Chromosome-level genomes of two Magnoliales species provide new insights into the holocentric transition
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Comparative genomics of holocentric Myristica fragrans and monocentric Cananga odorata reveals contrasting centromere, repeat, epigenetic, and genome-evolution landscapes.
view moreCredit: Jinyin Xing and Xing Guo
Beijing—Most plants pack their centromere into a single region of each chromosome, but a few Magnoliales species instead spread centromeric function along the entire chromosome. To understand the genomic basis of this difference, a research team from Northeast Forestry University and BGI Research assembled chromosome-level genomes for the holocentric species Myristica fragrans (nutmeg) and the monocentric species Cananga odorata (ylang-ylang), and compared them using integrated multi-omics analyses. The study was published in Journal of Systematics and Evolution.
“Most plants concentrate their centromere in one region of each chromosome, but some Magnoliales species have spread centromeric function along the whole chromosome,” says Jinyin Xing, first author of the study. “By comparing a holocentric species with a closely related monocentric one at the chromosome level, we could dissect the genomic changes underlying this remarkable reorganization.”
Two chromosome-level genomes, two ways to build a centromere
The team generated a 637 Mb, 22-chromosome assembly for M. fragrans and a 717 Mb, 8-chromosome assembly for C. odorata, both with high completeness (BUSCO 97.5%–98.6%). Hi-C contact maps confirmed the expected distinction: each C. odorata chromosome showed a single prominent heterochromatic block, a classic monocentric centromere feature, whereas M. fragrans showed no such concentrated signal, consistent with holocentric chromosomes. In silico centromere prediction with two independent tools recapitulated this pattern, identifying one centromere locus per chromosome in C. odorata but multiple loci per chromosome in M. fragrans.
Despite these structural differences, centromere-associated regions in both species were positively correlated with mCG/mCHG methylation and heterochromatin-related (B) chromatin compartments. The two species differed markedly elsewhere: C. odorata showed clustered heterochromatin and a dominant TE-rich plateau of LTR/Gypsy elements (Tekay, Athila, and SIRE), whereas M. fragrans displayed a dispersed chromatin organization with multiple discrete peaks of LTR/Copia elements (Ale and SIRE). Notably, mCHH was depleted within M. fragrans centromeres but enriched around those of C. odorata.
Shared centromere features, divergent repeat and methylation landscapes
The two major tandem-repeat families of M. fragrans (MF_351 and MF_269) were preferentially localized to chromosome termini, where they showed elevated mCG and mCHG, suggesting a structural role in chromosome stability. By contrast, tandem repeats in C. odorata accumulated predominantly in euchromatic regions, with negligible occupancy in heterochromatin.
Phylogenomic and Ks analyses showed that M. fragrans and C. odorata share an ancient whole-genome duplication (LAURb, ~115 million years ago), and that M. fragrans and M. yunnanensis also experienced two distinct waves of transposon expansion. These results suggest that the emergence of holocentricity is unlikely to be explained by a whole-genome duplication event alone.
The core kinetochore protein CENH3 is highly conserved between the two species, with only subtle lineage-specific differences in the centromere-recognition loop1 and N-terminal tail. The elongated NASP N-terminus appears to be a Magnoliales-wide feature rather than a holocentric signature, and no large-scale structural changes were detected in other core kinetochore proteins.
Lineage-specific rewiring, not a simple whole-genome story
Taken together, these results suggest that lineage-specific remodeling of repetitive sequences and epigenetic states, rather than whole-genome duplication or major changes in core kinetochore proteins, likely drove the reorganization of centromeric architecture in Myristica. The chromosome-level genomes and comparative framework generated here offer a foundation for future studies of chromosome biology and centromere diversification in non-model plant lineages.
Original Source:
Jinyin Xing, Qiongqiong Lin, Dongming Fang, Lingling Lin, Fang Wang, Jingwei Zhou, Handong Su, Wen-Bin Yu, Gang Hao, Tong Wei, Xing Guo. 2026. Comparative genomics with de novo genome assembly of two Magnoliales species: Insights into monocentric-to-holocentric transition. Journal of Systematics and Evolution 64(5): 929-947.
https://doi.org/10.1111/jse.70124
Keywords:
centromere evolution, comparative genomics, holocentromere, Magnoliales, transposable elements.
Author’s Institution:
Northeast Forestry University is a national key university in China recognized for its research strengths in forestry, life sciences, and ecology. BGI Research is a leading genomics research institute under BGI Group, specializing in genomics, multi-omics, and bioinformatics.
About JSE:
Journal of Systematics and Evolution (JSE) is a peer-reviewed, bi-monthly international English-language journal dedicated to the understanding of biodiversity and evolution. Papers in any of the following and related fields will be considered: systematics and biodiversity conservation, paleobiology and biogeography, adaptation, speciation and domestication, evolutionary genomics and Evo-Devo, theory and methods in evolutionary biology.
Journal
Journal of Systematics and Evolution
Article Title
Comparative genomics with de novo genome assembly of two Magnoliales species: Insights into monocentric-to-holocentric transition
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