The reference genome sequence of the scarlet follicle, Sterculia lanceolata, reveals a paleo-polyploidization and its impact on fruit quality and fruit dehiscence

TL;DR

This study provides a high-quality genome sequence for Sterculia lanceolata, revealing its evolutionary history and genes linked to fruit traits.

Contribution

The first chromosome-level genome assembly of Sterculia lanceolata, uncovering paleo-polyploidization and its impact on fruit quality.

Findings

A high-quality genome assembly of 602.8 Mb with 98.7% BUSCO completeness was achieved.

Ancient whole-genome duplication events were identified, influencing karyotype evolution in Malvaceae.

Key gene families related to fruit dehiscence were found to have expanded due to polyploidy.

Abstract

Sterculia lanceolata, a tree species of the Malvaceae family with notable ornamental and medicinal value, has long been constrained in genetic research and breeding applications due to the lack of genomic resources. In this study, we report for the first time a high-quality, chromosome-level genome assembly of this species, aimed at elucidating its evolutionary history and the genetic basis of key traits. We constructed the genome using PacBio HiFi sequencing and further assembled it into 20 pseudochromosomes with the aid of Hi-C technology, yielding a final genome assembly size of 602.8 Mb with a contig N50 of 29.3 Mb and a BUSCO completeness of 98.7%. The assembly includes the identification of 20 pseudochromosomes and the annotation of 35,873 protein-coding genes, with an annotation rate of 96.4%. By integrating genomic data from other Malvaceae species, we analyzed the karyotype evolution of S. lanceolata and revealed the basal ploidy level of the family. Comparative genomic analyses uncovered significant syntenic relationships and whole-genome duplication (WGD) events among Malvaceae species, thereby clarifying the trajectory of karyotype evolution. Moreover, the study identified key regulatory gene families associated with fruit dehiscence (homologs of SHP1/2, FUL, IND, and ALC) that have undergone extensive expansion in S. lanceolata as a consequence of ancient polyploidy events. The reference genome provided in this study not only serves as a critical resource for evolutionary research in Malvaceae but also establishes a foundational framework for molecular breeding, genetic improvement, and conservation of S. lanceolata and related species.

Figures