The genomes of chicory, endive, great burdock and yacon provide insights into Asteraceae palaeo‐polyploidization history and plant inulin production

Abstract

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.

EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends

“…Till now, EndHiC has also been applied to resolve the scaffolding assemblies of several other genomes, including 3 economic plants chicory ( Cichorium intybus , n = 9), endive ( Cichorium endivia , n = 9), yacon ( Smallanthus sonchifolius , n = 29) [ 4 ], and an invasive weed Ipomoea cairica (n = 15) [ 5 ], whose genome sizes are 1.3 Gb, 0.85 Gb, 2.6 Gb, and 0.73 Gb. Applying the contig error correction module of EndHiC, 3, 0, 0, and 1 contigs were identified with assembly errors for chicory, endive, yacon and Ipomoea cairica , respectively.…”

“…Then, what is the optimal size value? To answer this question, we calculated the contact values for contig ends with different contig end sizes ranging from 500-Kb to 40-Mb, using the human simulated data and the real great burdock ( Arctium lappa ) genome data that was finely assembled by Hifiasm and further scaffolded into 18 chromosomes [ 4 ]. We took the contact values from adjacent contig ends as signal contact values, while that from non-adjacent contigs ends as noise contact values.…”

“…The long accurate reads generated by PacBio High-Fidelity (HiFi) technology, with an average read length over 10-Kb and base accuracy over 99%, has been widely applied in the de novo assembly of plant and animal genomes [ 1 ]. Specific software for assembling HiFi reads have also been developed, such as Hifiasm [ 2 ] and HiCanu [ 3 ], which in general can produce large contigs with N50 size over tens of mega-bases for a substantial part of genomes [ 4 – 6 ]. Besides, the ultra-long noisy reads with an average length over 50-Kb from Oxford Nanopore Technology (ONT) and related software development such as wtdbg2 [ 7 ], also largely improve the contig continuity in genome assemblies.…”

“…Using the current long accurate HiFi reads, we can routinely generate highly continuous contigs with N50 size approaching or larger than 10 Mb and N90 size approaching or larger than 1 Mb for a certain part of plant and animal genomes [ 4 , 5 ]. Here we do not include complex genomes, such as polyploidy or those enriched in long repeats, which tend to generate more fragmental contig assemblies.…”

“…To resolve this problem, here we developed an independent Hi-C scaffolding tool EndHiC, which constructs scaffolds with only Hi-C links from the most effective region of contig ends. To illustrate the EndHiC method, we used the genome data of a medical and vegetable plant great burdock ( Arctium lappa ) sequenced by our group [ 4 ], which was EndHiC’s first successful application and also on which the inspiration of using contig end was born.…”