Complete sequencing of ape genomes Published: April, 2025 Abstract:
The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1,2,3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved refe... Read more »
Human de novo mutation rates from a four-generation pedigree reference Published: March, 2025 Abstract:
Understanding the human de novo mutation (DNM) rate requires complete sequence information1. Here using five complementary short-read and long-read sequencing technologies, we phased and assembled more than 95% of each diploid human genome in a fo... Read more »
Bat genomes illuminate adaptations to viral tolerance and disease resistance Published: January, 2025 Abstract:
Zoonoses are infectious diseases transmitted from animals to humans. Bats have been suggested to harbour more zoonotic viruses than any other mammalian order1. Infections in bats are largely asymptomatic2,3, indicating limited tissue-damaging infl... Read more »
Single chromatin fiber profiling and nucleosome position mapping in the human brain Published: December, 2024 Abstract:
Motivation
Nucleosomes are the basic unit of chromatin, but genome-scale maps of nucleosome positioning along chromatin fibers do not exist for brain and many other complex tissues. Conventional chromatin accessibility assays designed to map nu... Read more »
The genome sequence of the Turnip Sawfly, Athalia rosae(Linnaeus, 1758) Published: February, 2023 Abstract:
We present a genome assembly from an individual female Athalia rosae (the Turnip Sawfly; Arhropoda; Insecta; Hymenoptera; Athaliidae). The genome sequence is 172 megabases in span. Most of the assembly is scaffolded into eight chromosomal pseudomo... Read more »
The genome sequence of the malaria mosquito, Anopheles funestus,Giles, 1900 Published: November, 2022 Abstract:
We present a genome assembly from an individual female Anopheles funestus (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae). The genome sequence is 251 megabases in span. The majority of the assembly is scaffolded into three chromoso... Read more »
Detection and Quantitation of DNA Damage on a Genome-wide ScaleUsing RADAR-seq. Published: November, 2022 Abstract:
The formation and persistence of DNA damage can impact biological processes such as DNA replication and transcription. To maintain genome stability and integrity, organisms rely on robust DNA damage repair pathways. Techniques to detect and locate... Read more »
Mitochondrial RNA editing in Trypanoplasma borreli: new tools, newrevelations Published: November, 2022 Abstract:
The kinetoplastids are unicellular flagellates that derive their name from the ‘kinetoplast’, a region within their single mitochondrion harboring its organellar genome of high DNA content, called kinetoplast (k) DNA. Some protein prod... Read more »
Semi-automated assembly of high-quality diploid human reference genomes. Published: October, 2022 Abstract:
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a ble... Read more »
The genome sequence of the Arran brown, Erebia ligea (Linnaeus,1758) Published: October, 2022 Abstract:
We present a genome assembly from an individual male Erebia ligea (Arran brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 506 megabases in span. The majority (99.92\%) of the assembly is scaffolded into 29 chromosomal ... Read more »
Complete Genome Sequence of Strain DM083 Isolated from HumanTongue Coating. Published: September, 2022 Abstract:
We isolated Lactiplantibacillus plantarum DM083 from the human tongue coating to establish a strain library for oral probiotics. It has a single circular 3,197,299 bp chromosome with a guanine-cytosine (GC) content of 44.6\% without plasmids. Impo... Read more »
The genome sequence of the pale mottled willow, Caradrina clavipalpis(Scopoli, 1763) Published: September, 2022 Abstract:
We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100\%) is scaffolded into 31 chromoso... Read more »
The genome sequence of the smoky wainscot, Mythimna impura (Hubner,1808) Published: September, 2022 Abstract:
We present a genome assembly from an individual female Mythimna impura (smoky wainscot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 949 megabases in span. The majority of the assembly (98.39\%) is scaffolded into 32 chromo... Read more »
The genome sequence of the wall brown, Lasiommata megera (Linnaeus,1767) Published: September, 2022 Abstract:
We present a genome assembly from an individual female Lasiommata megera (the wall brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 488 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 30 ch... Read more »
The genome sequence of the sallow kitten, Furcula furcula (Clerck,1759) Published: September, 2022 Abstract:
We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100\%) is scaffolded into 29 chromosomal p... Read more »
The genome sequence of the peacock moth, Macaria notata (Linnaeus,1758) Published: September, 2022 Abstract:
We present a genome assembly from an individual male Macaria notata (the peacock moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 394 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 29 chrom... Read more »
Plant species-specific basecaller improves actual accuracy of nanoporesequencing Published: September, 2022 Abstract:
Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling,... Read more »
The genome sequence of the dun-bar pinion, Cosmia trapezina(Linnaeus, 1758) Published: July, 2022 Abstract:
We present a genome assembly from an individual male Cosmia trapezina (dun-bar pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 825 megabases in span. The majority of the assembly (99.87\%) is scaffolded into 32 chromos... Read more »
Familial long-read sequencing increases yield of de novo mutations. Published: April, 2022 Abstract:
Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide patt... Read more »
The genome sequence of Anoplius nigerrimus (Scopoli, 1763), a spiderwasp Published: April, 2022 Abstract:
We present a genome assembly from an individual Anoplius nigerrimus (Arthropoda; Insecta; Hymenoptera; Pompilidae) of unknown sex. The genome sequence is 624 megabases in span. In total, 45.75\% of the assembly is scaffolded into 15 chromosomal ps... Read more »
Haplotype-resolved Chinese male genome assembly based on high-fidelitysequencing Published: March, 2022 Abstract:
The advantages of both the length and accuracy of high-fidelity (HiFi) reads enable chromosome-scale haplotype-resolved genome assembly. In this study, we sequenced a cell line named HJ, established from a Chinese Han male individual by using HiFi... Read more »
Complete Genome Sequence of Herpes Simplex Virus 2 StrainG. Published: March, 2022 Abstract:
Herpes simplex virus type (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regi... Read more »
The genome sequence of a stonefly, Nemurella pictetii Klapalek, 1900 Published: February, 2022 Abstract:
We present a genome assembly from an individual male Nemurella pictetii (Arthropoda; Insecta; Plecoptera; Nemouridae). The genome sequence is 257 megabases in span. The majority of the assembly (99.79\%) is scaffolded into 12 chromosomal pseudomol... Read more »
The genome sequence of a parasitoid wasp, Forster, 1771. Published: January, 2022 Abstract:
We present a genome assembly from an individual female (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 315 megabases in span. The majority of the assembly (82.64\%) is scaffolded into 12 chromosomal pseudomolecules. Gene ... Read more »
The genome sequence of the brimstone moth, Opisthograptis luteolata(Linnaeus, 1758) Published: January, 2022 Abstract:
We present a genome assembly from an individual male (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99\%) is scaffolded into 31 chromosomal pseudo... Read more »
Reference genome assembly of the big berry Manzanita (Arctostaphylosglauca). Published: November, 2021 Abstract:
Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus ... Read more »
PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs,and methylation. Published: September, 2021 Abstract:
Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehens... Read more »
De novo genome assembly of the marine teleost, bluefin trevally (Caranxmelampygus). Published: September, 2021 Abstract:
The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and c... Read more »
Targeted long-read sequencing identifies missing disease-causingvariation. Published: August, 2021 Abstract:
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-eval... Read more »
Evidence of an epidemic spread of KPC-producing in Czech hospitals Published: August, 2021 Abstract:
The aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018–2019, a total of 108 KPC-producing Enterobacterales were recovered fr... Read more »
Chromosomal inversion polymorphisms in two sympatric ascidian lineages. Published: April, 2021 Abstract:
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 c... Read more »
Complete vertebrate mitogenomes reveal widespread repeats and geneduplications. Published: April, 2021 Abstract:
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 Genome... Read more »
Rapid and ongoing evolution of repetitive sequence structures in humancentromeres. Published: December, 2020 Abstract:
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 l... Read more »
Efficient hybrid de novo assembly of human genomes with WENGAN. Published: December, 2020 Abstract:
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 ... Read more »
Contrasting signatures of genomic divergence during sympatric speciation. Published: October, 2020 Abstract:
The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin. Gene flow count... Read more »
Genome structure and content of the rice root-knot nematode (). Published: October, 2020 Abstract:
Discovered in the 1960s, is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavaila... Read more »
Repeat expansions confer WRN dependence in microsatellite-unstablecancers. Published: October, 2020 Abstract:
The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair. Depletion of WRN induces widespread DNA double-strand break... Read more »
Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs. Published: July, 2020 Abstract:
Aberrant microsatellite repeat-expansions at specific loci within the human genome cause several distinct, heritable, and predominantly neurological, disorders. Creating models for these diseases poses a challenge, due to the instability of such r... Read more »
LongQC: A Quality Control Tool for Third GenerationSequencing Long Read Data Published: February, 2020 Abstract:
We propose LongQC as an easy and automated quality control tool for genomic datasets generated by third generation sequencing (TGS) technologies such as Oxford Nanopore technologies (ONT) and SMRT sequencing from Pacific Bioscience (PacBio). Key s... Read more »
Nanopore Sequencing and Its Clinical Applications. Published: January, 2020 Abstract:
Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore). Nanopore-based DNA... Read more »
Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull. Published: October, 2019 Abstract:
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 heterozygo... Read more »
A chromosome-scale genome assembly of cucumber (Cucumis sativus L.). Published: June, 2019 Abstract:
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-cove... Read more »
The alternative reality of plant mitochondrial DNA Published: March, 2019 Abstract:
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 mitochondri... Read more »
Characterizing the Major Structural Variant Alleles of the Human Genome. Published: January, 2019 Abstract:
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... Read more »
Improved reference genome of Aedes aegypti informs arbovirus vector control. Published: November, 2018 Abstract:
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... Read more »
Whole-genome landscape of Medicago truncatula symbiotic genes. Published: November, 2018 Abstract:
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 assemb... Read more »
The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird. Published: October, 2018 Abstract:
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 d... Read more »
Long-read sequence capture of the hemoglobin gene clusters across gadid species. Published: October, 2018 Abstract:
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 de... Read more »
Genomic Structural Variations Within Five Continental Populations of . Published: October, 2018 Abstract:
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 con... Read more »
Long-read sequence capture of the haemoglobin gene clusters across codfish species. Published: August, 2018 Abstract:
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 de... Read more »
A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Published: June, 2018 Abstract:
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 obje... Read more »
Draft genome of the Peruvian scallop Argopecten purpuratus. Published: April, 2018 Abstract:
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 t... Read more »
Overview of Next-Generation Sequencing Technologies. Published: April, 2018 Abstract:
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 correspondin... Read more »
Comparative Analysis of Ralstonia solanacearum Methylomes Published: April, 2017 Abstract:
Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identifie... Read more »
Microevolution of Burkholderia pseudomallei during an acute infection. Published: September, 2014 Abstract:
We used whole-genome sequencing to evaluate 69 independent colonies of Burkholderia pseudomallei isolated from seven body sites of a patient with acute disseminated melioidosis. Fourteen closely related genotypes were found, providing evidence for... Read more »
