A haplotype-resolved nutmeg genome reveals XY sex chromosome evolution and enables molecular sexing.

Katarina Matvijev, Sufang Wang, Mengjun Xiao, Ashini D Mahadura, Ray Ming, Dmitry A Filatov

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Article in Communications biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

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6 authors.

Katarina Matvijev *Department of Biology, University of Oxford, Oxford, UK.

Sufang Wang *Department of Biology, University of Oxford, Oxford, UK.

Mengjun Xiao *Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.

Ashini D MahaduraDepartment of Biology, University of Oxford, Oxford, UK.

Ray MingCentre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. rayming@illinois.edu.ORCID 0000-0002-9417-5789

Dmitry A FilatovDepartment of Biology, University of Oxford, Oxford, UK. dmitry.filatov@biology.ox.ac.uk.ORCID 0000-0001-8077-5452

Funding

RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/Y009169/1

6 · The paper itself

Abstract

Nutmeg (Myristica fragrans Houtt.) is a dioecious species that produces one of the most valuable spices and has peculiar holocentric chromosomes with diffuse centromere. The impact of holocentricity on the evolution of sex chromosomes is not well understood. Here, we present the first fully annotated haplotype-resolved chromosome-level genome of a male nutmeg plant, identify its sex chromosomes and analyse evolution of the sex-linked region (SLR). We demonstrate that nutmeg has a male heterogametic (XY) system, with a 0.23 Mb X-linked SLR and a 3.1 Mb Y-linked SLR with limited evidence for Y-degeneration. Low X:Y synonymous divergence for X- and Y-linked homologs (K

Indexed as

Chromosomes, PlantEvolution, MolecularGenome, PlantHaplotypesSex Chromosomes

Identifiers

PMID42209685

DOI10.1038/s42003-026-10355-0

PMCPMC13500479

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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 Socratic graph.