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Near-Complete Sumatran Tiger Genome Assembly Covered 17 of 19 Chromosomes From End to End

Sumatran tiger
Research · Genetics & genomics

Researchers have produced the first almost complete telomere-to-telomere genome assembly for the sumatran tiger (Panthera tigris sumatrae). The study, published on 21 March 2026 in BMC Genomics, used long-read Oxford Nanopore sequencing to build a substantially more continuous genomic reference for the subspecies.

Telomeres are repetitive DNA sequences at the ends of chromosomes. A telomere-to-telomere, or T2T, assembly aims to reconstruct an entire chromosome continuously from one end to the other, including repetitive regions that are difficult to assemble with shorter DNA reads.

The researchers generated high-coverage Nanopore long-read data and compared several ways of correcting sequencing errors and assembling the reads. Error correction was crucial: three of the best-performing approaches initially produced nine chromosomes as single, gapless T2T contigs — continuous DNA sequences extending from one telomere to the other. The authors argue that improved error correction could make highly complete reference genomes simpler and less costly to produce using a single widely available sequencing technology.

Seventeen of 19 chromosomes reached both telomeres

After the contigs were ordered and linked into chromosome-scale scaffolds using the published tiger genome as a guide, two of the strongest assemblies had 17 of the 19 tiger chromosomes represented from telomere to telomere. The previously published tiger reference had only one chromosome assembled from one telomere to the other as a single contig. An independent method based on three-dimensional DNA contacts also recovered all 19 chromosome types and found no indication of major large-scale errors in the selected assembly.

Telomeric repeat sequences and gaps across Sumatran tiger genome assemblies
Locations of telomeric repeat sequences and gaps in the genome assemblies compared in the study. Figure 1 from Dean et al. (2026), BMC Genomics, CC BY 4.0.

The assembly also revealed genes and potential structural differences

Genome annotation — identifying likely genes and their positions in the assembled DNA — predicted 23,737 complete genes. The comparison with domestic cat and the earlier tiger reference also supported two large suspected chromosomal inversions, regions where a stretch of DNA occurs in the opposite orientation. One inversion contained MAN1B1, involved in glycoprotein breakdown, together with DPP7 and UAP1L1, genes linked to immune or cell-survival processes in other mammals. The authors suggest that such regions could contribute to functional differences between domestic cats and tigers, while stressing that several additional apparent rearrangements in the Sumatran tiger assembly may still reflect assembly error and need further investigation.

Synteny and selected chromosomal rearrangements in domestic cat and tiger genome assemblies
Comparison of gene order (synteny) and selected chromosomal rearrangements among domestic cat and tiger genome assemblies. Figure 2 from Dean et al. (2026), BMC Genomics, CC BY 4.0.

The DNA came from a residual blood sample collected for clinical purposes from an adult female sumatran tiger at Twycross Zoo in the United Kingdom in 2020. The sample was later donated for genome sequencing; the study did not involve an experimental procedure performed for the genomic research itself.

The authors say the near-complete reference can provide a basis for identifying deleterious alleles — gene variants that may reduce health or fitness — maintaining genetic variation and informing mate selection in captive sumatran tiger populations.

Sources and image credit

  1. Dean, L. L., Holmes, N., Dobbs, P., & Loose, M. (2026). The tiger who came to T2T: Telomere-to-Telomere genome assembly of the Sumatran tiger (Panthera tigris sumatrae) using nanopore simplex reads. BMC Genomics, 27, 339. https://doi.org/10.1186/s12864-026-12703-0Primary peer-reviewed open-access article published 21 March 2026 under CC BY 4.0. The study generated about 158 Gb of ONT simplex data (~64× coverage); after homology-based scaffolding, two leading assemblies represented 17 of 19 tiger chromosomes as telomere-to-telomere scaffolds.

Image: Frank Kohn / U.S. Fish & Wildlife Service — Sumatran tiger photographed at the Smithsonian’s National Zoo, Washington, DC; representative image, not the individual used in the genome study · Public Domain · Source

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