Centromeres unmasked: the complete genome of weeping forsythia

A team of scientists has successfully completed the first gap-free, telomere-to-telomere (T2T) genome assembly for Forsythia suspensa, a widely used ornamental and medicinal shrub. This complete reference genome enabled them to map and analyze the plant’s functional centromeres—chromosomal regions critical for cell division—with unprecedented detail. Their work revealed an unusually rich and diverse array of centromeric satellite sequences and surprisingly old retrotransposon insertions. These features suggest that the species' predominant asexual reproduction may have slowed centromere evolution, leading to a unique chromosomal landscape. The study sets a new standard for plant genome assemblies and opens new avenues for investigating chromosomal stability and evolution.

Forsythia suspensa, or weeping forsythia, is prized for its vivid yellow blossoms and valued in traditional Chinese medicine for its anti-inflammatory properties. It also plays an important ecological role in erosion control due to its hardiness and resilience. Despite its wide utility, efforts to fully decode its genome have long been impeded by repetitive sequences and structural gaps, particularly in centromeric regions. These regions are notoriously difficult to assemble, yet are essential for accurate chromosome segregation during cell division. Advances in long-read sequencing and chromatin mapping technologies have recently made it possible to resolve these genomic “dark matter” regions. Due to these challenges, deeper investigations into centromere architecture and genome completeness in F. suspensa are urgently needed.

In a new study published (DOI: 10.1093/hr/uhae185) on July 10, 2024, in Horticulture Research, researchers from the Institute of Genetics and Developmental Biology at the Chinese Academy of Sciences, Inner Mongolia Normal University, and Qingdao Agricultural University unveiled the first complete genome of F. suspensa. By combining Oxford Nanopore, PacBio HiFi, and Hi-C technologies, the team produced a telomere-to-telomere genome assembly, named Fsus-CHAU. The new resource enabled high-resolution mapping of all 14 centromeres using a custom-developed CENH3 antibody, revealing an unexpected diversity of centromeric repeats and shedding light on how asexual reproduction may influence genome evolution.

The researchers constructed a 688.79 Mb genome encompassing 14 gap-free chromosomes with an impressive contig N50 of 48.48 Mb and 98.6% gene completeness. Using a peptide-specific antibody against FsCENH3, they precisely pinpointed all functional centromeres. High-resolution ChIP-seq and FISH experiments showed these regions contained a surprising mix of satellite sequences—some over twice the size of classic centromere repeats—and a unique pattern across different chromosomes. These findings point to a highly individualized centromere architecture within F. suspensa. Furthermore, contrary to patterns seen in species like maize or Arabidopsis, the retrotransposons within F. suspensa centromeres were significantly older, suggesting long-term stability. The authors hypothesize that this reflects the species’ reliance on asexual reproduction, which may slow the turnover of transposable elements and allow older centromeric features to persist. Additionally, phased nucleosome mapping revealed that CENH3 binding follows a structured, repeat-specific pattern, a feature vital for centromere function. Together, these insights suggest that F. suspensa harbors one of the most structurally complex and evolutionarily distinctive centromeres yet observed in flowering plants.

“Our study goes beyond genome assembly—it reshapes how we think about plant centromeres,” said Dr. Yang Liu, the study’s senior author. “We discovered that F. suspensa, with its dominant asexual reproduction, may retain much older centromeric retrotransposons than expected. This is a rare opportunity to study centromere evolution in slow-changing genomic environments. The unexpected diversity and size of its centromeric repeats may provide valuable clues about nucleosome organization and long-term chromosomal stability in plants.”

The Fsus-CHAU genome provides a foundational reference for Forsythia genetics, with implications extending into breeding, conservation, and synthetic biology. Understanding the plant’s centromere structure can inform artificial chromosome design and improve targeted gene insertion techniques. The findings may also guide breeding programs aimed at enhancing traits like stress tolerance, flowering time, and medicinal compound production. More broadly, this study contributes to evolutionary biology by illuminating how reproductive strategies such as asexual propagation influence chromosomal architecture over time. As sequencing technologies advance, F. suspensa may become a model for studying stable centromere dynamics in perennial, clonally propagated plant species.

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References

DOI

10.1093/hr/uhae185

Original Source URL

https://doi.org/10.1093/hr/uhae185

Funding information

A Circos plot. Starting from the outermost to the innermost ring: (a) chromosome, (b) gene number density, (c) LTR density, (d) GC content, and (e) syntenic block. B The phenotypes of different tissues, including flower, fruit, stem, leaf, and the whole plant in Forsythia suspensa. C The karyotype analysis of 14 chromosome pairs in F. suspensa. D Chromatin interaction map generated by Hi-C for the Fsus-CHAU genome.

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.