Evidence map›Paper›PMID 41975254›Full record

ArticleBMC genomics2026

The reference genome of the Asian Elephant (Elephas maximus): a foundation for conservation and genomic research.

Diego De Panis, Larissa S Arantes, Tom Brown, Elisa Somenzi, Gudrun Wibbelt, Jennifer Ballaco, Jacquelyn Mountcastle, Nadolina Brajuka, Vinita S Joardar, Olivier Fedrigo and 5 more

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Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Diego De Panis *Department of Evolutionary Genetics, Leibniz Institute for Zoo- and Wildlife Research (IZW), Berlin, Germany.
Larissa S Arantes *Department of Evolutionary Genetics, Leibniz Institute for Zoo- and Wildlife Research (IZW), Berlin, Germany.
Tom Brown *Department of Evolutionary Genetics, Leibniz Institute for Zoo- and Wildlife Research (IZW), Berlin, Germany.
Elisa SomenziDepartment of Biology, University of Turku, Turku, Finland.
Gudrun WibbeltDepartment of Wildlife Diseases, Leibniz Institute for Zoo- and Wildlife Research (IZW), Berlin, Germany.
Jennifer BallacoVertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
Jacquelyn MountcastleVertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
Nadolina BrajukaVertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
Vinita S JoardarNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
Olivier FedrigoVertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
Françoise Thibaud-NissenNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
Oliver A RyderConservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA.
Erich JarvisVertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
Virpi LummaaDepartment of Biology, University of Turku, Turku, Finland. virpi.lummaa@gmail.com.
Camila J MazzoniDepartment of Evolutionary Genetics, Leibniz Institute for Zoo- and Wildlife Research (IZW), Berlin, Germany. mazzoni@izw-berlin.de.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe Asian elephant (Elephas maximus), a keystone species with both ecological and cultural significance, is highly endangered and has disappeared from 95% of its historical range. In this study, we present a chromosome-level assembly and an annotation of the Asian elephant genome, providing a foundational resource for population genomics, conservation biology and evolutionary research.

resultsThe primary genome assembly spans 190 contigs, with an N50 of 87,987,108 bp and is scaffolded into 64 sequences, with an N50 of 127,432,672 bp. We also present two haplotype-resolved assemblies with contig N50s of 75,101,715 bp and 88,213,608 bp. The genome assemblies and annotated protein-coding models in the primary assembly are highly complete, with 98.2%, 98.2%, and 96.0% BUSCO single-copy orthologs identified in the primary and two haplotype genome assemblies, respectively, and 98.8% recovered in the protein-coding annotation. We showcase how this reference genome enables insights into functional and evolutionary genomics, including the transposable element landscape, demographic history, a comparison against an individual sequenced from another population, as well as an investigation into genomic regions with increased levels of heterozygosity that colocalise with multi-copy gene families associated with immune and sensory-responses.

conclusionThe development of a high-quality genome assembly and annotation for E. maximus gives researchers a valuable resource to help understand the evolutionary history of this iconic species as well as guide conservation efforts. Here we have shown that highly contiguous, complete and accurate chromosome sequences help uncover regions with increased levels of homozygosity, indicative of inbreeding, and areas of increased heterozygosity, enriched for genes key to the immune response and other sensory mechanisms.

Indexed as

Conservation of Natural ResourcesElephantsGenomeGenomicsAnimalsEvolution, MolecularHaplotypesMolecular Sequence AnnotationAsian elephantElephas maximusGenome AnnotationGenome AssemblyHeterozygosity

Identifiers

PMID41975254
PMCPMC13185315

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.