LAUSR

Inulin is an important reserve polysaccharide in Asteraceae plants, and is also widely used as a sweetener, a source of dietary fibre and prebiotic. Nevertheless, a lack of genomic resources for inulin‐producing plants has hindered extensive studies on inulin metabolism and regulation. Here, we present chromosome‐level reference genomes for four inulin‐producing plants: chicory (Cichorium intybus), endive (Cichorium endivia), great burdock (Arctium lappa) and yacon (Smallanthus sonchifolius), with assembled genome sizes of 1.28, 0.89, 1.73 and 2.72 Gb, respectively. We found that the chicory, endive and great burdock genomes were shaped by whole genome triplication (WGT‐1), and the yacon genome was shaped by WGT‐1 and two subsequent whole genome duplications (WGD‐2 and WGD‐3). A yacon unique whole genome duplication (WGD‐3) occurred 5.6–5.8 million years ago. Our results also showed the genome size difference between chicory and endive is largely due to LTR retrotransposons, and rejected a previous hypothesis that chicory is an ancestor of endive. Furthermore, we identified fructan‐active‐enzyme and transcription‐factor genes, and found there is one copy in chicory, endive and great burdock but two copies in yacon for most of these genes, except for the 1‐FEH II gene which is significantly expanded in chicory. Interestingly, inulin synthesis genes 1‐SST and 1‐FFT are located close to each other, as are the degradation genes 1‐FEH I and 1‐FEH II. Finally, we predicted protein structures for 1‐FFT genes to explore the mechanism determining inulin chain length.