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PubMed2003

An extensible application for assembling annotation for genomic data.

SUMMARY: AnnBuilder is an R package for assembling genomic annotation data. The system currently provides parsers to process annotation data from LocusLink, Gene Ontology Consortium, and Human Gene Project and can be extended to new data sources via user defined parsers. AnnBuilder differs from other existing systems in that it provides users with unlimited ability to assemble data from user selected sources. The products of AnnBuilder are files in XML format that can be easily used by different systems. AVAILABILITY: (http://www.bioconductor.org). Open source.

Database Management Systems↗

PubMed2026

The genome sequence of the Downland Conch, Aethes tesserana (Denis & Schiffermüller) , 1775 (Lepidoptera: Tortricidae).

We present a genome assembly from an individual male Aethes tesserana (Downland Conch; Arthropoda; Insecta; Lepidoptera; Tortricidae). The assembly contains two haplotypes with total lengths of 486.12 megabases and 482.92 megabases. Most of haplotype 1 (99.81%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.54 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Aethes tesserana↗

PubMed2026

The genome sequence of the Bluebell moth, Eana incanana (Stephens, 1852) (Lepidoptera: Tortricidae).

We present a genome assembly from an individual male Eana incanana (Bluebell moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The assembly contains two haplotypes with total lengths of 372.33 megabases and 373.40 megabases. Most of haplotype 1 (99.64%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.01 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Bluebell moth↗

PubMed2026

The genome sequence of the Marbled Maple moth, Altenia scriptella (Hübner, 1796) (Lepidoptera: Gelechiidae).

We present a genome assembly from an individual female Altenia scriptella (Marbled Maple moth; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The assembly contains two haplotypes with total lengths of 506.56 megabases and 440.34 megabases. Most of haplotype 1 (99.51%) is scaffolded into 33 chromosomal pseudomolecules, including the W and Z sex chromosomes. The assembly also includes two B chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.3 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Altenia scriptella↗

PubMed2026

The genome sequence of the Lesser noctule, Nyctalus leisleri (Kuhl, 1817) (Chiroptera: Vespertilionidae).

We present a genome assembly from an individual male Nyctalus leisleri (Leisler's bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The assembly contains two haplotypes with total lengths of 2 226.32 megabases and 2 021.25 megabases. Most of haplotype 1 (88.57%) is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.23 kilobases. Gene annotation of this assembly on Ensembl identified 18 985 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Chiroptera↗

PubMed2026

The genome sequence of the lesser white-fronted goose, Anser erythropus (Linnaeus, 1758) (Anseriformes: Anatidae).

We present a genome assembly from an individual female Anser erythropus (lesser white-fronted goose; Chordata; Aves; Anseriformes; Anatidae). The assembly contains two haplotypes with total lengths of 1 339.88 megabases and 1 168.02 megabases. Most of haplotype 1 (88.67%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.74 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Anser erythropus↗

PubMed2026

The genome sequence of the Royal Mantle, Catarhoe cuculata (Hufnagel, 1767) (Lepidoptera: Geometridae).

We present a genome assembly from an individual male Catarhoe cuculata (Royal Mantle; Arthropoda; Insecta; Lepidoptera; Geometridae). The assembly contains two haplotypes with total lengths of 297.56 megabases and 297.17 megabases. Most of haplotype 1 (99.41%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.67 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Catarhoe cuculata↗

PubMed2026

The genome sequence of the muscid fly, Hydrotaea similis Meade, 1887 (Diptera: Muscidae).

We present a genome assembly from an individual female Hydrotaea similis (muscid fly; Arthropoda; Insecta; Diptera; Muscidae). The assembly contains two haplotypes with total lengths of 884.66 megabases and 852.78 megabases. Most of haplotype 1 (90.83%) is scaffolded into 5 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 20.27 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Diptera↗

PubMed2026

The genome sequence of the Silver Colonel, Odontomyia argentata (Fabricius, 1794) (Diptera: Stratiomyidae).

We present a genome assembly from an individual female Odontomyia argentata (Silver Colonel; Arthropoda; Insecta; Diptera; Stratiomyidae). The assembly contains two haplotypes with total lengths of 1 950.48 megabases and 1 937.58 megabases. Most of haplotype 1 (95.92%) is scaffolded into 6 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.0 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Diptera↗

PubMed2026

The genome sequence of a muscid fly, Lispocephala verna (Fabricius, 1794) (Diptera: Muscidae).

We present a genome assembly from an individual female Lispocephala verna (muscid fly; Arthropoda; Insecta; Diptera; Muscidae). The assembly contains two haplotypes with total lengths of 987.71 megabases and 934.62 megabases. Most of haplotype 1 (95.8%) is scaffolded into 5 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.34 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Diptera↗

PubMed2026

The genome sequence of the Mallow Seed Moth, Platyedra subcinerea (Haworth, 1828) (Lepidoptera: Gelechiidae).

We present a genome assembly from an individual male Platyedra subcinerea (Mallow Seed Moth; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The assembly contains two haplotypes with total lengths of 555.70 megabases and 555.31 megabases. Most of haplotype 1 (99.98%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.25 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Lepidoptera↗

PubMed2026

The genome sequence of the Pale Eggar, Trichiura crataegi (Linnaeus, 1758) (Lepidoptera: Lasiocampidae).

We present a genome assembly from an individual male Trichiura crataegi (Pale Eggar; Arthropoda; Insecta; Lepidoptera; Lasiocampidae). The assembly contains two haplotypes with total lengths of 1 112.64 megabases and 1 115.22 megabases. Most of haplotype 1 (99.87%) is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.03 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Lepidoptera↗

PubMed2026

The genome sequence of Natterer's Bat, Myotis nattereri (Kuhl, 1817) (Chiroptera: Vespertilionidae).

We present a genome assembly from an individual male Myotis nattereri (Natterer's Bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The assembly contains two haplotypes with total lengths of 2 138.58 megabases and 1 932.61 megabases. Most of haplotype 1 (98.98%) is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.27 kilobases. Gene annotation of this assembly on Ensembl identified 19 245 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Chiroptera↗

PubMed2026

The genome sequence of a muscid fly, Hydrotaea militaris (Meigen, 1826) (Diptera: Muscidae).

We present a genome assembly from an individual female Hydrotaea militaris (Arthropoda; Insecta; Diptera; Muscidae). The assembly contains two haplotypes with total lengths of 1 703.03 megabases and 1 760.39 megabases. Most of haplotype 1 (96.2%) is scaffolded into 6 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 18.83 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Diptera↗

PubMed2025

Enhancing genome recovery across metagenomic samples using MAGmax.

SUMMARY: The number of metagenome-assembled genomes (MAGs) is rapidly increasing with the growing scale of metagenomic studies, driving fast progress in microbiome research. Sample-wise assembly has become the standard due to its computational efficiency and strain-level resolution. It requires dereplication, the removal of near-identical genomes assembled in different metagenomic samples. We present MAGmax, an efficient dereplication tool that enhances both the quantity and quality of MAGs through a strategy of bin merging and reassembly. Unlike dRep, which selects a single representative bin per genome cluster, MAGmax merges multiple bins within a cluster and reassembles them to increase coverage. MAGmax produces more dereplicated, higher-quality MAGs than dRep at 1.6× its speed and using three times less memory. AVAILABILITY AND IMPLEMENTATION: The MAGmax open source software, implemented in Rust, is available under the GPLv3 license at https://github.com/soedinglab/MAGmax.

Metagenomics↗

PubMed2025

The genome sequence of the comb-clawed beetle, Prionychus ater (Fabricius, 1775) (Coleoptera: Tenebrionidae).

We present a genome assembly from an individual male Prionychus ater (comb-clawed beetle; Arthropoda; Insecta; Coleoptera; Tenebrionidae). The assembly contains two haplotypes with total lengths of 385.22 megabases and 347.54 megabases. Most of haplotype 1 (97.6%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.26 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Prionychus ater; comb-clawed beetle; genome sequen↗

PubMed2025

The genome sequence of the Treble Lines, Charanyca trigrammica (Hufnagel, 1766) (Lepidoptera: Noctuidae).

We present a genome assembly from an individual male Charanyca trigrammica (Treble Lines; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 546.43 megabases and 546.58 megabases. Most of haplotype 1 (99.97%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.44 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Charanyca trigrammica; Treble Lines; genome sequen↗

PubMed2025

The genome sequence of the Eurasian Spoonbill, Platalea leucorodia Linnaeus, 1758 (Pelecaniformes: Threskiornithidae).

We present a genome assembly from an individual female Platalea leucorodia (Eurasian Spoonbill; Chordata; Aves; Pelecaniformes; Threskiornithidae). The assembly contains two haplotypes with total lengths of 1 345.83 megabases and 1 190.44 megabases. Most of haplotype 1 (95.57%) is scaffolded into 37 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.15 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Platalea leucorodia; Eurasian Spoonbill; genome se↗