(a) Phylogenetic tree built from 147 single copy orthologues (left; numbers at nodes indicate bootstrap support), and a histogram of introns present at 29,447 conserved positions identified by the software package Malin (right). (b) Phylogenetic tree with branch lengths labeled and scaled to the intron loss rate calculated by Malin. The unedited tree in both panels is given in Figure 2—figure supplement 3, and was, together with 2371 orthologous protein clusters (Supplementary file 2), used as input for Malin. (c) Alignment of A. lycopersici aculy03g01320 (which encodes an ADP-ribosylation factor-like 8, or Arl8, protein) with single copy orthologues from five other mite and insect species as indicated. Analogous positions of phase 0, 1, and 2 introns are denoted by colored triangles (legend, bottom right), with amino acids at the analogous intronic positions indicated beneath (identity, similarity, and non-similarity are indicated by ‘*', ‘:', and ‘.', respectively, for aculy03g01320 and its orthologue from D. pteronyssinus, the most closely related genome; in descending order, the sequence identifiers are aculy03g01320.1, g8154.t1, tetur10g00460, rna18006, BGIBMGA010943-RA, and FBtr0339723). The letter ‘E’ indicates that this intron position is conserved across other model organisms in Eukaryota; Dictyostelium purpureum (GenBank Accession XM_003283650), C. elegans (NM_070390.9), H. sapiens (NM_018184.3), Monosiga brevicollis (XM_001744342.1), and A. thaliana (NM_114847.5). (d) Local protein alignment, after panel c, revealing a candidate imprecise intron loss event in aculy04g10480 (which encodes a polymerase delta-interacting protein) in A. lycopersici (insertion of S and N amino acid residues, top). Numbers denote positions in the A. lycopersici orthologue; sequence identifiers, in descending order, are aculy04g10480.1, g5664.t1, tetur01g12540, rna9399, BGIBMGA013121-RA, and FBtr0078681. Panels (c) and (d) are drawn based on Malin output. Other findings for intronic features and factors contributing to A. lycopersici’s genome reduction, and the supporting analyses, are presented in Figure 2—figure supplements 1, 2, 4, 5 and 6.