M. Shakerkhatibi, N. Mohammadi, K. Zoroufchi Benis, A. B. Sarand, E. Fatehifar and A. A. Hashemi, Environ. Health Eng. Manage. J., 2015, 2, 117–122 CAS .

VanRaden, P. M. Efficient methods to compute genomic predictions. J. Dairy Sci. 91, 4414–4423 (2008). Khazaei, H. et al. Flanking SNP markers for vicine–convicine concentration in faba bean ( Vicia faba L.). Mol. Breeding 35, 38 (2015). Vondrak, T. et al. Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats. Plant J. 101, 484–500 (2020). I. Correia, A. Nunes, A. S. Barros and I. Delgadillo, J. Cereal Sci., 2010, 51, 146–151 CrossRef CAS .De novo repeat finding was done on Hedin/2 pseudomolecules with RepeatModeler v2.0.1 (ref. 68) with sample sizes of 1,000,000 bp and with LTR_retriever v2.9.0 (ref. 69) and LTRharvest 70. De novo elements were clustered with cd-hit-est v4.8.1 (ref. 71); element classification was aided by comparing to RepBase release 20181926, core-repeat domains from GyDB 2.0 (ref. 72) and REXdb Viridiplantae v3.0 (ref. 73). For the retrotransposons, sLTRs and full-length elements were specified as such by LTR_retriever and LTRharvest. Repeat masking was done with RepeatMasker v4.2.1 ( http://www.repeatmasker.org) using de novo repeat libraries. Transposable element sequences encoding conserved protein domains were also identified based on their similarities to the REXdb v3.0 database using DANTE v0.1.1 ( https://github.com/kavonrtep/dante). Satellite repeats were annotated using similarity searches to a custom database of satellite DNA families described in our previous studies 18, 31, 74, 75. The distribution of satellite repeats on metaphase chromosomes of V. faba was examined using fluorescence in situ hybridization (FISH). Chromosome preparation, probe labelling and FISH were performed as previously described 31, with hybridization and washing temperatures adjusted to account for the probe AT/CG content to allow for 10–20% mismatches. Chromosomes were counterstained with 4′,6-diamidino-2-phenylindole (DAPI), mounted in Vectashield medium (Vector Laboratories) and examined using a Zeiss AxioImager.Z2 microscope with an Axiocam 506 mono camera. Images were captured and processed using ZEN 3.2 software (Carl Zeiss). Gene model annotation Fig. 5 Volume average droplet size ( D 4,3) of emulsions prepared using different commercial pulse proteins samples. Droplet size of freshly prepared emulsions and as a function of storage time (day 7 and 14) is shown at (a) pH 2 and (b) pH 7. The effect of (c) heat treatment (90 °C for 30 min) and (d) the addition of 1 wt% salt on the average droplet size at pH 2 and pH 7 are also shown. Means that do not share a letter are significantly different by Tukey's test at p< 0.05 significance level. See Table 1 for sample identification.

Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451–9457 (2020).

Xi, H., Nguyen, V., Ward, C., Lui, Z. & Searle, I. R. Chromosome-level assembly of the common vetch ( Vicia sativa) reference genome. Gigabyte https://doi.org/10.46471/gigabyte.38 (2022). Approximately 79% of the Hedin/2 assembly was annotated as transposon-derived (Supplementary Table 8). By far, the largest group is the LTR retrotransposons (RLX), accounting for 63.7% of the genome sequence. Other groups of TEs represent only minor fractions of the genome (Supplementary Table 8). Among the RLX, those of the Gypsy (RLG) superfamily outnumber Copia (RLC) elements by more than 2:1 (Fig. 1d and Extended Data Fig. 3). The Ogre family of Gypsy elements alone make up almost half (44%) of the genome, confirming its status as a major determinant of genome size in the Fabaceae 18 (Fig. 2f). The great length of individual elements (up to 35 kb for Ogre and 32 kb of SIRE, the longest and second-longest elements, respectively), together with their abundance, partially explains the large size of the faba bean genome (Supplementary Fig. 5). In addition, a large and diverse set of satellite repeat families that differ in their monomer sequences and genome abundance 31 accounted for 9.4% of the total assembly length, with the most abundant satellite family FokI representing 4% (0.475 Gb). FokI, together with several other highly amplified satellites, forms prominent heterochromatic bands on faba bean chromosomes (Fig. 1c). The TE density was remarkably invariable along all six chromosomes, mirroring gene density and recombination rate, and inverse to the density of satellite arrays (Fig. 1d and Extended Data Fig. 3).