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New Shiqi Pigeon Genome Placed 97.8% of Its Sequence on 41 Chromosomes

Rock dove in profile at Waterlow Park, London
Research · Genetics & genomics

A chromosome-level reference genome has been assembled from a female Shiqi pigeon, a domestic meat breed of rock dove (Columba livia) from Zhongshan in southern China. The bird was sampled in Zhongshan, and the study was published in Scientific Data on 25 July 2026.

The researchers combined PacBio HiFi long reads with Hi-C data. HiFi reads provide long, highly accurate stretches of DNA sequence, while Hi-C helps determine which sequence blocks belong together on the same chromosome.

Most of the genome was anchored to chromosomes

The final assembly spans 1.244 gigabases, or about 1.24 billion DNA bases. About 97.8% of the assembled sequence was placed on 41 chromosomes, and the researchers annotated 15,184 protein-coding genes. BUSCO analysis found 97.7% of the conserved genes expected in a high-quality bird genome, supporting the completeness of the assembly.

A reference genome provides a map for later genetic studies

Shiqi pigeons are an economically important Chinese meat breed. A chromosome-level genome gives researchers a clearer reference for locating genes, comparing chromosome structure and studying genetic differences among pigeon breeds and populations.

The study itself did not identify genes for a particular production trait or reconstruct the breed’s full domestication history. Its main contribution is the reference genome, which can now support future work on genetic architecture, artificial selection, breed evolution and molecular breeding in domestic pigeons.

Sources and image credit

  1. Liang, Y., Lu, H., Zhang, W. et al. (2026). Chromosome-level genome assembly of the Shiqi pigeon (Columba livia).Primary open-access Data Descriptor. The 1.244-Gb assembly placed 97.81% of sequence on 41 chromosomes, reached 97.7% BUSCO completeness and annotated 15,184 protein-coding genes.
  2. NCBI BioSample SAMN56644893: Shiqi pigeon genome.Official sample record confirming a female Shiqi pigeon sampled in Zhongshan, China, in September 2022.

Image: Rock dove (Columba livia) in Waterlow Park, London, United Kingdom, 28 July 2022. Photo: Satdeep Gill / Wikimedia Commons. CC BY-SA 4.0; Commons Quality Image. Representative species image; this is not a Shiqi pigeon or the bird used for genome sequencing. · CC BY-SA 4.0 · Source

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