Relevant bibliographies by topics / Chromosome-level genome assembly

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  1. Journal articles
  2. Dissertations / Theses
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  4. Conference papers

Academic literature on the topic 'Chromosome-level genome assembly'

Author: Grafiati
Published: 4 June 2025
Last updated: 1 August 2025

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Journal articles on the topic "Chromosome-level genome assembly"

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Arkhipov, Alexander A., Elena N. Pushkova, Nadezhda L. Bolsheva, et al. "Nanopore Data-Driven Chromosome-Level Assembly of Flax Genome." Plants 13, no. 24 (2024): 3465. https://doi.org/10.3390/plants13243465.

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Flax is an important crop grown for seed and fiber. Flax chromosome number is 2n = 30, and its genome size is about 450–480 Mb. To date, the genomes of several flax varieties have been sequenced and assembled. However, the obtained assemblies are still far from the telomere-to-telomere (T2T) level. We sequenced the genome of flax variety K-3018 on the Oxford Nanopore Technologies (ONT) platform and obtained 57.7 Gb of R10 simplex reads with an N50 = 18.4 kb (~120× genome coverage). ONT reads longer than 50 kb were kept as ultra-long ones (~10× genome coverage), and the rest of the ONT reads we
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Collins, Andrew. "The Challenge of Genome Sequence Assembly." Open Bioinformatics Journal 11, no. 1 (2018): 231–39. http://dx.doi.org/10.2174/1875036201811010231.

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Background: Although whole genome sequencing is enabling numerous advances in many fields achieving complete chromosome-level sequence assemblies for diverse species presents difficulties. The problems in part reflect the limitations of current sequencing technologies. Chromosome assembly from ‘short read’ sequence data is confounded by the presence of repetitive genome regions with numerous similar sequence tracts which cannot be accurately positioned in the assembled sequence. Longer sequence reads often have higher error rates and may still be too short to span the larger gaps between conti
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Coelho, Laís, Lukas Musher, and Joel Cracraft. "A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)." Diversity 11, no. 9 (2019): 144. http://dx.doi.org/10.3390/d11090144.

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Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophi
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Fu, Xinhua, Victor Benno Meyer-Rochow, Lesley Ballantyne, and Xinlei Zhu. "An Improved Chromosome-Level Genome Assembly of the Firefly Pyrocoelia pectoralis." Insects 15, no. 1 (2024): 43. http://dx.doi.org/10.3390/insects15010043.

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The endemic and endangered Chinese firefly Pyrocoelia pectoralis is a sexually dimorphic, nocturnal species. A previous attempt by this team to assemble a draft genome of P. pectoralis using PacBio and Illumina HiSeq X Ten platforms was limited in its usefulness by high redundancy and contamination. This prompted us to conduct an improved chromosome-level genome assembly of P. pectoralis. Ten chromosomes were further assembled based on Hi-C data to a 532.25 Mb final size with a 52.87 Mb scaffold N50. The total repeat lengths in the genome of P. pectoralis amount to 227.69 Mb; 42.78%. In total,
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Gao, Haiyu, Hui Kang, Yaolei Zhang, et al. "Chromosome-Level Genome Assembly of the Rough-Toothed Dolphin (Steno bredanensis)." Journal of Marine Science and Engineering 11, no. 2 (2023): 418. http://dx.doi.org/10.3390/jmse11020418.

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The rough-toothed dolphin (Steno bredanensis), the single extant species of the genus Steno, inhabits tropical and subtropical oceans. It is an attractive species for studying aquatic adaptation and evolution. The latest advances in high-throughput sequencing are transforming the study of marine mammals and contributing to understanding various phenomena at the species and population level by determining high-quality genomes. Here, to comprehensively understand the genetic features and explore the molecular basis of aquatic adaption, the chromosome-level genome assembly and comparative genomic
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Chen, Yutang, Roland Kölliker, Martin Mascher, et al. "An improved chromosome-level genome assembly of perennial ryegrass (Lolium perenne L.)." Gigabyte 2024 (March 6, 2024): 1–11. http://dx.doi.org/10.46471/gigabyte.112.

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This work is an update and extension of the previously published article “Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly” by Frei et al. The published genome assembly of the doubled haploid perennial ryegrass (Lolium perenne L.) genotype Kyuss (Kyuss v1.0) marked a milestone for forage grass research and breeding. However, order and orientation errors may exist in the pseudo-chromosomes of Kyuss, since barley (Hordeum vulgare L.), which diverged 30 million years ago from perennial ryegrass, was used as the reference to scaffold Ky
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Li, Yiyuan, Hyunjin Park, Thomas E. Smith, and Nancy A. Moran. "Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly." Molecular Biology and Evolution 36, no. 10 (2019): 2143–56. http://dx.doi.org/10.1093/molbev/msz138.

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Abstract Genome structural variations, including duplications, deletions, insertions, and inversions, are central in the evolution of eukaryotic genomes. However, structural variations present challenges for high-quality genome assembly, hampering efforts to understand the evolution of gene families and genome architecture. An example is the genome of the pea aphid (Acyrthosiphon pisum) for which the current assembly is composed of thousands of short scaffolds, many of which are known to be misassembled. Here, we present an improved version of the A. pisum genome based on the use of two long-r
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Yurchenko, Andrey A., Hans Recknagel, and Kathryn R. Elmer. "Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome." Genome Biology and Evolution 12, no. 11 (2020): 1953–60. http://dx.doi.org/10.1093/gbe/evaa161.

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Abstract Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a
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Teterina, Anastasia A., John H. Willis, and Patrick C. Phillips. "Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization." Genetics 214, no. 4 (2020): 769–80. http://dx.doi.org/10.1534/genetics.119.303018.

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The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and
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Zhu, Xiangyun, Yanping Luo, Baoshan Ma, et al. "Chromosome-Level Assembly and Annotation of the Endangered Red-Wing Fish (Distoechodon macrophthalmus)." Genes 15, no. 12 (2024): 1536. http://dx.doi.org/10.3390/genes15121536.

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Background/Objectives: The red-wing fish (Distoechodon macrophthalmus), an endangered species native to Yunnan, is endemic to Chenghai Lake. The natural population of this species has suffered a sharp decline due to the invasion of alien fish species. Fortunately, the artificial domestication and reproduction of D. macrophthalmus have been successful and this species has become an economic species locally. However, there is still little research on D. macrophthalmus. Methods: In this study, a high-quality genome of D. macrophthalmus was assembled and annotated. The genome was sequenced and ass
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Dissertations / Theses on the topic "Chromosome-level genome assembly"

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SECOMANDI, SIMONA. "CHROMOSOME-LEVEL DE NOVO GENOME ASSEMBLIES OF AVIAN SPECIES AND THEIR RELEVANCE FOR COMPARATIVE GENOMICS, PANGENOMICS, POPULATION GENOMICS AND SPECIES CONSERVATION." Doctoral thesis, Università degli Studi di Milano, 2022. http://hdl.handle.net/2434/931506.

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Life on Earth is currently experiencing the sixth mass extinction. A major loss of species is being caused by anthropogenic habitat destruction, illegal wildlife trade, overfishing, massive fossil fuel consumption and the consequent climate changes, leading to a progressive collapse of biodiversity. The establishment of conservation initiatives is now more crucial than ever and the genetic management of threatened species is currently gaining critical significance. Previous genetic studies have been limited by the lack of complete reference genomes, thus having to focus on a limited number of
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Gapa, Liubov. "Short-read Chromosome Level Genome Assembly of Digitaria exilis." Thesis, 2019. http://hdl.handle.net/10754/660202.

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Genomics has become an important tool in agriculture. Many modern crop breeding approaches such as genomic selection and genome editing require detailed information of the genomic composition of a crop species. However, the assembly of high-quality genome sequences is prone to technical artifacts that arise from inaccuracies in the sequencing technology and assembly algorithms. This is particularly true for the genomes of cereal crops, which are often very large, repeat-rich, and polyploid. Until recently, the highly continuous assembly of such cereal crop genomes from short-read data was main
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Book chapters on the topic "Chromosome-level genome assembly"

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Tilghman, Shirley M., and Huntington F. Willard. "Epigenetic regulation in mammals." In Chromatin Structure and Gene Expression. Oxford University PressOxford, 1995. http://dx.doi.org/10.1093/oso/9780199635764.003.0010.

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Abstract The term ‘epigenetic’ when applied to mammalian genes refers to different stable states of phenotypic expression usually thought to be due to differential effects of chromosome or chromatin packaging, and determined or influenced by control mechanisms which can be manifested over exceptionally long distances. Both the recognition of epigenetic states and the design of tractable experimental approaches to analyse them require an appreciation for mammalian gene expression in its dynamic setting. One must consider those aspects of chromatin assembly, structure, and replication (see Chapt
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Schedl, Paul, and Frank Grosveld. "Domains and boundaries." In Chromatin Structure and Gene Expression. Oxford University PressOxford, 1995. http://dx.doi.org/10.1093/oso/9780199635764.003.0009.

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Abstract The very large genomes found in many higher eukaryotes must be condensed into a relatively small volume inside the nucleus. This is accomplished by packaging the DNA into a complex, multi-level nucleoprotein structure, chromatin. At the first level of organization the DNA is assembled into a beads-on-a-string nucleosome array, the 10 nm fibre visualized by electron microscopy (see Chapter 1). In the second level of organization, the 10 nm fibre is coiled into a 30 nm fibre. While this transition is thought to be facilitated by Hl binding (1), the precise organization of the nucleosome
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Conference papers on the topic "Chromosome-level genome assembly"

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Zaccaron, Alex. "Impact of genomic structural variations on virulence of the tomato pathogen Cladosporium fulvum." In IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-1.

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Cladosporium fulvum causes tomato leaf mold and has been extensively used in the past as a model species to study plant-microbe interactions. Although the first chromosome-scale reference genome of the fungus was released in 2022, still little is known about how its genome architecture and structural variations (SVs) thereof impact its virulence. In this study, we used PacBio HiFi to sequence the genomes of four additional C. fulvum isolates and further assembled them at chromosome level. Comparative genome analyses revealed high chromosomal synteny among the five isolates, and a set of 13 cor
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Sadler, J. Evan. "THE MOLECULAR BIOLOGY OF VON WILLEBRAND FACTOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643930.

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Human von Willebrand factor (vWF) is a plasma glycoprotein that is synthesized by endothelial cells and megakaryocytes, and perhaps by syncytiotrophoblast of placenta. The biosynthesis of vWF is very complex, involving proteolytic processing, glycosyla-tion, disulfide bond formation, and sulfation. Mature vWF consists of a single subunit of ∼ 250,000 daltons that is assembled into multimer ranging from dimers to species of over 10 million daltons. vWF performs its essential hemostatic function through several binding interactions, forming a bridge between specific receptors on the platelet sur
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