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. 2019 Feb 15;8:e41556. doi: 10.7554/eLife.41556

Figure 6. Members of a lineage-specific expansion of Ependymin-related proteins are subject to circalunar regulation on RNA and protein level.

(a) Unrooted maximum likelihood phyolgenetic tree of Ependymin-related proteins based on the analysis published by Suárez-Castillo and García-Arrarás, 2007 including eleven of 15 Platynereis Ependymin-related proteins (ERP4.1–4.10; ERP3; blue boxes) and various additional invertebrate Ependymin sequences. The phylogeny reveals four distinct groups of Ependymin-related proteins (ERP) that are termed ERP1, ERP2, ERP3/4 and fish-specific ERPs; group-specific expansions of ERPs is observed at several places in the phylogeny. All identified Platynereis Ependymins (blue) fall into the ERP3/4 clade. A full tree with un-collapsed nodes, the alignment, NCBI accession numbers and the Platynereis sequence identifiers are provided in Figure 6—figure supplement 1 and Figure 6—source datas 1 and 2. (b,b’) Protein and RNA-Seq expression profiles validate Platynereis ERP4.9 as a new target of circalunar phase on RNA and protein level. (b) Normalised protein expression profile; (b’) DESeq2 normalised RNA expression profile. The graphs show the arithmetic mean with standard deviation, together with individual data points. (c–e) RNA expression pattern of erp4.9 in immature adult Platynereis heads. a.e.: anterior eye; p.e.: posterior eye; n.o.: nuchal organ. (c) Dorsal view, anterior to the top. Characteristic expression is observed around the dorsal blood vessel (central arrow), anterior of the nuchal organ (arrowheads) and next to the anterior eyes (arrows). Scale bar: 250 µm. (d) Dorsal view of the base of a prostomial cirrus, scale bar: 50 µm. (e) Ventral view, anterior to the top. Expression is observed in a plate-like structure at the bottom of the head, as well as around the mouth opening (arrows) and the palps (arrow heads). Scale bar: 250 µm. For additional circalunar-regulated ERPs see Figure 6—figure supplement 2 and Figure 5—source datas 16 and 17.

Figure 6—source data 1. Ependymins alignment.
Fasta-file containing the ependymin protein alignement; used for the ERP trees in Figs. 6 and Figure 6-figure supplement 1.
elife-41556-fig6-data1.txt (74KB, txt)
DOI: 10.7554/eLife.41556.074
Figure 6—source data 2. Ependymins alignment sequence IDs/accession numbers.
Table containing the TS_v5 IDs for the Platynereis Ependymins as well as the NCBI IDs for the other ERPs.
elife-41556-fig6-data2.csv (27.8KB, csv)
DOI: 10.7554/eLife.41556.075

Figure 6.

Figure 6—figure supplement 1. Maximum likelihood phylogeny of Ependymin-related proteins using the same alignment and settings as in Figure 6a.

Figure 6—figure supplement 1.

For better visibility, the tree is shown as rooted at the split between ERP group one and ERP group 2. Platynereis sequences are labelled with a systematic nomenclature following the apparent phylogeny, all other entries are labelled with genus_and Accession-Number. For cases in which translated (tr) genomic regions were initially used, two accession numbers are given.
Figure 6—figure supplement 2. ERP4.10 is regulated in both protein and RNA expression by circalunar phase.

Figure 6—figure supplement 2.

(a,b) Normalised values for abundance of ERP4.10 on protein (a) and RNASeq (b) level. (c–c’’) Results of a whole mount in-situ hybridisation on immature Platynereis heads. a.e.: anterior adult eye; p.e.: posterior adult eye; n.o.: nuchal organ. (c) Dorsal view, anterior to the top. Characteristic expression is observed around the dorsal blood vessel (central arrow), anterior of the nuchal organ (arrow heads) and next to the anterior adult eyes (arrows). Scale bar: 250 µm. (c’) Ventral view, anterior to the top. Expression is observed in a plate-like structure at the bottom of the head. Scale bar: 250 µm. (c’’) Dorsal view of cirrus; Scale bar: 50 µm.