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The genome sequence of the Orange Underwing, Archiearis parthenias (Linnaeus, 1761) (Lepidoptera: Geometridae).

We present a genome assembly from an individual female Archiearis parthenias (Orange Underwing; Arthropoda; Insecta; Lepidoptera; Geometridae). The assembly contains two haplotypes with total lengths of 528.46 megabases and 426.17 megabases. Most of haplotype 1 (99.61%) is scaffolded into 26 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 17.24 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.

Archiearis parthenias↗

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↗

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↗

The genome sequence of a blow fly, Melanomya nana (Meigen, 1826) (Diptera: Calliphoridae).

We present a genome assembly from an individual male Melanomya nana (blow fly; Arthropoda; Insecta; Diptera; Calliphoridae). The assembly contains two haplotypes with total lengths of 1 391.98 megabases and 1 424.34 megabases. Most of haplotype 1 (99.62%) is scaffolded into 5 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 27.12 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.

Diptera↗

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↗

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↗

Computational prediction of methylation status in human genomic sequences.

Epigenetic effects in mammals depend largely on heritable genomic methylation patterns. We describe a computational pattern recognition method that is used to predict the methylation landscape of human brain DNA. This method can be applied both to CpG islands and to non-CpG island regions. It computes the methylation propensity for an 800-bp region centered on a CpG dinucleotide based on specific sequence features within the region. We tested several classifiers for classification performance, including K means clustering, linear discriminant analysis, logistic regression, and support vector machine. The best performing classifier used the support vector machine approach. Our program (called hdfinder) presently has a prediction accuracy of 86%, as validated with CpG regions for which methylation status has been experimentally determined. Using hdfinder, we have depicted the entire genomic methylation patterns for all 22 human autosomes.

Algorithms↗

Bacteriophage P100 for control of Listeria monocytogenes in foods: genome sequence, bioinformatic analyses, oral toxicity study, and application.

Listeria monocytogenes is an opportunistic foodborne pathogen responsible for Listeriosis, a frequently fatal infection. This investigation represents a comprehensive approach to characterize and evaluate the broad host range, strictly virulent phage P100, which can infect and kill a majority of Listeria monocytogenes strains. First, the complete nucleotide sequence (131,384 basepairs) of the genome of P100 was determined, predicted to encode 174 gene products and 18 tRNAs. Bioinformatic analyses revealed that none of the putative phage proteins has any homologies to genes or proteins of Listeria or any other bacteria which are known or suspected to be toxins, pathogenicity factors, antibiotic resistance determinants, or any known allergens. Next, a repeated dose oral toxicity study in rats was conducted, which did not produce any abnormal histological changes, morbidity or mortality. Therefore, no indications for any potential risk associated with using P100 as a food additive were found. As proof of concept, and to determine the parameters for application of P100 to foods sensitive to Listeria contamination, surface-ripened red-smear soft cheese was produced. Cheeses were contaminated with low concentrations of L. monocytogenes at the beginning of the ripening period, and P100 was applied to the surface during the rind washings. Depending on the time points, frequency and dose of phage applications, we were able to obtain a significant reduction (at least 3.5 logs) or a complete eradication of Listeria viable counts, respectively. We found no evidence for phage resistance in the Listeria isolates recovered from samples. Taken together, our results indicate that P100 can provide an effective and safe measure for the control of Listeria contamination in foods and production equipment.

Animals↗

Complete genome sequence of transmissible gastroenteritis coronavirus PUR46-MAD clone and evolution of the purdue virus cluster.

The complete sequence (28580 nt) of the PUR46-MAD clone of the Purdue cluster of transmissible gastroenteritis coronavirus (TGEV) has been determined and compared with members of this cluster and other coronaviruses. The computing distances among their S gene sequences resulted in the grouping of these coronaviruses into four clusters, one of them exclusively formed by the Purdue viruses. Three new potential sequence motifs with homology to the alpha-subunit of the polymerase-associated nucleocapsid phosphoprotein of rinderpest virus, the Bowman-Birk type of proteinase inhibitors, and the metallothionein superfamily of cysteine rich chelating proteins have been identified. Comparison of the TGEV polymerase sequence with that of other RNA viruses revealed high sequence homology with the A-E domains of the palm subdomain of nucleic acid polymerases.

Amino Acid Sequence↗

The complete chloroplast genome sequence and phylogenetic position of Mallotus apelta.

Mallotus apelta is a perennial species of Euphorbiaceae widely distributed in subtropical East and Southeast Asia. In this study, we sequenced and analyzed its complete chloroplast genome. The genome was 164,055 bp in length and exhibited a typical quadripartite structure, comprising an LSC region of 88,899 bp, an SSC region of 18,494 bp, and two IR regions of 28,331 bp each. A total of 124 genes were annotated. Comparative analyses revealed conserved genome organization and IR boundaries among Mallotus species. Phylogenetic analysis showed that M. apelta was closely related to M. paniculatus, providing valuable resources for Mallotus phylogenetic studies.

Euphorbiaceae↗

Complete mitochondrial genomic sequence of Lenzites betulinus (Polyporales, Basidiomycota).

Lenzites betulinus is a medicinal fungus in the Polyporaceae. Here, we report the first complete mitochondrial sequencing of this species. The circular genome is 61,288 bp in length, with a GC content of 26.32% and base composition of A (36.98%), T (36.70%), G (12.96%), and C (13.36%). It contains 14 core protein-coding genes (PCGs), 26 tRNA genes, two rRNA genes, and nine intronic ORFs within the cox1 gene. A maximum-likelihood phylogenetic tree based on 14 PCGs from 17 mitochondrial genomes confirmed that L. betulinus clusters within the Polyporaceae, closely related to Trametes and Fomitopsis. This served as a significant reference for ongoing research into other species within the Polyporales order.

Mitochondrial genome↗