Relevant bibliographies by topics / Draft genome assembly

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
  5. Reports

Academic literature on the topic 'Draft genome assembly'

Author: Grafiati
Published: 3 June 2025
Last updated: 31 July 2025

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Journal articles on the topic "Draft genome assembly"

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Li, Qiye, Qunfei Guo, Yang Zhou, et al. "A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)." Gigabyte 2020 (July 1, 2020): 1–13. http://dx.doi.org/10.46471/gigabyte.2.

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Amphibian genomes are usually challenging to assemble due to their large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of
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Longmuir, Amy L., Peter L. Beech, and Mark F. Richardson. "Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi." F1000Research 6 (February 28, 2018): 1972. http://dx.doi.org/10.12688/f1000research.12867.2.

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Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The current reference genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, robust genome assemblies of more typical strains are required. Here we report the genome sequencing, draft assembly, and prel
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Zhang, Aidi, Hui Zhou, Xiaohan Jiang, Yuepeng Han, and Xiujun Zhang. "The Draft Genome of a Flat Peach (Prunus persica L. cv. ‘124 Pan’) Provides Insights into Its Good Fruit Flavor Traits." Plants 10, no. 3 (2021): 538. http://dx.doi.org/10.3390/plants10030538.

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The flat peach has become more and more popular worldwide for its fruit quality with relatively low acidity, high sugar content and rich flavor. However, the draft genome assembly of flat peach is still unavailable and the genetic basis for its fruit flavor remains unclear. In this study, the draft genome of a flat peach cultivar ‘124 Pan’ was assembled by using a hybrid assembly algorithm. The final assembly resulted in a total size of 206 Mb with a N50 of 26.3 Mb containing eight chromosomes and seven scaffolds. Genome annotation revealed that a total of 25,233 protein-coding genes were pred
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Longmuir, Amy L., Peter L. Beech, and Mark F. Richardson. "Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi." F1000Research 6 (November 8, 2017): 1972. http://dx.doi.org/10.12688/f1000research.12867.1.

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Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The currently available genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, more robust assemblies of the genomes of more typical strains are required. Here we report the genome sequencing, draft ass
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Braich, Shivraj, Rebecca C. Baillie, German C. Spangenberg, and Noel O. I. Cogan. "A new and improved genome sequence of Cannabis sativa." Gigabyte 2020 (December 23, 2020): 1–13. http://dx.doi.org/10.46471/gigabyte.10.

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Cannabis is a diploid species (2n = 20), the estimated haploid genome sizes of the female and male plants using flow cytometry are 818 and 843 Mb respectively. Although the genome of Cannabis has been sequenced (from hemp, wild and high-THC strains), all assemblies have significant gaps. In addition, there are inconsistencies in the chromosome numbering which limits their use. A new comprehensive draft genome sequence assembly (∼900 Mb) has been generated from the medicinal cannabis strain Cannbio-2, that produces a balanced ratio of cannabidiol and delta-9-tetrahydrocannabinol using long-read
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Cui, Chenming, John H. Herlihy, Aureliano Bombarely, John M. McDowell, and David C. Haak. "Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity." Molecular Plant-Microbe Interactions® 32, no. 12 (2019): 1559–63. http://dx.doi.org/10.1094/mpmi-04-19-0103-ta.

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Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits widespread fungicide resistance and a broad host range. As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome. Here, we leverage Oxford Nanopore Technologies and existing short-read resources to rapidly generate a low-cost, improved as
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Okamoto, Kenichi, Nichole Dopkins, and Elias Kinfu. "A draft genome sequence of the common, or spectacled caiman Caiman crocodilus." F1000Research 10 (December 2, 2021): 1230. http://dx.doi.org/10.12688/f1000research.73066.1.

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The common, or spectacled, caiman Caiman crocodilus is an abundant, widely distributed Neotropical crocodilian exhibiting notable morphological and molecular diversification. The species also accounts by far for the largest share of crocodilian hides on the global market, with the C. crocodilus hide trade alone valued at about US$86.5 million per year. We obtained 239,911,946 paired-end reads comprising approximately 72 G bases using IlluminaTM sequencing of tissue sampled from a single Caiman crocodilus individual. These reads were de-novo assembled and progressively aligned against the genom
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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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Gan, Han Ming, and Christopher M. Austin. "Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease." F1000Research 8 (December 16, 2019): 2108. http://dx.doi.org/10.12688/f1000research.21570.1.

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Background: The genome of Vibrio parahaemolyticus MVP1, isolated from a Malaysian aquaculture farm with shrimp acute hepatopancreatic necrosis disease (AHPND), was previously sequenced using Illumina MiSeq and assembled de novo, producing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood. Methods: The genome of MVP1 was sequenced on Nanopore MinION to obtain long reads to improve genome contiguity. De novo genome a
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Gim, Jeong-An, Kyung-Wan Baek, Young-Sool Hah, Ho Jin Choo, Ji-Seok Kim, and Jun-Il Yoo. "Draft genome of Semisulcospira libertina, a species of freshwater snail." Genomics & Informatics 19, no. 3 (2021): e32. http://dx.doi.org/10.5808/gi.21039.

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Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Although S. libertina has ecological, commercial, and clinical importance, its whole-genome has not been reported yet. Here, we revealed the genome of S. libertina through de novo assembly. We assembled the whole-genome of S. libertina and determined its transcriptome for the first time using Illumina NovaSeq 6000 platform. According to the k-mer analysis, the genome size of S.
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Dissertations / Theses on the topic "Draft genome assembly"

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Freeman, Alex J. "The Genome Sequence of Gossypium herbaceum (A1), a Domesticated Diploid Cotton." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7329.

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Gossypium herbaceum is a species of cotton native to Africa and Asia. As part of a larger effort to investigate structural variation in assorted diploid and polyploid cotton genomes we have sequenced and assembled the genome of G. herbaceum. Cultivated G. herbaceum is an A1-genome diploid from the Old World (Africa) with a genome size of approximately 1.7 Gb. Long range information is essential in constructing a high-quality assembly, especially when the genome is expected to be highly repetitive. Here we present a quality draft genome of G. herbaceum (cv. Wagad) using a multi-platform sequenc
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Jugas, Robin. "Metody pro vylepšení genomového sestavení založené na signálovém zpracování." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2016. http://www.nusl.cz/ntk/nusl-241090.

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The diploma thesis deals with sequencing methods and genome assembly methods including usage of numerical representations. The theoretical part of thesis describes the history of DNA research, generations of sequencing methods, the assembly methods themselves and definiton of numerical representations. Numerical represenatations serve to convert character form of DNA to numerical form and so allow to use digital signal processing methods. There is an algorithm for genome assembly using numerical represenatation proposed in thesis, which is later tested at sequence data.
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Hackl, Thomas Verfasser], Jörg [Gutachter] Schultz, and Rainer Franz [Gutachter] [Hedrich. "A draft genome for the Venus flytrap, Dionaea muscipula : Evaluation of assembly strategies for a complex Genome – Development of novel approaches and bioinformatics solutions / Thomas Hackl. Gutachter: Jörg Schultz ; Rainer Hedrich." Würzburg : Universität Würzburg, 2016. http://d-nb.info/1111888663/34.

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Ribeiro, Stela Barros. "Sequenciamento e caracterização parcial do genoma de cagaiteira (Eugenia dysenterica DC.)." Universidade Federal de Goiás, 2016. http://repositorio.bc.ufg.br/tede/handle/tede/6232.

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Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2016-09-19T11:37:57Z No. of bitstreams: 2 Dissertação - Stela Barros RIbeiro - 2016.pdf: 2466812 bytes, checksum: 6dcf03c36d51185279b526d71c61bd43 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)<br>Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-09-19T11:38:26Z (GMT) No. of bitstreams: 2 Dissertação - Stela Barros RIbeiro - 2016.pdf: 2466812 bytes, checksum: 6dcf03c36d51185279b526d71c61bd43 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)<br>Made avail
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Hackl, Thomas. "A draft genome for the Venus flytrap, Dionaea muscipula : Evaluation of assembly strategies for a complex Genome – Development of novel approaches and bioinformatics solutions." Doctoral thesis, 2016. https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-133149.

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The Venus flytrap, \textit{Dionaea muscipula}, with its carnivorous life-style and its highly specialized snap-traps has fascinated biologist since the days of Charles Darwin. The goal of the \textit{D. muscipula} genome project is to gain comprehensive insights into the genomic landscape of this remarkable plant. The genome of the diploid Venus flytrap with an estimated size between 2.6 Gbp to 3.0 Gbp is comparatively large and comprises more than 70 % of repetitive regions. Sequencing and assembly of genomes of this scale are even with state-of-the-art technology and software challenging. In
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Huang, Yi-Chen, and 黃亦晨. "Gap-Centered Local Assembly: Gap Filling in Genome Drafts with Linked Reads." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/ujfcbz.

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碩士<br>國立臺灣大學<br>生醫電子與資訊學研究所<br>107<br>De novo assembly of short reads that accompanies with scaffolding algorithm often produces lots of gaps due to a lack of information to determine the sequences between contigs which leads to an incomplete draft of genomes. Here, we present a protocol for filling the gaps in genome that utilizes linked-read information contained in barcoded short reads. We validate our protocol with Japanese eel genome and show how the gaps can be filled using 10x Chromium linked reads with our local assembly methods. We expect this gap-filling protocol can be utilized for
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Hefer, Charles Amadeus. "Assembly, annotation and polymorphism analysis of a draft transcriptome sequence for a fast-growing Eucalyptus plantation tree." Thesis, 2011. http://hdl.handle.net/2263/28833.

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Ultra-high throughput DNA sequencing technologies have rapidly changed the face of genomic research projects. Technologies such as mRNA-Seq have the potential to rapidly profile the expressed gene-catalog of non-model organisms, albeit with significant bioinformatics related costs and support required. This study developed automated data analysis workflows focused on the quality evaluation of mRNA-Seq reads, de novo transcriptome assembly, transcriptome annotation and digital gene expression profiling making use of data analysis tools available in the public domain and novel tools developed fo
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Book chapters on the topic "Draft genome assembly"

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Joets, Johann, Clémentine Vitte, and Alain Charcosset. "Draft Assembly of the F2 European Maize Genome Sequence and Its Comparison to the B73 Genome Sequence: A Characterization of Genotype-Specific Regions." In Compendium of Plant Genomes. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-97427-9_1.

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Polano, Cesare, and Giuseppe Firrao. "Assembly of Phytoplasma Genome Drafts from Illumina Reads Using Phytoassembly." In Phytoplasmas. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8837-2_16.

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Shieh, Yi-Kung, Shu-Cheng Liu, and Chin Lung Lu. "Scaffolding Contigs Using Multiple Reference Genomes." In Computational Biology and Chemistry. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.93456.

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Scaffolding is an important step of the genome assembly and its function is to order and orient the contigs in the assembly of a draft genome into larger scaffolds. Several single reference-based scaffolders have currently been proposed. However, a single reference genome may not be sufficient alone for a scaffolder to correctly scaffold a target draft genome, especially when the target genome and the reference genome have distant evolutionary relationship or some rearrangements. This motivates researchers to develop the so-called multiple reference-based scaffolders that can utilize multiple
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Conference papers on the topic "Draft genome assembly"

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"Annotation of Siberian larch genome draft assembly." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-024.

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McGrath, J. Mitchell, Nizar Drou, Darren Waite, and David Swarbreck. "THE 'C869' SUGAR BEET GENOME: A DRAFT ASSEMBLY." In 37th Biennial Meeting of American Society of Sugarbeet Technologist. ASSBT, 2013. http://dx.doi.org/10.5274/assbt.2013.29.

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Reports on the topic "Draft genome assembly"

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Sherman, A., D. N. Kuhn, Y. Cohen, R. Ophir, and R. Goenaga. Exploring the polyembryonic seed trait in mango as a basis for a biotechnology platform for fruit tree crops. United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134176.bard.

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Mango is one of the most important fruit crops. However, the biology of this fruit tree is under studied. The lack of genetic and genomic resources has limited progress in mango research and breeding. Several research groups have recently started developing genomic tools for mango by creating transcriptome and genomic data. Sexual reproduction in plants is the main pathway for the creation of new genetic combinations. In modern agriculture, breeders exploit the genetic diversity generated through sexual reproduction to develop elite cultivars; however, these cultivars require genetic stabiliza
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