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Journal articles on the topic 'Draft genome assembly'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

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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Coombe, Lauren, Vladimir Nikolić, Justin Chu, Inanc Birol, and René L. Warren. "ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs." Bioinformatics 36, no. 12 (2020): 3885–87. http://dx.doi.org/10.1093/bioinformatics/btaa253.

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Abstract Summary The ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of

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Landi, Lucia, Stefania Pollastro, Caterina Rotolo, Gianfranco Romanazzi, Francesco Faretra, and Rita Milvia De Miccolis Angelini. "Draft Genomic Resources for the Brown Rot Fungal Pathogen Monilinia laxa." Molecular Plant-Microbe Interactions® 33, no. 2 (2020): 145–48. http://dx.doi.org/10.1094/mpmi-08-19-0225-a.

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Monilinia laxa is the causal agent of brown rot on stone fruit, and it can cause heavy yield losses during field production and postharvest storage. This article reports the draft genome assembly of the M. laxa Mlax316 strain, obtained using a hybrid genome assembly with both Illumina short-reads and PacBio long-reads sequencing technologies. The complete draft genome consists of 49 scaffolds with total size of 42.81 Mb, and scaffold N50 of 2,449.4 kb. Annotation of the M. laxa assembly identified 11,163 genes and 12,424 proteins which were functionally annotated. This new genome draft improve

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Nguinkal, Julien Alban, Ronald Marco Brunner, Marieke Verleih, et al. "The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe." Genes 10, no. 9 (2019): 708. http://dx.doi.org/10.3390/genes10090708.

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The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 6

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Cortese, Iliana Julieta, María Lorena Castrillo, Andrea Liliana Onetto, Gustavo Ángel Bich, Pedro Darío Zapata, and Margarita Ester Laczeski. "De novo genome assembly of Bacillus altitudinis 19RS3 and Bacillus altitudinis T5S-T4, two plant growth-promoting bacteria isolated from Ilex paraguariensis St. Hil. (yerba mate)." PLOS ONE 16, no. 3 (2021): e0248274. http://dx.doi.org/10.1371/journal.pone.0248274.

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Plant growth-promoting bacteria (PGPB) are a heterogeneous group of bacteria that can exert beneficial effects on plant growth directly or indirectly by different mechanisms. PGPB-based inoculant formulation has been used to replace chemical fertilizers and pesticides. In our previous studies, two endophytic endospore-forming bacteria identified as Bacillus altitudinis were isolated from roots of Ilex paraguariensis St. Hil. seedlings and selected for their plant growth-promoting (PGP) properties shown in vitro and in vivo. The purposes of this work were to assemble the genomes of B. altitudin

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Upadhyay, Maulik, Andreas Hauser, Elisabeth Kunz, et al. "The First Draft Genome Assembly of Snow Sheep (Ovis nivicola)." Genome Biology and Evolution 12, no. 8 (2020): 1330–36. http://dx.doi.org/10.1093/gbe/evaa124.

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Abstract The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was ∼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised

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Amses, Kevin R., William J. Davis, and Timothy Y. James. "SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes." Bioinformatics 36, no. 7 (2019): 1994–2000. http://dx.doi.org/10.1093/bioinformatics/btz866.

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Abstract Motivation Whole-genome sequencing of uncultured eukaryotic genomes is complicated by difficulties in acquiring sufficient amounts of tissue. Single-cell genomics (SCG) by multiple displacement amplification provides a technical workaround, yielding whole-genome libraries which can be assembled de novo. Downsides of multiple displacement amplification include coverage biases and exacerbation of contamination. These factors affect assembly continuity and fidelity, complicating discrimination of genomes from contamination and noise by available tools. Uncultured eukaryotes and their rel

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Mollah, Md Bazlur Rahman, Mohd Golam Quader Khan, Md Shahidul Islam, and Md Samsul Alam. "First draft genome assembly and identification of SNPs from hilsa shad (Tenualosa ilisha) of the Bay of Bengal." F1000Research 8 (March 22, 2019): 320. http://dx.doi.org/10.12688/f1000research.18325.1.

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Background: Hilsa shad (Tenualosa ilisha), a widely distributed migratory fish, contributes substantially to the economy of Bangladesh. The harvest of hilsa from inland waters has been fluctuating due to anthropological and climate change-induced degradation of the riverine habitats. The whole genome sequence of this valuable fish could provide genomic tools for sustainable harvest, conservation and productivity cycle maintenance. Here, we report the first draft genome of T. ilisha from the Bay of Bengal, the largest reservoir of the migratory fish. Methods: A live specimen of T. ilisha was co

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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 (January 15, 2025): 1230. https://doi.org/10.12688/f1000research.73066.2.

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The common, or spectacled, caiman Caiman crocodilus is an abundant, widely distributed Neotropical crocodilian exhibiting notable morphological and molecular diversification. As the type species for the Caimaninae subfamily - the sister taxa for the subfamily to which members of the genus Alligator belong - C. crocodilus occupies a key position in our understanding of crocodilian and archosaur genetics and evolution. 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.

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Khayi, Slimane, Nour Elhouda Azza, Fatima Gaboun, et al. "First draft genome assembly of the Argane tree (Argania spinosa)." F1000Research 7 (August 17, 2018): 1310. http://dx.doi.org/10.12688/f1000research.15719.1.

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Background: The Argane tree (Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinde

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Khayi, Slimane, Nour Elhouda Azza, Fatima Gaboun, et al. "First draft genome assembly of the Argane tree (Argania spinosa)." F1000Research 7 (May 4, 2020): 1310. http://dx.doi.org/10.12688/f1000research.15719.2.

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Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinde

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Zhuo, Degen, Wei D. Zhao, Fred A. Wright, et al. "Assembly, Annotation, and Integration of UNIGENE Clusters into the Human Genome Draft." Genome Research 11, no. 5 (2001): 904–18. http://dx.doi.org/10.1101/gr.164501.

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The recent release of the first draft of the human genome provides an unprecedented opportunity to integrate human genes and their functions in a complete positional context. However, at least three significant technical hurdles remain: first, to assemble a complete and nonredundant human transcript index; second, to accurately place the individual transcript indices on the human genome; and third, to functionally annotate all human genes. Here, we report the extension of the UNIGENE database through the assembly of its sequence clusters into nonredundant sequence contigs. Each resulting conse

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Delmont, Tom O., and A. Murat Eren. "Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies." PeerJ 4 (March 29, 2016): e1839. http://dx.doi.org/10.7717/peerj.1839.

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High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigradeHypsibius dujardini,and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of

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Karimi, Karim, Duy Ngoc Do, and Younes Miar. "PSVIII-9 Genome assembly of American mink (Neovison vison) using high-fidelity long reads." Journal of Animal Science 99, Supplement_3 (2021): 241–42. http://dx.doi.org/10.1093/jas/skab235.440.

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Abstract Development of genome-enabled selection and providing new insights in the genetic architecture of economically important traits are essential parts of mink breeding programs. Availability of a contagious genome assembly would guarantee the fundamental genomic studies in American mink (Neovison vison). Advances in long-read sequencing technologies have provided the opportunity to obtain high quality and free-gaps assemblies for different species. The objective of this study was to generate an accurate genome assembly using Single Molecule High-Fidelity (HiFi) Sequencing for American mi

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Bogoyavlenskiy, Andrey P., Madina S. Alexyuk, Amankeldi K. Sadanov, Vladimir E. Berezin, Lyudmila P. Trenozhnikova, and Gul B. Baymakhanova. "Draft Genome Sequence Data of Streptomyces anulatus, Strain K-31." Data 8, no. 8 (2023): 131. http://dx.doi.org/10.3390/data8080131.

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Streptomyces anulatus is a typical representative of the Streptomyces genus synthesizing a large number of biologically active compounds. In this study, the draft genome of Streptomyces anulatus, strain K-31 is presented, generated from Illumina reads by SPAdes software. The size of the assembled genome was 8.548838 Mb. Annotation of the S. anulatus genome assembly identified C. hemipterus genome 7749 genes, including 7149 protein-coding genes and 92 RNA genes. This genome will be helpful to further understand Streptomyces genetics and evolution and can be useful for obtained biological active

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Liu, Yuling, Zhen Liu, Renhai Peng, et al. "Cytogenetic maps of homoeologous chromosomes A h01 and D h01 and their integration with the genome assembly in Gossypium hirsutum." Comparative Cytogenetics 11, no. (2) (2017): 405–20. https://doi.org/10.3897/CompCytogen.v11i2.12824.

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Cytogenetic maps of Gossypium hirsutum (Linnaeus, 1753) homoeologous chromosomes A<sub>h</sub>01 and D<sub>h</sub>01 were constructed by fluorescence in situ hybridization (FISH), using eleven homoeologous-chromosomes-shared bacterial artificial chromosomes (BACs) clones and one chromosome-specific BAC clone respectively. We compared the cytogenetic maps with the genetic linkage and draft genome assembly maps based on a standardized map unit, relative map position (RMP), which allowed a global view of the relationship of genetic and physical distances along each chromosome, and assembly qualit

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Yu, Jin, Linzhou Li, Sibo Wang, et al. "Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)." Gigabyte 2020 (November 16, 2020): 1–9. http://dx.doi.org/10.46471/gigabyte.8.

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Mosses comprise one of three lineages forming a sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to, and colonization of, land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss that is widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo-assembled its genome using the 10X Genomics method. The genome comprises 385.2 Mbp, with a scaffo

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Helmkampf, Martin, M. Renee Bellinger, Scott M. Geib, Sheina B. Sim, and Misaki Takabayashi. "Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing." Genome Biology and Evolution 11, no. 7 (2019): 2045–54. http://dx.doi.org/10.1093/gbe/evz135.

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Abstract The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here, we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds with a N50 size of 186 kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615 Mb) and read k-mer profiles, we estimated the genome size to fall between 600 and 700 Mb, although

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Duan, Yajuan, Yue Li, Jing Zhang, et al. "Genome Survey and Chromosome-Level Draft Genome Assembly of Glycine max var. Dongfudou 3: Insights into Genome Characteristics and Protein Deficiencies." Plants 12, no. 16 (2023): 2994. http://dx.doi.org/10.3390/plants12162994.

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Dongfudou 3 is a highly sought-after soybean variety due to its lack of beany flavor. To support molecular breeding efforts, we conducted a genomic survey using next-generation sequencing. We determined the genome size, complexity, and characteristics of Dongfudou 3. Furthermore, we constructed a chromosome-level draft genome and speculated on the molecular basis of protein deficiency in GmLOX1, GmLOX2, and GmLOX3. These findings set the stage for high-quality genome analysis using third-generation sequencing. The estimated genome size is approximately 1.07 Gb, with repetitive sequences accoun

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Sowdhamini, Ramanathan. "Draft genome sequence of an invasive plant Lantana camara L." Bioinformation 18, no. 9 (2022): 739–41. http://dx.doi.org/10.6026/97320630018739.

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Lantana camara L. is an invasive species of global concern. An ornamental plant originating from central America, it has now spread across natural and human-dominated habitats across tropical and subtropical regions globally. Understanding the population and evolutionary genetics of this species could help gain deeper insights into invasion biology, and provide tools for more effective management. Such investigation would require a relatively good quality genome assembly. While there have been reports of a transcriptome, it has been challenging to construct the genome assembly because of the l

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Shu, Ruihao, Jihong Zhang, Qian Meng, et al. "A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis." Genome Biology and Evolution 12, no. 7 (2020): 1074–79. http://dx.doi.org/10.1093/gbe/evaa112.

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Abstract Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or “DongChongXiaCao,” is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genome assembly of O. sinensis. The assembly of 23 contigs was ∼110.8 Mb with a N50 length of 18

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Briskine, Roman V., and Kentaro K. Shimizu. "Positional bias in variant calls against draft reference assemblies." BMC Genomics 18, no. 1 (2017): 263. https://doi.org/10.1186/s12864-017-3637-2.

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<strong>Background: </strong>Whole genome resequencing projects may implement variant calling using draft reference genomes assembled de novo from short-read libraries. Despite lower quality of such assemblies, they allowed researchers to extend a wide range of population genetic and genome-wide association analyses to non-model species. As the variant calling pipelines are complex and involve many software packages, it is important to understand inherent biases and limitations at each step of the analysis.<strong>Results: </strong>In this article, we report a positional bias present in varian

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Voelker, Julia, Mervyn Shepherd, and Ramil Mauleon. "A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species." Gigabyte 2021 (August 9, 2021): 1–15. http://dx.doi.org/10.46471/gigabyte.28.

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The economically important Melaleuca alternifolia (tea tree) is the source of a terpene-rich essential oil with therapeutic and cosmetic uses around the world. Tea tree has been cultivated and bred in Australia since the 1990s. It has been extensively studied for the genetics and biochemistry of terpene biosynthesis. Here, we report a high quality de novo genome assembly using Pacific Biosciences and Illumina sequencing. The genome was assembled into 3128 scaffolds with a total length of 362 Mb (N50 = 1.9 Mb), with significantly higher contiguity than a previous assembly (N50 = 8.7 Kb). Using

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Osipowski, Paweł, Magdalena Pawełkowicz, Michał Wojcieszek, Agnieszka Skarzyńska, Zbigniew Przybecki, and Wojciech Pląder. "A high-quality cucumber genome assembly enhances computational comparative genomics." Molecular Genetics and Genomics 295, no. 1 (2019): 177–93. http://dx.doi.org/10.1007/s00438-019-01614-3.

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Abstract Genetic variation is expressed by the presence of polymorphisms in compared genomes of individuals that can be transferred to next generations. The aim of this work was to reveal genome dynamics by predicting polymorphisms among the genomes of three individuals of the highly inbred B10 cucumber (Cucumis sativus L.) line. In this study, bioinformatic comparative genomics was used to uncover cucumber genome dynamics (also called real-time evolution). We obtained a new genome draft assembly from long single molecule real-time (SMRT) sequencing reads and used short paired-end read data fr

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Coff, Lachlan, Andrew J. Guy, Bronwyn E. Campbell, Barbara F. Nowak, Paul A. Ramsland, and Nathan J. Bott. "Draft genome of the bluefin tuna blood fluke, Cardicola forsteri." PLOS ONE 17, no. 10 (2022): e0276287. http://dx.doi.org/10.1371/journal.pone.0276287.

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The blood fluke Cardicola forsteri (Trematoda: Aporocotylidae) is a pathogen of ranched bluefin tuna in Japan and Australia. Genomics of Cardicola spp. have thus far been limited to molecular phylogenetics of select gene sequences. In this study, sequencing of the C. forsteri genome was performed using Illumina short-read and Oxford Nanopore long-read technologies. The sequences were assembled de novo using a hybrid of short and long reads, which produced a high-quality contig-level assembly (N50 > 430 kb and L50 = 138). The assembly was also relatively complete and unfragmented, comprising

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Karimi, Karim, Duy Ngoc Do, Jingy Wang, et al. "A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison)." Communications Biology 5, no. 1 (2022). http://dx.doi.org/10.1038/s42003-022-04341-5.

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AbstractAvailability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole geno

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Marla, Soma S., Pallavi Mishra, Ranjeet Maurya, et al. "Refinement of Draft Genome Assemblies of Pigeonpea (Cajanus cajan)." Frontiers in Genetics 11 (December 15, 2020). http://dx.doi.org/10.3389/fgene.2020.607432.

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Genome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in next generation sequencing. Of late several draft assemblies have been reported in sequenced plant genomes. The reported draft genome assemblies of Cajanus cajan have different levels of genome completeness, a large number of repeats, gaps, and segmental duplications. Draft assemblies with portions of genome missing are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and the prediction

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Marla, Soma S., Pallavi Mishra, Ranjeet Maurya, et al. "Refinement of Draft Genome Assemblies of Pigeonpea (Cajanus cajan)." Frontiers in Genetics 11 (December 15, 2020). http://dx.doi.org/10.3389/fgene.2020.607432.

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Genome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in next generation sequencing. Of late several draft assemblies have been reported in sequenced plant genomes. The reported draft genome assemblies of Cajanus cajan have different levels of genome completeness, a large number of repeats, gaps, and segmental duplications. Draft assemblies with portions of genome missing are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and the prediction

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Davis, John T., Ruijuan Li, Seungmo Kim, Richard Michelmore, Shinje Kim, and Julin N. Maloof. "Whole genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae." G3 Genes|Genomes|Genetics, February 1, 2023. http://dx.doi.org/10.1093/g3journal/jkad026.

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Abstract Brassica napus, a globally important oilseed crop, is an allotetraploid hybrid species with two subgenomes originating from B. rapa and B. oleracea. The presence of two highly similar subgenomes has made the assembly of a complete draft genome challenging and has also resulted in natural homoeologous exchanges between the genomes, resulting in variations in gene copy number, which further complicates assigning sequences to correct chromosomes. Despite these challenges, high quality draft genomes of this species have been released. Using third generation sequencing and assembly technol

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Manee, M. Manee, M. Al-Shomrani Badr, A. Altammami Musaad, A. F. El-Shafie Hamadttu, and H. Alqahtani Fahad. "Draft genome assembly of adult female red palm weevil Rhynchophorus ferrugineus." July 22, 2022. https://doi.org/10.5281/zenodo.6878576.

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Chueca, Luis J., Tilman Schell, and Markus Pfenninger. "De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)." G3 Genes|Genomes|Genetics 11, no. 8 (2021). http://dx.doi.org/10.1093/g3journal/jkab180.

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Abstract Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxf

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Shearman, Jeremy R., Wirulda Pootakham, Chutima Sonthirod, et al. "A draft chromosome-scale genome assembly of a commercial sugarcane." Scientific Reports 12, no. 1 (2022). http://dx.doi.org/10.1038/s41598-022-24823-0.

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AbstractSugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum, S. spontaneum, and several other Saccharum species, resulting in an auto-allopolyploid with 8–12 copies of each chromosome. The current genome assembly gold standard is to generate a long read assembly followed by chromatin conformation capture sequencing to scaffold. We used the PacBio RSII and chromatin conformation capture sequencing to sequence and assemble the genome of a South East Asian commercial sugarcane cultivar, known as Khon Kaen 3. The

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Karam, Qusaie, Vinod Kumar, Anisha B. Shajan, Sabeeka Al-Nuaimi, Zainab Sattari, and Saleem El-Dakour. "De-novo genome assembly and annotation of sobaity seabream Sparidentex hasta." Frontiers in Genetics 13 (October 31, 2022). http://dx.doi.org/10.3389/fgene.2022.988488.

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Sparidentexhasta (Valenciennes, 1830) of the Sparidae family, is an economically important fish species. However, the genomic studies on S. hasta are limited due to the absence of its complete genome. The goal of the current study was to sequence, assemble, and annotate the genome of S. hasta that will fuel further research related to this seabream. The assembled draft genome of S. hasta was 686 Mb with an N50 of 80 Kb. The draft genome contained approximately 22% repeats, and 41,201 genes coding for 44,555 transcripts. Furthermore, the assessment of the assembly completeness was estimated bas

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Guyomar, Cervin, Wesley Delage, Fabrice Legeai, Christophe Mougel, Jean-Christophe Simon, and Claire Lemaitre. "MinYS: mine your symbiont by targeted genome assembly in symbiotic communities." NAR Genomics and Bioinformatics 2, no. 3 (2020). http://dx.doi.org/10.1093/nargab/lqaa047.

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Abstract Most metazoans are associated with symbionts. Characterizing the effect of a particular symbiont often requires getting access to its genome, which is usually done by sequencing the whole community. We present MinYS, a targeted assembly approach to assemble a particular genome of interest from such metagenomic data. First, taking advantage of a reference genome, a subset of the reads is assembled into a set of backbone contigs. Then, this draft assembly is completed using the whole metagenomic readset in a de novo manner. The resulting assembly is output as a genome graph, enabling di

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Li, Kunpeng, Peng Xu, Jinpeng Wang, Xin Yi, and Yuannian Jiao. "Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement." Nature Communications 14, no. 1 (2023). http://dx.doi.org/10.1038/s41467-023-42336-w.

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AbstractAssembly of a high-quality genome is important for downstream comparative and functional genomic studies. However, most tools for genome assembly assessment only give qualitative reports, which do not pinpoint assembly errors at specific regions. Here, we develop a new reference-free tool, Clipping information for Revealing Assembly Quality (CRAQ), which maps raw reads back to assembled sequences to identify regional and structural assembly errors based on effective clipped alignment information. Error counts are transformed into corresponding assembly evaluation indexes to reflect the

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Chakravarty, Sakshar, Glennis Logsdon, and Stefano Lonardi. "RAmbler resolves complex repeats in human Chromosomes 8, 19, and X." Genome Research, March 4, 2025, gr.279308.124. https://doi.org/10.1101/gr.279308.124.

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Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from PacBio HiFi reads. RAmbler (i) identifies repetitive regions by detecting unusually high coverage regions after mapping

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Luo, Haoran, Qingxian Lin, Wenzhen Fang, Xiaolin Chen, and Xiaoping Zhou. "Genomic insights into the endangered white-eared night heron (Gorsachius magnificus)." BMC Genomic Data 25, no. 1 (2024). http://dx.doi.org/10.1186/s12863-024-01194-1.

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Abstract Objectives A genome sequence of a threatened species can provide valuable genetic information that is important for improving the conservation strategies. The white-eared night heron (Gorsachius magnificus) is an endangered and poorly known ardeid bird. In order to support future studies on conservation genetics and evolutionary adaptation of this species, we have reported a de novo assembled and annotated whole-genome sequence of the G. magnificus. Data description The final draft genome assembly of the G. magnificus was 1.19 Gb in size, with a contig N50 of 187.69 kb and a scaffold

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Poisson, William, Julien Prunier, Alexandra Carrier, et al. "Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights." BMC Genomics 24, no. 1 (2023). http://dx.doi.org/10.1186/s12864-023-09189-5.

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Abstract Background Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since

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Saito, Daniel, Cristiane Pereira Borges Saito, Fabiana de Souza Cannavan, and Siu Mui Tsai. "Draft genome sequences of 13 putatively novel Haemophilus species and strains assembled from human saliva." Microbiology Resource Announcements, February 20, 2024. http://dx.doi.org/10.1128/mra.00945-23.

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ABSTRACT We present the draft metagenome-assembled genomes (MAGs) of 13 Haemophilus representatives from human saliva. MAGs were reconstructed by a streamlined pre-assembly mapping approach performed against 9 clinically relevant reference genomes. Overall, genomes belonging to 2 potentially novel Haemophilus species and 11 strains were recovered, as determined by genome-wide ANI analysis.

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Yepes-Blandón, Jonny Andrés, Chao Bian, María José Benítez-Galeano, et al. "Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae." Frontiers in Genetics 13 (January 19, 2023). http://dx.doi.org/10.3389/fgene.2022.989788.

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We report the first draft genome assembly for Prochilodus magdalenae, the leading representative species of the Prochilodontidae family in Colombia. This 1.2-Gb assembly, with a GC content of 42.0% and a repetitive content of around 31.0%, is in the range of previously reported characid species genomes. Annotation identified 34,725 nuclear genes, and BUSCO completeness value was 94.9%. Gene ontology and primary metabolic pathway annotations indicate similar gene profiles for P. magdalenae and the closest species with annotated genomes: blind cave fish (Astyanax mexicanus) and red piranha (Pygo

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Wood, Jason M., Julian B. Peres, John Bateh, et al. "Draft Genome Sequences of Heat Shock-Tolerant Microbes Isolated from a Spacecraft Assembly Facility." Microbiology Resource Announcements 10, no. 36 (2021). http://dx.doi.org/10.1128/mra.00653-21.

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Heat shock-tolerant microorganisms belonging to the orders Bacillales and Micrococcales were isolated from the Spacecraft Assembly Facility at the Jet Propulsion Laboratory, and 63 draft genome sequences were assembled and identified. Further analyses of these genomes can provide insight into methods for preventing forward contamination.

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