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

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

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1

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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2

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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3

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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7

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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8

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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9

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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10

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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11

Liu, Qing, Gui Xiong, Ziwei Wang, et al. "Chromosome-level genome assembly of the diploid oat species Avena longiglumis." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03248-6.

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AbstractDiploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate
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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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Liu, Shuya, and Nansheng Chen. "Chromosome-level genome assembly of marine diatom Skeletonema tropicum." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03238-8.

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AbstractSkeletonema tropicum is a marine diatom of the genus Skeletonema that also includes many well-known species including S. marinoi. S. tropicum is a high temperature preferring species thriving in tropical ocean regions or temperate ocean regions during summer-autumn. However, mechanisms of ecological adaptation of S. tropicum remain poorly understood due partially to the lack of a high-quality whole genome assembly. Here, we report the first high-quality chromosome-scale genome assembly for S. tropicum, using cutting-edge technologies including PacBio single molecular sequencing and hig
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14

Zhong, Yu-Wei, Yun-Yun Fan, Zhang-Qi Zuo, et al. "A chromosome-level genome assembly of the parasitoid wasp Eretmocerus hayati." Scientific Data 10, no. 1 (2023). http://dx.doi.org/10.1038/s41597-023-02450-2.

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AbstractHymenoptera is an order accounting for a large proportion of species in Insecta, among which Chalcidoidea contains many parasitoid species of biocontrol significance. Currently, some species genomes in Chalcidoidea have been assembled, but the chromosome-level genomes of Aphelinidae are not yet available. Using Illumina, PacBio HiFi and Hi-C technologies, we assembled a genome assembly of Eretmocerus hayati (Aphelinidae, Hymenoptera), a worldwide biocontrol agent of whiteflies, at the chromosome level. The assembled genome size is 692.1 Mb with a contig N50 of 7.96 Mb. After Hi-C scaff
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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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Li, Hongran, Yan Peng, Chao Wu, et al. "A chromosome-level genome assembly of Sesamia inferens." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-02937-6.

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AbstractThe pink stem borer, Sesamia inferens (Walker), is a significant polyphagous pest historically restricted to regions south of N34° latitude. However, with changes in global climate and farming practices, the distribution of this moth has progressively exceeded its traditional limit of 34° N and encompassed most regions in North China. The genetic adaptations of S. inferens remain incompletely understood due to the lack of high-quality genome resources. Here, we sequenced the genome of S. inferens using PacBio and Hi-C technology, yielding a genome assembly of 865.04 Mb with contig N50
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Zhang, Xinhua, MingZhi Li, Zhan Bian, et al. "Improved chromosome-level genome assembly of Indian sandalwood (Santalum album)." Scientific Data 10, no. 1 (2023). http://dx.doi.org/10.1038/s41597-023-02849-x.

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AbstractSantalum album is a well-known aromatic and medicinal plant that is highly valued for the essential oil (EO) extracted from its heartwood. In this study, we present a high-quality chromosome-level genome assembly of S. album after integrating PacBio Sequel, Illumina HiSeq paired-end and high-throughput chromosome conformation capture sequencing technologies. The assembled genome size is 207.39 M with a contig N50 of 7.33 M and scaffold N50 size of 18.31 M. Compared with three previously published sandalwood genomes, the N50 length of the genome assembly was longer. In total, 94.26% of
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18

Kuhl, Heiner, Ling Li, Sven Wuertz, Matthias Stöck, Xu-Fang Liang, and Christophe Klopp. "CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes." GigaScience 9, no. 5 (2020). http://dx.doi.org/10.1093/gigascience/giaa034.

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Abstract Background Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce. Result Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-
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Zhao, Shihu, Xiufeng Yang, Bo Pang, et al. "A chromosome-level genome assembly of the redfin culter (Chanodichthys erythropterus)." Scientific Data 9, no. 1 (2022). http://dx.doi.org/10.1038/s41597-022-01648-0.

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AbstractChanodichthys erythropterus is a fierce carnivorous fish widely found in East Asian waters. It is not only a popular food fish in China, it is also a representative victim of overfishing. Genetic breeding programs launched to meet market demands urgently require high-quality genomes to facilitate genomic selection and genetic research. In this study, we constructed a chromosome-level reference genome of C. erythropterus by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. The 1.085 Gb C. erythropterus genome was
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Rai, Amit, Hideki Hirakawa, Ryo Nakabayashi, et al. "Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis." Nature Communications 12, no. 1 (2021). http://dx.doi.org/10.1038/s41467-020-20508-2.

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AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach i
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Li, Meifei, Yingmin Zhang, Yi Wang, Yue Yin, Meijun Zhou, and Yonghong Zhang. "Chromosome-level genome assembly of Aquilaria yunnanensis." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03635-z.

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AbstractAquilaria yunnanensis is an endangered agarwood-producing tree currently listed on the IUCN Red List of Threatened Species. The agarwood it produces has important medicinal and economic value, but its population has sharply declined due to human destruction and habitat reduction. Therefore, obtaining genomic information on A. yunnanensis is beneficial for its protection work. We assembled a chromosome-level reference genome of A. yunnanensis by using BGI short reads, PacBio HiFi long reads, coupled with Hi-C technology. The final genome assembly of A. yunnanensis is 847.04 Mb, with N50
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Huang, Tianqing, Enhui Liu, Baorui Cao, et al. "A chromosome-level genome assembly and evolutionary analysis of Coregonus ussuriensis Berg." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03642-0.

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AbstractCoregonus ussuriensis Berg, distributed widely in cold waters above 45° N latitude, is a savored freshwater whitefish that has been included in the list of endangered animals as a consequence of overfishing. Lack of genomic information seriously hampers evolutionary and genetic research on C. ussuriensis warranting the need to assemble a high-quality reference genome to promote its genetic breeding. We assembled and constructed a reference chromosome-level C. ussuriensis genome (sequence length, 2.51 Gb; contig N50 length, 4.27 Mb) using PacBio sequencing and Hi-C assembly technology,
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Xu, Xiaojun, Jing Chen, Wenzhi Guan, Baolong Niu, Shaokui Yi, and Bao Lou. "A chromosome-level genome assembly of East Asia endemic minnow Zacco platypus." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03163-w.

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AbstractZacco platypus is an endemic colorful freshwater minnow that is intensively distributed in East Asia. In this study, two adult female individuals collected from Haihe River basin were used for karyotypic study and genome sequencing, respectively. The karyotype formula of Z. platypus is 2N = 48 = 18 M + 24SM/ST + 6 T. We used PacBio long-read sequencing and Hi-C technology to assemble a chromosome-level genome of Z. platypus. As a result, an 814.87 Mb genome was assembled with the PacBio long reads. Subsequently, 98.64% assembled sequences were anchored into 24 chromosomes based on the
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Lü, Zhenming, Ziwei Yu, Wenkai Luo, et al. "Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca)." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-02997-8.

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AbstractThe eel gobies fascinate researchers with many important features, including its unique body structure, benthic lifestyle, and degenerated eyes. However, genome assembly and exploration of the unique genomic composition of the eel gobies are still in their infancy. This has severely limited research progress on gobies. In this study, multi-platform sequencing data were generated and used to assemble and annotate the genome of O. rebecca at the chromosome-level. The assembled genome size of O. rebecca is 918.57 Mbp, which is similar to the estimated genome size (903.03 Mbp) using 17-mer
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Shu, Xiaohan, Ruizhong Yuan, Boying Zheng, et al. "Chromosome-level genome assembly of Microplitis manilae Ashmead, 1904 (Hymenoptera: Braconidae)." Scientific Data 10, no. 1 (2023). http://dx.doi.org/10.1038/s41597-023-02190-3.

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AbstractMicroplitis manilae Ashmead (Hymenoptera: Braconidae) is an important parasitoid of agricultural pests in lepidopteran species. So far, two extant genome assembles from the genus Microplitis are fragmented. Here, we offered a high-quality genome assembly of M. manilae at the chromosome level with high accuracy and contiguity, assembled by ONT long-read, MGI-SEQ short-read, and Hi-C sequencing methods. The final assembled genome size was 282.85 Mb, with 268.17 Mb assigned to 11 pseudochromosomes. The scaffold N50 length was 25.23 Mb, and the complete BUSCO score was 98.61%. The genome c
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Fu, Luyao, Changjin Lin, Wenyan Xu, et al. "Chromosome-level genome assembly of predatory Arma chinensis." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03837-5.

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AbstractArma chinensis is a natural enemy that preys on various species and can suppress agricultural and forest pests in the orders Lepidoptera and Coleoptera. Here, we aimed to determine the genome of A. chinensis assembled at the chromosome-level using PacBio and Hi-C technologies. The assembled genome was 986 Mb, with a contig N50 of 2.40 Mb, scaffold N50 of 134.98 Mb, and BUSCO completeness of 96.10%. Hi-C data aided in anchoring the assembly onto seven chromosomes. A sequence of ~ 496.2 Mb was annotated as a repeat element, constituting 51.15% of the genome. We functionally annotated 84.
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Song, Yongli, Jian-Ping Huang, Yong-Jiang Wang, and Sheng-Xiong Huang. "Chromosome level genome assembly of endangered medicinal plant Anisodus tanguticus." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03007-7.

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AbstractAnisodus tanguticus is a medicinal herb that belongs to the Anisodus genus of the Solanaceae family. This endangered herb is mainly distributed in Qinghai–Tibet Plateau. In this study, we combined the Illumina short-read, Nanopore long-read and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to de novo assemble the A. tanguticus genome. A high-quality chromosomal-level genome assembly was obtained with a genome size of 1.26 Gb and a contig N50 of 25.07 Mb. Of the draft genome sequences, 97.47% were anchored to 24 pseudochromosomes with a scaffold N50 of 5
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Zhao, Hang, Wenzheng Wang, Yirong Yang, et al. "A high-quality chromosome-level wild rice genome of Oryza coarctata." Scientific Data 10, no. 1 (2023). http://dx.doi.org/10.1038/s41597-023-02594-1.

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AbstractOryza coarctata (2n = 4X = 48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of O. coarctata. PacBio high-quality HiFi reads generated 460 contigs with a total length of 573.4 Mb
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Zhang, Dongdong, Zhenfan Yu, Xingyue Liu, Yong Li, Bin Zeng, and Lirong Wang. "Chromosome level genome assembly of ‘Wanfeng’ almond (Prunus dulcis)." Scientific Data 12, no. 1 (2025). https://doi.org/10.1038/s41597-025-04480-4.

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Abstract We assembled a chromosome-level genome of Chinese native ‘Wanfeng’ almond, with a size of 288.53 Mb and a contig N50 of 30.48 Mb. Approximately 270 Mb (93.58%) of the sequences are anchored on 8 Superscaffolds, and 174.59 Mb (60.51%) of the sequences are repetitive sequences. BUSCO assessment revealed that the ‘Wanfeng’ almond genome assembly included 99.3% complete BUSCOs. A total of 24,230 protein-coding genes were annotated, and 24,033 were functional. The assembly of the ‘Wanfeng’ almond genome provides a valuable genetic resource for molecular breeding of native almonds in China.
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Bachvaroff, Tsvetan R., Ryan C. McDonald, Louis V. Plough, and J. Sook Chung. "Chromosome-level genome assembly of the blue crab, Callinectes sapidus." G3 Genes|Genomes|Genetics 11, no. 9 (2021). http://dx.doi.org/10.1093/g3journal/jkab212.

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Abstract The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200× coverage Illumina paired-end reads, a 60× 8 kb mate-paired library, and 50× PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chrom
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Xie, Hongxin, Zixuan Chen, Shuai Pang, and Weiguo Du. "Efficient and highly continuous chromosome-level genome assembly of the first chameleon genome." Genome Biology and Evolution, July 22, 2023. http://dx.doi.org/10.1093/gbe/evad131.

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Abstract Most amniote genomes are diploid, moderate in size (approximately 1–6 Gbp), and contain a large proportion of repetitive sequences. The development of next-generation sequencing technology, especially the emergence of high-fidelity (HiFi) long-read data, has made it feasible to resolve high-quality genome assembly for non-model species efficiently. However, reference genomes for squamate reptiles has lagged behind other amniote lineages. Here we de novo assembled the first genome from the Chameleonidae family, the panther chameleon (Furcifer pardalis). We obtained telomere-to-telomere
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Wang, Yi-Ting, Li-Jun Cao, Jin-Cui Chen, et al. "Chromosome-level genome assembly of an agricultural pest Zeugodacus tau (Diptera: Tephritidae)." Scientific Data 10, no. 1 (2023). http://dx.doi.org/10.1038/s41597-023-02765-0.

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AbstractThe fruit fly Zeugodacus tau (Diptera: Tephritidae) is a major pest of melons and other cucurbits in Southeast Asia. In this study, we used Illumina, Nanopore, and Hi-C sequencing technologies to assemble a reference genome of Z. tau at the chromosomal level. The assembled genome was 421.79 Mb and consisted of six chromosomes (one X-chromosome + five autosomes). The contig N50 was 4.23 Mb. We identified 20,922 protein-coding genes, of which 17,251 (82.45%) were functionally annotated. Additionally, we found 247 rRNAs, 435 tRNAs, 67 small nuclear RNAs, and 829 small RNAs in the genome.
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Martin, Plasil, Winter Sven, Stejskalova Karla, et al. "A Chromosome-Level Genome Assembly of the Snow Leopard, Panthera Uncia." Journal of Heredity, July 9, 2025. https://doi.org/10.1093/jhered/esaf046.

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Abstract The snow leopard (Panthera uncia), a vulnerable big cat native to Central Asia, faces an ongoing population decline due to habitat loss and human activities. Despite its conservation importance, genomic resources for this species remain limited. High-quality reference genomes are essential for assessing genetic diversity, structural variation, and evolutionary history. To address this gap, we have generated a long-read-based and proximity-ligation scaffolded de novo genome assembly of a male snow leopard. The final assembly has a total length of 2.46 Gb in 280 scaffolds, of which the
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Kim, Jungeun, Hui-Su Kim, Jae-Pil Choi, et al. "Chromosome-Level Genome Assembly of the Butter Clam Saxidomus purpuratus." Genome Biology and Evolution 14, no. 7 (2022). http://dx.doi.org/10.1093/gbe/evac106.

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Abstract Herein, we provide the first whole-genome sequence of the purple butter clam (Saxidomus purpuratus), an economically important bivalve shellfish. Specifically, we sequenced and de novo assembled the genome of Sa. purpuratus based on PromethION long reads and Hi-C data. The 978-Mb genome of Sa. purpuratus comprises 19 chromosomes with 36,591 predicted protein-coding genes. The N50 length of Sa. purpuratus genome is 52 Mb, showing the highest continuous assembly among bivalve genomes. The Benchmarking by Universal Single-Copy Orthologs assessment indicated that 95.07% of complete metazo
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35

Xu, Shifen, Liyun Jiang, Zhengting Zou, Ming Zou, Gexia Qiao, and Jing Chen. "Two chromosome-level genome assemblies of galling aphids Slavum lentiscoides and Chaetogeoica ovagalla." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03653-x.

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AbstractSlavum lentiscoides and Chaetogeoica ovagalla are two aphid species from the subtribe Fordina of Fordini within the subfamily Eriosomatinae, and they produce galls on their primary host plants Pistacia. We assembled chromosome-level genomes of these two species using Nanopore long-read sequencing and Hi-C technology. A 332 Mb genome assembly of S. lentiscoides with a scaffold N50 of 19.77 Mb, including 11,747 genes, and a 289 Mb genome assembly of C. ovagalla with a scaffold N50 of 11.85 Mb, containing 14,492 genes, were obtained. The Benchmarking Universal Single-Copy Orthologs (BUSCO
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36

Sun, Lina, Chunxi Jiang, Fang Su, Wei Cui, and Hongsheng Yang. "Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus." Scientific Data 10, no. 1 (2023). http://dx.doi.org/10.1038/s41597-023-02368-9.

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AbstractSea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. In this study, we produced a high-quality chromosome-level genome of A. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. The assembled A. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb
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Cheng, Yunying, Ruanni Chen, Jinlin Chen, Wanlong Huang, and Jianming Chen. "A chromosome-level genome assembly of the Echiura Urechis unicinctus." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-023-02885-7.

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AbstractEchiura is a distinctive family of unsegmented sausage-shaped marine worms whose phylogenetic relationship still needs strong evidence from the phylogenomic analysis. In this family, Urechis unicinctus is known for its high nutritional and medicinal value and adaptation to harsh intertidal conditions. Herein, we combined PacBio long-read, short-read Illumina and Hi-C sequencing, generating a high-quality chromosome-level genome assembly of U. unicinctus. The assembled genome spans ~1,138.6 Mb with a scaffold N50 of 68.3 Mb, of which 1,113.8 Mb (97.82%) were anchored into 17 pseudo-chro
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Zhou, Huijuan, Xuedong Zhang, Hengzhao Liu, et al. "Chromosome-level genome assembly of Platycarya strobilacea." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03107-4.

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AbstractPlatycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six
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39

Xu, Chao, Jichao Ji, Xiangzhen Zhu, et al. "Chromosome level genome assembly of oriental armyworm Mythimna separata." Scientific Data 10, no. 1 (2023). http://dx.doi.org/10.1038/s41597-023-02506-3.

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AbstractThe oriental armyworm, Mythimna separata, is an extremely destructive polyphagous pest with a broad host range that seriously threatens the safety of agricultural production. Here, a high-quality chromosome-level genome was assembled using Illumina, PacBio HiFi long sequencing, and Hi-C scaffolding technologies. The genome size was 706.30 Mb with a contig N50 of 22.08 Mb, and 99.2% of the assembled sequences were anchored to 31 chromosomes. In addition, 20,375 protein-coding genes and 258.68 Mb transposable elements were identified. The chromosome-level genome assembly of M. separata p
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Han, Hongyu, Xiuhong Li, Tianze Li, et al. "Chromosome-level genome assembly of Solanum pimpinellifolium." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03442-6.

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AbstractSolanum pimpinellifolium, the closest wild relative of the domesticated tomato, has high potential for use in breeding programs aimed at developing multi-pathogen resistance and quality improvement. We generated a chromosome-level genome assembly of S. pimpinellifolium LA1589, with a size of 833 Mb and a contig N50 of 31 Mb. We anchored 98.80% of the contigs into 12 pseudo-chromosomes, and identified 74.47% of the sequences as repetitive sequences. The genome evaluation revealed BUSCO and LAI score of 98.3% and 14.49, respectively, indicating high quality of this assembly. A total of 4
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Chen, Mingyue, Danni Yang, Shihai Yang, et al. "Chromosome-level genome assembly of Hippophae gyantsensis." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-02909-w.

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AbstractHippophae gyantsensis, which is a native tree species in China, is ideal for windbreak and sand-fixing forests. It is an economically and ecologically valuable tree species distributed exclusively in the Qinghai-Tibet Plateau in China. In our study, we assembled a chromosome-level genome of H. gyantsensis using Illumina sequencing, Nanopore sequencing and chromosome structure capture technique. The genome was 716.32 Mb in size with scaffold N50 length of 64.84 Mb. A total of 716.25 Mb genome data was anchored and orientated onto 12 chromosomes with a mounting rate of up to 99.99%. Addi
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Pu, De-Qiang, Xing-Long Wu, Zhi-Teng Chen, Shu-Jun Wei, Peng Cai, and Hong-Ling Liu. "Chromosome-level genome assembly of the giant ladybug Megalocaria dilatata." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-02990-1.

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AbstractThe giant ladybug Megalocaria dilatata (Fabricius) is a potential biocontrol agent and a valuable model for coccinellid genomics and evolutionary biology. However, the lack of a reference genome for M. dilatata has impeded further explorations into its evolution and constrained its use in pest management. Here, we assembled and annotated a high-quality, chromosome-level genome of M. dilatata. The resulting assembly spans 772.3 Mb, with a scaffold N50 of 72.48 Mb and a GC content of 34.23%. The Hi-C data aided in anchoring the assembly onto 10 chromosomes ranging from 43.35 to 108.16 Mb
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43

Pinto, Brendan J., Jerome J. Weis, Tony Gamble, Paul J. Ode, Ryan Paul, and Jennifer M. Zaspel. "A Chromosome-Level Genome Assembly of the Parasitoid Wasp, Cotesia glomerata (Hymenoptera: Braconidae)." Journal of Heredity, May 27, 2021. http://dx.doi.org/10.1093/jhered/esab032.

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Abstract Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet understudied hymenopterans are parasitoid wasps in the family Braconidae. Among this understudied group is the genus Cotesia, a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia
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Li, Yunfeng, Lei Gao, Yongjia Pan, et al. "Chromosome-level reference genome of the jellyfish Rhopilema esculentum." GigaScience 9, no. 4 (2020). http://dx.doi.org/10.1093/gigascience/giaa036.

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Abstract Background Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. Findings In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ∼275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among
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45

Wang, Fayan, Lihan Wang, Dan Liu, et al. "Chromosome-level assembly of Gymnocypris eckloni genome." Scientific Data 9, no. 1 (2022). http://dx.doi.org/10.1038/s41597-022-01595-w.

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AbstractGymnocypris eckloni is widely distributed in isolated lakes and the upper reaches of the Yellow River and play significant roles in the trophic web of freshwater communities. In this study, we generated a chromosome-level genome of G. eckloni using PacBio, Illumina and Hi-C sequencing data. The genome consists of 23 pseudo-chromosomes that contain 918.68 Mb of sequence, with a scaffold N50 length of 43.54 Mb. In total, 23,157 genes were annotated, representing 94.80% of the total predicted protein-coding genes. The phylogenetic analysis showed that G. eckloni was most closely related t
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46

Choi, Sehyun, Yuna Kang, and Changsoo Kim. "Chromosome-level genome assembly of Salvia sclarea." Scientific Data 12, no. 1 (2025). https://doi.org/10.1038/s41597-024-04347-0.

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47

Liang, Ying, Shanshan Chen, Kunhua Wei, et al. "Chromosome Level Genome Assembly of Andrographis paniculata." Frontiers in Genetics 11 (June 30, 2020). http://dx.doi.org/10.3389/fgene.2020.00701.

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48

Gao, Yubang, Jingzhao Li, Yuli Xie, et al. "Chromosome-level genome assembly of Ajuga decumbens." Frontiers in Plant Science 15 (June 19, 2024). http://dx.doi.org/10.3389/fpls.2024.1413468.

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Qiu, Shaolong, Ningning Wu, Xiaodong Sun, Yongguo Xue, and Jixing Xia. "Chromosome-level genome assembly of soybean aphid." Scientific Data 12, no. 1 (2025). https://doi.org/10.1038/s41597-025-04711-8.

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50

Feng, Xiu, Ren Zhu, Yintao Jia, et al. "Chromosome-level genome assembly of Triplophysa scleroptera." Scientific Data 12, no. 1 (2025). https://doi.org/10.1038/s41597-025-05122-5.

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