Megaruptor® 2

 DNA Shearing, RNA shearing and Chromatin shearing
Tight fragment size distribution
Hydropores eliminate clogging
High quality libraires
Tuneable to between 3 - 75 kb
1 to 2 samples in series
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  •  Documents
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Catalog Number
1 unit

The Megaruptor® 2 was designed to provide the best experience with the fragmentation of DNA from 3 kb - 75 kb. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly interface allows for two samples to be processed sequentially without additional user input and without cross-contamination. Just set the desired parameters and the automated system takes care of the rest. Clogging issues are eliminated in this design. The shearing with the Megaruptor leads to optimal long-read sequencing using PacBio®'s, and Oxford Nanopore™ technologies' systems.


Established in March 15th 2000, DNA Link, Inc. has developed as one of the leading full genomic service provider with its extensive 17 years of experience. DNA Link has been involved in numerous genomic researches including many national projects, and contributed to the expansion of the genomic industry.

On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that are controlled under strict criteria and successfully assisted numerous research projects.

PacBio platforms’ strongest upside is that it generates the longest reads among all sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.

DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable hydropores, which contributes to the overall efficiency of the laboratory logistics.

Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices

Hyeyoon, Jang - Lab Manager - Seoul, Korea
  • Demonstrated shearing to fragment sizes between 10 kb and 75 kb with Megaruptor® 2
    DNA Shearing Device
    Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. A: DNA was analyzed by pulsedfield gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software. B: Fragment Analyzer profiles of human genomic DNA (25 ng/μl; 200 μl/sample) sheared at different software settings of 10, 15, 20, 30 and 40 kb. (High Sensitivity Large Fragment Analysis Kit; Advanced Analytical Technologies, Inc. was used for separation and fragment sizing).
    * indicates unsheared DNA
  •  Testimonials

    The system performance was very good. High molecular weight DNA of different plants (Arabidopsis Alm, Hops polaris and wine Villard Blanc) was isolated and diluted to 50ng/µl or 70ng/µl. We aimed for fragment length 30kb at the volume 150µl.
    We achieved good results and we will continue with bead purification and library preps for PacBio sequencing.  I like the user friendly interface of the Megaruptor® 2. Just two parameters had to be specified: volume of each sample and desired mean fragment size. The processed DNA has a narrow size distribution at around 30kb.

    Christa Lanz and Julia Hildebrandt, Max Planck Institute for Developmental Biology, Tübingen, Germany
  •  Documents
    Megaruptor® 2 Quick guide MANUAL
    We have designed the Megaruptor® 2 using our highest level of knowledge in shearin...
    Megaruptor® 2 Manual MANUAL
    The Megaruptor® 2 was designed to provide researchers with a simple, automated, and r...
    Megaruptor 2 Flyer FLYER
    Application of the Megaruptor® for shearing of ultra-long DNA fragments in the context of Long Read Sequencing using 3rd Gen Sequencing Technologies APPLICATION NOTE
    The Megaruptor® provides a simple, robust, and straight forward method for reproducible DNA s...
    Megaruptor genomic DNA shearing for large insert sequencing library preparation APPLICATION NOTE
    Wageningen University has a strong background in plant genome sequencing including contributions ...
    Bioruptor ® Sonicator Brochure BROCHURE
    Diagenode’s Bioruptor® uses state-of-the-art shearing device to disrupt, disp...
    Optimal long DNA fragment generation prior to SMRTbell® library preparation APPLICATION NOTE
    Several methods exist today for shearing genomic DNA, but few are reliable for generating DNA fra...
  •  Publications

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    Chromosomal inversion polymorphisms in two sympatric ascidian lineages.
    Satou, Yutaka and Sato, Atsuko and Yasuo, Hitoyoshi and Mihirogi, Yukie andBishop, John and Fujie, Manabu and Kawamitsu, Mayumi and Hisata, Kanako andSatoh, Noriyuki
    Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partia...

    Complete vertebrate mitogenomes reveal widespread repeats and geneduplications.
    Formenti G. et al.
    BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for sim...

    Chromosomal rearrangements but no change of genes and transposable elementsrepertoires in an invasive forest-pathogenic fungus
    Demené, A. et al.
    Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, that may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut ...

    A single nucleotide polymorphism variant located in the cis-regulatoryregion of the ABCG2 gene is associated with mallard egg colour.
    Liu H. et al.
    Avian egg coloration is shaped by natural selection, but its genetic basis remains unclear. Here, we used genome-wide association analysis and identity by descent to finely map green egg colour to a 179-kb region of Chr4 based on the resequencing of 352 ducks (Anas platyrhynchos) from a segregating population result...

    Genomic Characterization of VIM and MCR Co-Producers: The First TwoClinical Cases, in Italy.
    Marchetti, Vittoria Mattioni and Bitar, Ibrahim and Sarti, Mario andFogato, Elena and Scaltriti, Erika and Bracchi, Chiara and Hrabak, Jaroslavand Pongolini, Stefano and Migliavacca, Roberta
    BACKGROUND: the co-production of carbapenemases and -genes represents a worrisome event in the treatment of infections. The aim of the study was to characterize the genomic features of two clinical complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. METHODS: species identification and antibiotic susc...

    Chromosome-scale genome assembly provides insights into the evolution andflavor synthesis of passion fruit (Passiflora edulis Sims).
    Xia Z. et al.
    Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91\% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. T...

    Rapid and ongoing evolution of repetitive sequence structures in humancentromeres.
    Suzuki Y. et al.
    Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations i...

    Efficient hybrid de novo assembly of human genomes with WENGAN.
    Di Genova A. et al.
    Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very hi...

    Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.
    von der Heyde B, Emmanouilidou A, Mazzaferro E, Vicenzi S, Höijer I, Klingström T, Jumaa S, Dethlefsen O, Snieder H, de Geus E, Ameur A, Ingelsson E, Allalou A, Brooke HL, den Hoed M
    A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafi...

    Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69Escherichia coli Strain in Italy
    Mattioni, Marchetti Vittoria and Bitar, Ibrahim and Piazza, Aurora andMercato, Alessandra and Fogato, Elena and Hrabak, Jaroslav and Migliavacca,Roberta
    Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia col...

    Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.
    Oulghazi S, Moumni M, Khayi S, Robic K, Sarfraz S, Lopez-Roques C, Vandecasteele C, Faure D
    Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major...

    Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.
    Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, Ranallo-Benavidez TR, Lemmon ZH, Kim J
    Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new referen...

    Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.
    Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J
    Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the&nb...

    Genome Sequence of sp. Strain JOR-1, an Extremely Halophilic Archaeon from the Dead Sea.
    Anton BP, DasSarma P, Martinez FL, DasSarma SL, Al Madadha M, Roberts RJ, DasSarma S
    An extremely halophilic archaeon, sp. strain JOR-1, was isolated from the east coast of the Dead Sea, Kingdom of Jordan, and sequenced using single-molecule real-time (SMRT) sequencing. The GC-rich 2.5-Mbp genome was composed of a circular chromosome and a megaplasmid. The genome contained 2,633 genes and was incorp...

    The round goby genome provides insights into mechanisms that may facilitate biological invasions.
    Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S
    BACKGROUND: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecologi...

    The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome.
    Kan SL, Shen TT, Gong P, Ran JH, Wang XQ
    BACKGROUND: Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major...

    A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).
    Pippel M, Jebb D, Patzold F, Winkler S, Vogel H, Myers G, Hiller M, Hundsdoerfer AK
    BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of s...

    Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of .
    Hovde BT, Daligault HE, Hanschen ER, Kunde YA, Johnson MB, Starkenburg SR, Johnson SL
    The sequenced genome and the leaf transcriptome of a near relative of and was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like hom...

    NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.
    De Roeck A, De Coster W, Bossaerts L, Cacace R, De Pooter T, Van Dongen J, D'Hert S, De Rijk P, Strazisar M, Van Broeckhoven C, Sleegers K
    Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats inclu...

    Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull.
    Young AE, Mansour TA, McNabb BR, Owen JR, Trott JF, Brown CT, Van Eenennaam AL
    Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant P Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (Pp) polled calves. The calves had no horns and were otherwise heal...

    Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef.
    Sekizuka T, Lee K, Kimata K, Isobe J, Kuroda M, Iyoda S, Ohnishi M, Sata T, Watahiki M
    We present the complete genome sequence of an enterohemorrhagic O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011.

    Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions.
    Zhang S, Liang F, Lei C, Wu J, Fu J, Yang Q, Luo X, Yu G, Wang D, Zhang Y, Lu D, Sun X, Liang Y, Xu C
    BACKGROUND: Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capable of reliably distinguishing embryos that carry balanced inversion f...

    Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
    Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, L
    The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelit...

    Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine.
    Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC
    BACKGROUND: Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG ...

    Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.
    Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH
    BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co...

    A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).
    Li Q, Li H, Huang W, Xu Y, Zhou Q, Wang S, Ruan J, Huang S, Zhang Z
    BACKGROUND: Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumbe...

    Genome Sequence and Methylation Patterns of sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.
    Priya DasSarma, Anton BP, DasSarma S, Laye VJ, Guzman D, Roberts RJ, DasSarma S
    sp. strain BOL3-1 was isolated from Salar de Uyuni, Bolivia, and sequenced using single-molecule real-time sequencing. Its 3.7-Mbp genome was analyzed for gene content and methylation patterns and incorporated into the Haloarchaeal Genomes Database (http://halo.umbc.edu). The polyextremophilic character and high-ele...

    The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.
    Zhao Q, Yang J, Cui MY, Liu J, Fang Y, Yan M, Qiu W, Shang H, Xu Z, Yidiresi R, Weng JK, Pluskal T, Vigouroux M, Steuernagel B, Wei Y, Yang L, Hu Y, Chen XY, Martin C
    Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been a...

    Biocompatible N-acetyl cysteine reduces graphene oxide and persists at the surface as a green radical scavenger.
    Palmieri V, Dalchiele EA, Perini G, Motta A, De Spirito M, Zanoni R, Marrani AG, Papi M
    We demonstrate that N-acetyl cysteine (NAC) reduces graphene oxide (GO) at room temperature. This represents a new green method to produce reduced GO (rGO). NAC adheres to the rGO surface as demonstrated by several spectroscopy techniques and avoids GO-mediated oxidation of glutathione. This method offers new opport...

    The alternative reality of plant mitochondrial DNA
    Alexander Kozik, Beth A. Rowan, Dean Lavelle, Lidija Berke, M. Eric Schranz, Richard W. Michelmore, and Alan C. Christensen
    Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sit...

    Characterizing the Major Structural Variant Alleles of the Human Genome.
    Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE
    In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional...

    Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina.
    Martínez FL, Anton BP, DasSarma P, Rajal V, Irazusta V, Roberts RJ, DasSarma S
    Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-time sequencing.

    Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine
    Katlyn Borgersa,Jheng-Yang Ouc, Po-Xing Zhengc, Petra Tielsa, Annelies Van Heckea, Evelyn Pletsa, Gitte Michielsena, Nele Festjensa, Nico Callewaerta, Yao-Cheng Lin
    Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). This study reports on an integrated genome analysis workflow for BCG, resulting in the completely assembled genome sequence of BCG Danish 1331 (07/270), one of the WHO reference strains for BCG...

    SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).
    Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N
    Background: The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference genome assembly for the European subspecies (H. r. rustica). Findings...

    Improved reference genome of Aedes aegypti informs arbovirus vector control.
    Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gl
    Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assem...

    Whole-genome landscape of Medicago truncatula symbiotic genes.
    Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Mu
    Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene e...

    Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.
    Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M,
    Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies ...

    The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird.
    Gautier M, Yamaguchi J, Foucaud J, Loiseau A, Ausset A, Facon B, Gschloessl B, Lagnel J, Loire E, Parrinello H, Severac D, Lopez-Roques C, Donnadieu C, Manno M, Berges H, Gharbi K, Lawson-Handley L, Zang LS, Vogel H, Estoup A, Prud'homme B
    Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is f...

    Long-read sequence capture of the hemoglobin gene clusters across gadid species.
    Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S
    Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic org...

    Genomic Structural Variations Within Five Continental Populations of .
    Long E, Evans C, Chaston J, Udall JA
    Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations containing genes. Large structural variations represent a significant amo...

    Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis.
    Miao H, Zhou J, Yang Q, Liang F, Wang D, Ma N, Gao B, Du J, Lin G, Wang K, Zhang Q
    Background: For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and genetic counseling. One possible reason is the limited ability to detect d...

    Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease.
    Ebbert MTW, Farrugia SL, Sens JP, Jansen-West K, Gendron TF, Prudencio M, McLaughlin IJ, Bowman B, Seetin M, DeJesus-Hernandez M, Jackson J, Brown PH, Dickson DW, van Blitterswijk M, Rademakers R, Petrucelli L, Fryer JD
    BACKGROUND: Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (GC) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing te...

    The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.
    Payelleville A, Legrand L, Ogier JC, Roques C, Roulet A, Bouchez O, Mouammine A, Givaudan A, Brillard J
    DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the l...

    Long-read sequence capture of the haemoglobin gene clusters across codfish species.
    Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S
    Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic org...

    A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.
    Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Are
    Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for th...

    Overview of Next-Generation Sequencing Technologies.
    Slatko BE, Gardner AF, Ausubel FM
    High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this revi...

    Draft genome of the Peruvian scallop Argopecten purpuratus.
    Li C, Liu X, Liu B, Ma B, Liu F, Liu G, Shi Q, Wang C
    Background: The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybri...

    Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.
    Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F
    BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a majo...

    Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.
    Rödelsperger C. et al.
    The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicate...

    De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads
    Korlach J. et al.
    Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-r...

    DNA fragmentation and quality control analysis
    Wassim Lakhal, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen, Steve Siembieda, Markus Tilmes & Jonathan Hagopian
    Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor®, Megaruptor®, and Fragment Analyzer™ by Advanced Analytical ensure that these first cri...

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