here.

Keywords: polyploid root; genome assemblies; telomeric repeats; assemblies polyploid ... See more keywords

High-quality phased genome assemblies of line-bred Korean Hanwoo cattle

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recommendations! Published in 2025 at "Scientific Data"

DOI: 10.1038/s41597-025-06069-3

Abstract: The Korean cattle breed, Hanwoo, has been selected as a meat cattle breed since the late 1980s in Korea, but has suffered from reduced genetic diversity due to repeated selection within a single population. In… read more here.

Keywords: genome assemblies; high quality; phased genome; hrc hanwoo ... See more keywords

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btad198

Abstract: Summary Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created… read more here.

Keywords: exclusion; exclusion sets; grcm39; genome assemblies ... See more keywords

Chromosome-Level Genome Assemblies of Two Hypnales (Mosses) Reveal High Intergeneric Synteny

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recommendations! Published in 2022 at "Genome Biology and Evolution"

DOI: 10.1093/gbe/evac020

Abstract: Abstract Mosses compose one of the three lineages of bryophytes. Today, about 13,000 species of mosses are recognized from across the globe, and at least one-third of this diversity composes the Hypnales, a lineage characterized… read more here.

Keywords: genome assemblies; curvifolium; chromosome level; level genome ... See more keywords

Highly Contiguous Genome Assemblies of the Guinea Paper Wasp (Polistes exclamans) and Mischocyttarus mexicanus

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recommendations! Published in 2022 at "Genome Biology and Evolution"

DOI: 10.1093/gbe/evac110

Abstract: Abstract Paper wasps are a model system for the study of social evolution due to a high degree of inter- and intraspecific variation in cooperation, aggression, and visual signals of social status. Increasing the taxonomic… read more here.

Keywords: polistes exclamans; genome assemblies; mexicanus; genome ... See more keywords

polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies

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recommendations! Published in 2022 at "Genome Biology and Evolution"

DOI: 10.1093/gbe/evad020

Abstract: Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) Continuous Long Reads (CLR), have a high error rate. Such… read more here.

Keywords: polishclr; nextflow workflow; clr; genome assemblies ... See more keywords

Tapping Culture Collections for Fungal Endophytes: First Genome Assemblies for Three Genera and Five Species in the Ascomycota

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recommendations! Published in 2023 at "Genome Biology and Evolution"

DOI: 10.1093/gbe/evad038

Abstract: Abstract The Ascomycota form the largest phylum in the fungal kingdom and show a wide diversity of lifestyles, some involving associations with plants. Genomic data are available for many ascomycetes that are pathogenic to plants,… read more here.

Keywords: culture; fungal endophytes; culture collections; tapping culture ... See more keywords

The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)

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recommendations! Published in 2018 at "GigaScience"

DOI: 10.1093/gigascience/giy097

Abstract: Abstract Background Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied… read more here.

Keywords: simplicifolius daemonorops; daemonorops jenkinsiana; simplicifolius jenkinsiana; calamus simplicifolius ... See more keywords

Hi-C techniques: from genome assemblies to transcription regulation.

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recommendations! Published in 2024 at "Journal of experimental botany"

DOI: 10.1093/jxb/erae085

Abstract: The invention of chromosome-conformation capture (3C) techniques, in particular the key method Hi-C providing genome-wide information about chromatin contacts, revolutionized the way we study the three-dimensional (3D) organization of the nuclear genome and how it… read more here.

Keywords: techniques genome; transcription regulation; genome assemblies; botany ... See more keywords