The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae

Hilary S Ireland,Ross N Crowhurst,Robert J Schaffer,Ali Saei,Sylvia Erasmuson,Karine M David,Cecilia H Deng,David Chagné,Elena Hilario,Chen Wu

doi:10.1038/s41438-021-00662-4

Hilary S Ireland, Ross N Crowhurst + Show 8 more

Open Access

https://doi.org/10.1038/s41438-021-00662-4

Copy DOI

Abstract

The Rosaceae family has striking phenotypic diversity and high syntenic conservation. Gillenia trifoliata is sister species to the Maleae tribe of apple and ~1000 other species. Gillenia has many putative ancestral features, such as herb/sub-shrub habit, dry fruit-bearing and nine base chromosomes. This coalescence of ancestral characters in a phylogenetically important species, positions Gillenia as a ‘rosetta stone’ for translational science within Rosaceae. We present genomic and phenological resources to facilitate the use of Gillenia for this purpose. The Gillenia genome is the first fully annotated chromosome-level assembly with an ancestral genome complement (x = 9), and with it we developed an improved model of the Rosaceae ancestral genome. MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fleshy fruit development in Rosaceae.

Highlights

The Rosaceae family has striking phenotypic diversity and high syntenic conservation
The combination of phenotypic and genomic resources provided here will facilitate the use of G. trifoliata as a model species and ‘rosetta stone’ for translational science
The phenotype of G. trifoliata has been described in detail in a BBCH framework, to enhance comparative studies within Rosaceae, and to characterise the development of characters of interest, such as annual bearing, cane-like habit, and dry fruit development

Summary

Introduction

The Rosaceae family has striking phenotypic diversity and high syntenic conservation. Gillenia has many putative ancestral features, such as herb/subshrub habit, dry fruit-bearing and nine base chromosomes. This coalescence of ancestral characters in a phylogenetically important species, positions Gillenia as a ‘rosetta stone’ for translational science within Rosaceae. The Gillenia genome is the first fully annotated chromosome-level assembly with an ancestral genome complement (x = 9), and with it we developed an improved model of the Rosaceae ancestral genome. MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fleshy fruit development in Rosaceae. The phenotype and genome of G. trifoliata has potential to provide a ‘rosetta stone’ for translational science within Rosaceae.

Methods

Results

Conclusion