Marl├ętaz et al., 2018 - Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature   564:64-70 Full text @ Nature

Fig. 1

a, Summary of the 94 amphioxus samples generated in this study, comprising eight functional-genomic datasets. The number of biological replicates is indicated for each sample type. div., diverticulum; MethylC/RRBS, methylC sequencing and reduced representation bisulfite sequencing; Premet., premetamorphic. b, Genome browser excerpt showing a selection of available tracks, including gene annotation, sequence conservation (using phastCons), repeats and several epigenomic and transcriptomic datasets. Green rectangle highlights the APRE tested in ec, Numbers and proportions of amphioxus and zebrafish APREs according to their genomic location. Promoters, within 1-kbp upstream and 0.5-kbp downstream of an annotated TSS; gene body, within an orthology-supported gene; proximal, within 5-kbp upstream of (but not overlapping with) a TSS; distal, not in the aforementioned categories. d, Cumulative distributions of the distance between each APRE and the closest annotated TSS in each species. e, Lateral view of a representative transgenic zebrafish 26-hpf embryo showing GFP expression driven by an amphioxus APRE associated with Pax1/9 (‘Pax1/9-126’, highlighted in b) in pharyngeal arches (PA; n = 4/4). Positive-control enhancer was expressed in the midbrain (MB). Scale bar, 250 μm

Fig. S9

In situ hybridization assays for specialized zebrafish families In situ hybridization for multiple amphioxus stages for 11 genes whose zebrafish orthologous family has undergone specialization of at least one member. Only the positive control (Mlc, bottom) showed clearly restricted expression in amphioxus. The experiment was performed once, using 10 embryos per probe, all of which showed the same pattern for each distinct probe. In situ hybridization data for zebrafish was obtained from Zfin, with the exception of Kif5 genes 133 and the Atl strongly specialized ohnolog atl1 134, which have been reported before and are not shown here

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