Chromosome level assembly and annotation of the genome of the endangered giant Patagonian bumble bee Bombus dahlbomii DOI Creative Commons

Lican Martínez,

Eduardo E. Zattara, Marina P. Arbetman

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(7)

Published: July 1, 2024

This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from single, haploid male collected in Argentina was used PacBio (HiFi) sequencing, Hi-C technology then to map chromatin contacts. Using Juicer manual curation, scaffolded into 18 main pseudomolecules, representing high-quality, near chromosome-level assembly. The sequenced size is estimated at 265 Mb. annotated based on RNA sequencing data of another Argentina, BRAKER3 produced 15,767 genes. show high completeness, with >95% BUSCO scores both genes (based conserved Hymenoptera). provides valuable resource studying biology this iconic endangered species, as well understanding impacts its decline designing strategies preservation.

Language: Английский

Klumpy: A tool to evaluate the integrity of long‐read genome assemblies and illusive sequence motifs DOI Creative Commons
Giovanni Madrigal, Bushra Fazal Minhas, Julian Catchen

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 25(1)

Published: May 27, 2024

Abstract The improvement and decreasing costs of third‐generation sequencing technologies has widened the scope biological questions researchers can address with de novo genome assemblies. With increasing number reference genomes, validating their integrity minimal overhead is vital for establishing confident results in applications. Here, we present Klumpy, a tool detecting visualizing both misassembled regions assembly genetic elements (e.g. genes) interest set sequences. By leveraging initial raw reads combination respective assembly, illustrate Klumpy's utility by investigating antifreeze glycoprotein ( afgp ) loci across two icefishes, searching reported absent gene northern snakehead fish, scanning genomes mudskipper bumblebee regions. In former cases, were able to provide support noncanonical placement an locus icefishes locate missing gene. Furthermore, our scans identify unmappable putative repetitive element shared among several species bees.

Language: Английский

Citations

4
The genome sequence of the Large Red Tailed Bumble Bee, Bombus lapidarius (Linnaeus, 1758) DOI Creative Commons
Olga Sivell,

Duncan Sivell,

Matthew Noah Smith

et al.

Wellcome Open Research, Journal Year: 2025, Volume and Issue: 10, P. 67 - 67

Published: Feb. 12, 2025

We present a genome assembly from an individual female specimen of Bombus lapidarius (Large Red Tailed Bumble Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The sequence has total length 368.50 megabases. Most the (81.04%) is scaffolded into 18 chromosomal pseudomolecules. mitochondrial also been assembled and 28.11 kilobases in length.

Language: Английский

Citations

0
Klumpy: A Tool to Evaluate the Integrity of Long-Read Genome Assemblies and Illusive Sequence Motifs DOI Open Access
Giovanni Madrigal, Bushra Fazal Minhas, Julian Catchen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 15, 2024

Abstract The improvement and decreasing costs of third-generation sequencing technologies has widened the scope biological questions researchers can address with de novo genome assemblies. With increasing number reference genomes, validating their integrity minimal overhead is vital for establishing confident results in applications. Here, we present Klumpy, a tool detecting visualizing both misassembled regions assembly genetic elements (e.g., genes, promotors, or transposable elements) interest set sequences. By leveraging initial raw reads combination respective assembly, illustrate Klumpy’s utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, searching reported absent gene northern snakehead fish, scanning genomes mudskipper bumblebee regions. In former cases, were able to provide support noncanonical placement an afgp locus icefishes locate missing gene. Furthermore, our scans identify cryptic genome, putative repetitive element shared amongst several species bees.

Language: Английский

Citations

0
Chromosome level assembly and annotation of the genome of the endangered giant Patagonian bumble bee Bombus dahlbomii DOI Creative Commons

Lican Martínez,

Eduardo E. Zattara, Marina P. Arbetman

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(7)

Published: July 1, 2024

This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from single, haploid male collected in Argentina was used PacBio (HiFi) sequencing, Hi-C technology then to map chromatin contacts. Using Juicer manual curation, scaffolded into 18 main pseudomolecules, representing high-quality, near chromosome-level assembly. The sequenced size is estimated at 265 Mb. annotated based on RNA sequencing data of another Argentina, BRAKER3 produced 15,767 genes. show high completeness, with >95% BUSCO scores both genes (based conserved Hymenoptera). provides valuable resource studying biology this iconic endangered species, as well understanding impacts its decline designing strategies preservation.

Language: Английский

Citations

0