Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 4, 2025

The taxonomic classification of a falcon population found in the Mongolian Altai region Asia has been heavily debated for two centuries and previous studies have inconclusive, hindering more informed conservation approach. Here, we generated chromosome-level gyrfalcon reference genome using Vertebrate Genomes Project (VGP) assembly pipeline. Using whole sequences 49 falcons from different species populations, including "Altai" falcons, analyzed their structure, admixture patterns, demographic history. We find that are genomic mosaics saker ancestries, carry distinct W mitochondrial haplotypes cluster with lanner falcon. maternally-inherited diverged 422,000 years before present (290,000–550,000 YBP) ancestor sakers gyrfalcons, both which, turn, split 109,000 YBP (70,000–150,000 YBP). chromosome 31 coding variants 29 genes may possibly influence important structural, behavioral, reproductive traits. These findings provide insights into question as candidate species.

Language: Английский

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Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 14, 2025

Abstract Background Advancing our knowledge of vector species genomes is a key step in battle against the spread diseases. Biting midges genus Culicoides are vectors arboviruses that significantly affect livestock worldwide. stellifer suspected with wide range distribution North America, for which cryptic diversity has been described. Results With just one specimen C. , we assembled and annotated nuclear mitochondrial genome using ultra-low input DNA PacBio protocol. The assembly 119 Mb length contig N50 value 479.3 kb, contains 11% repeat sequences 18,895 protein-coding genes. To further elucidate role this as vector, provide genomic evidence non-retroviral endogenous viral element integrated into corresponds to rhabdovirus nucleocapsid proteins, same family vesicular stomatitis virus. Conclusions This information will pave way future investigations species’s putative role. We also demonstrate practicability completing studies small dipterans single specimens preserved ethanol well introduce workflow data analysis considers challenges insect assembly.

Language: Английский

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A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens)

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 27, 2024

The Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened, cooperatively-breeding bird, is an emerging model system in evolutionary biology and ecology. Extensive individual-based monitoring genetic sampling for decades has yielded wealth of data, allowing the detailed study social behavior, demography, population genetics this natural population. Here, we report linkage map chromosome-level genome assembly annotation female made with long-read sequencing technology, chromatin conformation map. We constructed comprising 4,468 SNPs that had 34 groups total sex-averaged autosomal length 2446.78 cM. new 1.33 Gb length, consisting 33 complete or near-complete autosomes sex chromosomes (ZW). This highly contiguous NG50 68 Mb Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score 97.1% respect to Aves database. annotated gene set BUSCO transcriptome 95.5% 17,964 identified protein-coding genes, 92.5% which have associated functional annotations. new, high-quality provides valuable tools future research into dynamics small, populations conservation concern.

Language: Английский

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Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: July 16, 2024

Background Advancing our knowledge of vector species genomes is a key step in battle against the spread diseases. Biting midges genus Culicoides are vectors arboviruses that significantly affect livestock worldwide. Culicoides stellifer suspected with wide range distribution North America, for which cryptic diversity has been described.Results With just one specimen C. stellifer, we assembled and annotated both high-quality nuclear mitochondrial genome using ultra-low input DNA PacBio protocol. The assembly 119 Mb length contig N50 value 479.3 kb, contains 11% repeat sequences 18,895 protein-coding genes. To further elucidate role this as vector, provide genomic evidence non-retroviral endogenous viral element integrated into corresponds to rhabdovirus nucleocapsid proteins, same family Vesicular Stomatitis Virus.Conclusions This information will pave way future investigations species's putative role. We also demonstrate practicability completing studies small dipterans single specimens preserved ethanol well introduce workflow data analysis considers challenges insect assembly.

Language: Английский

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De novo genome assembly of a Geomyid rodent, Botta’s pocket gopher (Thomomys bottae bottae)

Journal of Heredity, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 20, 2024

Botta's pocket gopher (Thomomys bottae) is a common and widespread subterranean rodent of the North American west. The species has been long interest to evolutionary biologists due phenotypic diversity across its range unusual levels variation in chromosome number composition. Here, we present high-quality reference genome from male T. b. bottae individual captured San Francisco Bay Area. assembly comprised 2,792 scaffolds, with scaffold N50 value 23.6 Mb BUSCO score 91.0%. This helps fill significant taxonomic sampling gap resources. With this genome, envision new opportunities investigate questions regarding genomics adaptation belowground niche. Further, can begin explore impact associated life history traits, such as limited dispersal low population connectivity, on intraspecific genetic variation, evolution, speciation, phylogenetic relationships Geomyoidea.

Language: Английский

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A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Sept. 11, 2024

Language: Английский

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