Extended Data Figure 5: Annotation of repeats and non-coding RNA genes.
From: The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

a, Repeat content of the sugar beet genome assembly. A total of 252 Mb (42.3%) of the genome assembly consist of repetitive DNA with retrotransposons as the most abundant repeat fraction. All major superfamilies of DNA transposons were represented, showing a dispersed or slightly centromere-enriched distribution along the chromosomes. Microsatellites and minisatellites were well represented owing to flanking heterogeneous sequences, which allowed their assembly. The remaining repetitive sequences (‘Unknown’) in 459 families represent potentially new repeats, most likely rearranged or truncated retrotransposons. b, Summary of non-coding RNA gene annotations. For different classes (miRNA, microRNA; rRNA, ribosomal RNA; snRNA, spliceosomal RNA; snoRNA, small nucleolar RNA; tRNA, transfer RNA) the number of predictions, the number and percentage of predictions with overlapping small RNA reads, and the number of families/subtypes are listed. c, Proportion of annotated tRNAs by amino acid for the five species studied (At, Arabidopsis thaliana; Pt, Populus trichocarpa; Bv, Beta vulgaris; Vv, Vitis vinifera; Zm, Zea mays). d, Absolute numbers of annotated tRNAs by amino acid. Except for pseudogenes the proportion of tRNAs is relatively constant among all species (species names as in c). e, Number of annotated tRNAs by amino acid and species (as predicted by tRNAscan-SE). The total is computed without the last two rows containing pseudogenes and presumably defunct tRNAs with undetermined anti-codon. f, Number and size of Beta vulgaris gene clusters of at least 10 members representing expanded gene families. A total of 1,274 genes are contained in 97 clusters.