Extended Data Fig. 1. Lineage specific OT-VT specializations.

a, Protein phylogenetic tree for VT in hagfish and lamprey relative to other vertebrates. Maximum likelihood amino acid phylogenetic tree generated via the Ensembl ‘Gene tree’ tool (gene tree identifier: ENSGT00390000004511) that uses the Gene Orthology/Paralogy prediction method pipeline. The longest available protein of each species was used. The tree is reconciled with a species tree, generated by TreeBeST. Left, red boxes, inferred gene duplication node; blue boxes, inferred speciation events; turquoise boxes, ambiguous nodes. Right, green bars, multiple amino acid alignment made with MUSCLE; white areas, gaps in the alignment; dark green bars, consensus alignments. We curated the tree and renamed genes using the universal nomenclature proposed in this Article. The tree with the current nomenclature used in the annotations of these genomes can be found at http://www.ensembl.org/Multi/GeneTree/Image?collapse=none;db=core;gt=ENSGT00390000004511. b, Triplication of the pale spear-nosed bat OT-VT region. An approximately10-gene window of synteny between human, megabat and pale spear-nosed bat is shown. In megabat, OT, VT and their syntenic genes are found in three different scaffolds (three boxes). In the pale spear-nosed bat with a higher-quality assembly, a syntenic triplication of the OT-VT region is found. c, gEVAL alignment analyses (https://geval.sanger.ac.uk/index.html). This panel shows gapless Pacbio-based long-read contigs (dark blue) and gapless Bionano optical maps (yellow), which span through the entire region with the OT and VT duplications in the pale spear-nosed bat, without any noticeable assembly errors.