Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

First annotated genome of a mandibulate moth, Neomicropteryx cornuta, generated using PacBio HiFi sequencing.

ABSTRACT: We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called "mandibulate archaic moths" (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 million years ago and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly-contiguous genome with a contig N50 of nearly 17 Mbp. The assembled genome length of 541,115,538 bp is about half the length of the largest published Amphiesmenoptera genome (Limnephilus lunatus, Trichoptera) and double the length of the smallest (Papilio polytes, Lepidoptera). We find high recovery of universal single copy orthologs with 98.1% of BUSCO genes present and provide a genome annotation of 15,643 genes aided by resolved isoforms from PacBio IsoSeq data. This high-quality genome assembly provides an important resource for studying ecological and evolutionary transitions in the early evolution of Amphiesmenoptera.

SUBMITTER: Li X

PROVIDER: S-EPMC8557830 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

First genome assembly of the order Strepsiptera using PacBio HiFi reads reveals a miniature genome.

Project description:Twisted-wing insects (Strepsiptera) are an enigmatic order of parasites with unusual life histories and striking sexual dimorphism. Males emerge from hosts as free-living winged adults, while females from most species remain as endoparasites that retain larval traits. Due to scarce genomic data and phylogenetic controversies, Strepsiptera was only recently placed as the closest living relative to beetles (Coleoptera). Here, we report the first PacBio HiFi genome assembly of the strepsipteran Xenos peckii (Xenidae). This de novo assembly size is 72.1 Mb, with a BUSCO score of 87.4%, N50 of 7.3 Mb, 23.4% GC content, and 38.41% repeat content. We identified 8 contigs that contain >75% of the assembly and reflect the haploid chromosome number reported from karyotypic data, and 3 contigs that exhibit sex chromosome coverage patterns. Additionally, the mitochondrial genome is 16,111 bp long and has 37 genes. This long-read assembly for Strepsiptera reveals a miniature genome and provides a unique tool to understand complex genome evolution associated with a parasitic lifestyle and extreme sexual dimorphism.

| S-EPMC11358474 | biostudies-literature

Complete Genome Assembly of Myxococcus xanthus Strain DZ2 Using Long High-Fidelity (HiFi) Reads Generated with PacBio Technology.

Project description:Myxococcus xanthus is a Gram-negative social bacterium belonging to the order Myxococcales of the class Deltaproteobacteria. It is a facultative social predator found in soils across the globe and is thought to be crucial for the microbial ecosystem. Here, we report a complete high-quality reference genome of the M. xanthus strain DZ2.

| S-EPMC8281077 | biostudies-literature

Chromosome-level genome assembly of Plagiognathops microlepis based on PacBio HiFi and Hi-C sequencing.

Project description:Plagiognathops microlepis is an economic freshwater fish in the subfamily Xenocyprinae of Cyprinidae. It is widely distributed in the freshwater ecosystem of China, with moderate economic value and broad development prospects. However, the lack of genomic resources has limited our understanding on the genetic basis, phylogenetic status and adaptive evolution strategies of this fish. Here, we assembled a chromosome-level reference genome of P. microlepis by integrating Pacbio HiFi long-reads, Illumina short-reads and Hi-C sequencing data. The size of this genome is 1004.34 Mb with a contig N50 of 38.80 Mb. Using Hi-C sequencing data, 99.59% of the assembled sequences were further anchored to 24 chromosomes. A total of 578.91 Mb repeat sequences and 28,337 protein-coding genes were predicted in the current genome, of which, 26,929 genes were functionally annotated. This genome provides valuable information for investigating the phylogeny and evolutionary history of cyprinid fishes, as well as the genetic basis of adaptive strategies and special traits in P. microlepis.

| S-EPMC11271555 | biostudies-literature

Assembly and comparative analysis of the complete mitochondrial genome of <i>Salix wilsonii</i> using PacBio HiFi sequencing.

Project description:Salix L. (willows) is one of the most taxonomically complex genera of flowering plants, including shrubs, tall trees, bushes, and prostrate plants. Despite the high species diversity, only five mitochondrial genomes (mitogenomes) have been released in this genus. Salix wilsonii is an important ornamental and economic willow tree in section Wilsonia of the genus Salix. In this study, the S. wilsonii mitogenome was assembled into a typical circular structure with a size of 711,456 bp using PacBio HiFi sequencing. A total of 58 genes were annotated in the S. wilsonii mitogenome, including 33 protein-coding genes (PCGs), 22 tRNAs, and 3 rRNAs. In the S. wilsonii mitogenome, four genes (mttB, nad3, nad4, and sdh4) were found to play important roles in its evolution through selection pressure analysis. Collinearity analysis of six Salix mitogenomes revealed high structural variability. To determine the evolutionary position of S. wilsonii, we conducted a phylogenetic analysis of the mitogenomes of S. wilsonii and 12 other species in the order Malpighiales. Results strongly supported the segregation of S. wilsonii and other five Salix species with 100% bootstrap support. The comparative analysis of the S. wilsonii mitogenome not only sheds light on the functional and structural features of S. wilsonii but also provides essential information for genetic studies of the genus Salix.

| S-EPMC9709322 | biostudies-literature

First whole genome assembly and annotation of a European common bean cultivar using PacBio HiFi and Iso-Seq data.

Project description:Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption worldwide. Flageolet bean originates from France and presents typical organoleptic properties, including the remarkable feature of having small pale green colored seeds. Here, we report the whole-genome data, assembly and annotation of the flageolet bean accession 'Flavert'. High molecular weight DNA and RNA were extracted and subjected to long-read sequencing using PacBio Sequel II platform. The genome consisted of 566,238,753 bp assembled in 13 molecules, including 11 chromosomes plus the mitochondrial and chloroplastic genomes. Annotation predicted 29,549 protein coding genes and 6,958 non-coding RNA. This high-quality genome (99.2% BUSCO completeness) represents a valuable data set for further genomic and genetic studies on common bean and more generally on legumes. To our knowledge, this is the first whole-genome sequence of a common bean accession originating from Europe.

| S-EPMC10293967 | biostudies-literature

Complete genome sequence of <i>Citrobacter braakii</i> ASE1 generated by PacBio sequencing.

Project description:We report the complete genome sequence of Citrobacter braakii ASE1 generated by the PacBio Sequel II platform. This bacterium was isolated from the soil of a lettuce farm in Salinas, CA, USA, in 2020. The genome consists of a single circular chromosome of 5,021,820 bp with a 52.2% GC content.

| S-EPMC10927685 | biostudies-literature

Complete Genome Sequence of Lanthionine-Producing Lactobacillus brevis Strain 100D8, Generated by PacBio Sequencing.

Project description:Lactobacillus brevis strain 100D8 was isolated from rye silage and showed rapid acidification ability in vitro and antifungal activity against mycotoxin-producing fungi. We report here the complete genome sequence of L. brevis strain 100D8, which has a circular chromosome (2,351,988?bp, 2,304 coding sequences [CDSs]) and three plasmids (45,061?bp, 57 CDSs; 40,740?bp, 40 CDSs; and 39,943?bp, 57 CDSs).

| S-EPMC6256641 | biostudies-literature

High-Quality Whole-Genome Sequences for 59 Historical Shigella Strains Generated with PacBio Sequencing.

Project description:Shigella spp. are enteric pathogens that cause shigellosis. We report here the high-quality whole-genome sequences of 59 historical Shigella strains that represent the four species and a variety of serotypes.

| S-EPMC5897796 | biostudies-literature

High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing.

Project description:Enterotoxigenic Escherichia coli (ETEC) is an important diarrheagenic pathogen. We report here the high-quality whole-genome sequences of 21 ETEC strains isolated from patients in the United States, international diarrheal surveillance studies, and cruise ship outbreaks.

| S-EPMC5764927 | biostudies-literature

Complete Genome Sequence and Annotation of Malacoplasma iowae Type Strain 695, Generated Using PacBio Sequencing.

Project description:Malacoplasma iowae, previously known as "Mycoplasma iowae," is associated with embryo mortality, reduced hatchability, and leg abnormalities in turkeys, leading to considerable economic losses. Here, we report the complete and annotated genome sequence of Malacoplasma iowae type strain 695.

| S-EPMC9872633 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data