# Whole genome sequencing and assembly of the house sparrow, Passer domesticus

**Authors:** Vikas Kumar, Gopesh Sharma, Sankalp Sharma, Samvrutha Prasad, Shailesh Desai, Toral Vaishnani, Dalia Vishnudasan, Gopinathan Maheswaran, Kaomud Tyagi, Inderjeet Tyagi, Polavarapu B Kavi Kishor, Gyaneshwer Chaubey, Prashanth Suravajhala, Prashanth Suravajhala, Prashanth Suravajhala, Prashanth Suravajhala

PMC · DOI: 10.46471/gigabyte.161 · GigaByte · 2025-07-21

## TL;DR

This paper presents a high-quality genome assembly for the house sparrow, which will aid in studying bird and vertebrate evolution.

## Contribution

The paper provides a new annotated genome assembly for the house sparrow using advanced sequencing and assembly tools.

## Key findings

- The genome assembly spans 922 MB with contigs totaling 268,193 bases.
- The assembly shows significant similarity to the chicken and zebra finch genomes.
- Functional annotations were added to enhance the genome's utility for comparative studies.

## Abstract

The common house sparrow, Passer domesticus, is a small bird belonging to the family Passeridae. Here, we provide high-quality whole-genome sequencing data along with its assembly for the house sparrow. The final genome assembly was generated using a workflow that included Shovill, SPAdes, MaSuRCA, and BUSCO. The assembly consists of contigs spanning 268,193 bases and coalescing around a 922 MB sized reference genome. We used rigorous statistical thresholds to check the coverage, as the Passer genome showed considerable similarity to the Gallus gallus (chicken) and Taeniopygia guttata (Zebra finch) genomes, also providing functional annotations. This new annotated genome assembly will be a valuable resource for comparative and population genomic analyses of passerine, avian, and vertebrate evolution.

## Linked entities

- **Species:** Passer domesticus (taxon 48849), Gallus gallus (taxon 9031), Taeniopygia guttata (taxon 59729)

## Full-text entities

- **Genes:** ARNTL (aryl hydrocarbon receptor nuclear translocator like) [NCBI Gene 374115] {aka BMAL1}, cox1 [NCBI Gene 22162590], Cox3 [NCBI Gene 22162593], Atp6 [NCBI Gene 22162597], TLR4 (toll like receptor 4) [NCBI Gene 417241]
- **Diseases:** dead (MESH:D001926), toxicity (MESH:D064420), parasitic infection (MESH:D010272)
- **Chemicals:** nitrogen (MESH:D009584), oxygen (MESH:D010100), GC (MESH:C057580), amino acid (MESH:D000596)
- **Species:** Gallus gallus (bantam, species) [taxon 9031], Accipiter nisus (Eurasian sparrowhawk, species) [taxon 211598], Fringilla polatzeki (Gran Canaria teydefinch, species) [taxon 1896334], Pyrgilauda ruficollis (rufous-necked snowfinch, species) [taxon 221976], Buteo (hawks, genus) [taxon 30396], Spizella passerina (chipping sparrow, species) [taxon 40210], Agelaioides badius (bay-winged cowbird, species) [taxon 84835], Acanthisitta chloris (rifleman, species) [taxon 57068], Anthus cervinus (species) [taxon 45805], Passer ammodendri (species) [taxon 150914], Passer montanus saturatus (subspecies) [taxon 353272], Plasmodium relictum (species) [taxon 85471], Pyrgilauda blanfordi (plain-backed snowfinch, species) [taxon 667180], Meleagris gallopavo (common turkey, species) [taxon 9103], Homo sapiens (human, species) [taxon 9606], Felis catus (cat, species) [taxon 9685], Limosa lapponica baueri (subspecies) [taxon 1758121], Dives dives (Melodious blackbird, species) [taxon 504886], Passer montanus (Eurasian tree sparrow, species) [taxon 9160], Passeridae (sparrows, family) [taxon 9158], Montifringilla adamsi (black-winged snowfinch, species) [taxon 356906], Chloebia gouldiae (Gouldian finch, species) [taxon 44316], Quiscalus quiscula (common grackle, species) [taxon 84782], Nymphalis io (European peacock, species) [taxon 171585], Streptopelia orientalis (eastern turtle dove, species) [taxon 36243], Pseudoleistes guirahuro (yellow-rumped marshbird, species) [taxon 84849], Emberiza fucata (species) [taxon 337179], Taeniopygia guttata (zebra finch, species) [taxon 59729], Gymnomystax mexicanus (oriole blackbird, species) [taxon 84819], Motacilla alba (Bachstelze, species) [taxon 45807], Hirundo rustica rustica (subspecies) [taxon 333673], Petronia petronia (species) [taxon 150913], Euphagus cyanocephalus (Brewer's blackbird, species) [taxon 84817], Lonchura striata domestica [taxon 299123], Passer domesticus (Haussperling, species) [taxon 48849], Agelaius phoeniceus (red-winged blackbird, species) [taxon 39638], Chrysomus icterocephalus (yellow-hooded blackbird, species) [taxon 993346], Gallus (genus) [taxon 9030]

## Full text

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## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12308067/full.md

## References

62 references — full list in the complete paper: https://tomesphere.com/paper/PMC12308067/full.md

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Source: https://tomesphere.com/paper/PMC12308067