Figure 1.
Species and genes included in this study.
Phylogenetic relationship of the five studied species. Numbers represent relative conservation of protein sequences (compared to C. elegans) based on the BLOSUM matrix.
Figure 2.
Functional conservation and divergence of unc-46 regulation.
(A) Vista plots represent primary sequence conservation in the intergenic region upstream of unc-46, relative to C. elegans. Window size = 20 bp, threshold: 70%. From top to bottom: C. briggsae, C. remanei, C. brenneri, C. japonica. (B) Expression patterns driven by the C. elegans (Cel), C. briggsae (Cbr), C. remanei (Cre), C. brenneri (Cbn), and C. japonica (Cja) CREs of unc-46. For all cells, frequency of expression is indicated, except for D-type neurons for which the median number of expressing cells in shown. For groups of multiple cells, percentages represent frequency of expression in at least one of these cells: RMEs(RMED/V/L/R), SIADs (SIADL/R), OLQDs (OLQDL/R), Lat. gang. (unidentified pair of neurons in the lateral ganglion), HSNs (HSNL/R). Detailed data are shown in Table S3.
Figure 3.
Functional conservation and divergence of acr-14 regulation.
(A) Vista plots represent primary sequence conservation in the intergenic region upstream of acr-14, relative to C. elegans. Window size = 20 bp, threshold: 70%. From top to bottom: C. briggsae, C. remanei, C. brenneri, C. japonica. (B) Expression patterns driven by the C. elegans (Cel), C. briggsae (Cbr), C. remanei (Cre), C. brenneri (Cbn), and C. japonica (Cja) CREs of acr-14. For all cells, frequency of expression is indicated, except for the ventral nerve cord (VNC) for which the median number of expressing cells in shown. For groups of multiple cells, percentages represent frequency of expression in at least one of these cells: AVAs (AVAL/R), AFDs (AFDL/R), CEPs (CEPD/V L/R), AVns (AVHL/R or AVJL/R or AVDL/R), PVNs (PVNL/R). Reductions of expression compared to the endogenous pattern are circled. Detailed data are shown in Table S4.
Figure 4.
Functional conservation and divergence of unc-47 regulation.
(A) Vista plots represent primary sequence conservation in the intergenic region upstream of unc-47, relative to C. elegans. Window size = 20 bp, threshold: 70%. From top to bottom: C. briggsae, C. remanei, C. brenneri, C. japonica. (B) Expression patterns driven by the C. elegans (Cel), C. briggsae (Cbr), C. remanei (Cre), C. brenneri (Cbn), and C. japonica (Cja) CREs of unc-47. For all cells, frequency of expression is indicated, except for D-type neurons for which the median number of expressing cells in shown. For groups of multiple cells, percentages represent frequency of expression in at least one of these cells: RMEs (RMED/V/L/R), SIADs (SIADL/R), CEPs (CEPD/V L/R), SDQs (SDQL/R), PVNs (PVNL/R). It is unclear whether expression in the SIADs is endogenous [56], [57], [68]. However, since it is consistently seen with the C. elegans CRE, we included it in the endogenous pattern. We classified the strong expression of the C. briggsae unc-47 CRE in SDQL/R as ectopic, even though weak SDQR expression was observed with the C. elegans CRE, because of the dramatic differences in the frequency and intensity of expression [22]. Reduction and losses of expression compared to the endogenous pattern are circled. Detailed data are shown in Table S5.
Figure 5.
Functional conservation and divergence of kat-1 regulation.
(A) Vista plots represent primary sequence conservation in the intergenic region upstream of kat-1, relative to C. elegans. Window size = 20 bp, threshold: 70%. From top to bottom: C. briggsae, C. remanei, C. brenneri, C. japonica. (B) Expression patterns driven by the C. elegans (Cel), C. briggsae (Cbr), C. remanei (Cre), C. brenneri (Cbn), and C. japonica (Cja) CREs of kat-1. Frequency of expression in different tissues is shown: Pha. (pharynx), Int. (intestine), Gon. sheath (gonadal sheath), Head musc. (head muscles), Hypod. (hypodermis), Head neur. (head neurons), VNC (ventral nerve cord). Losses of expression compared to the endogenous pattern are circled. Detailed data are shown in Table S6.
Figure 6.
Functional conservation and divergence of unc-25 regulation.
(A) Vista plots represent primary sequence conservation in the intergenic region upstream of unc-25, relative to C. elegans. Window size = 20 bp, threshold: 70%. From top to bottom: C. briggsae, C. remanei, C. brenneri, C. japonica. (B) Expression patterns driven by the C. elegans (Cel), C. briggsae (Cbr), C. remanei (Cre), C. brenneri (Cbn), and C. japonica (Cja) CREs of unc-25. For all cells, frequency of expression is indicated, except for D-type neurons for which the median number of expressing cells in shown. For groups of multiple cells, percentages represent frequency of expression in at least one of these cells: RMEs (RMED/V/L/R), SIADs (SIADL/R). Detailed data are shown in Table S7.
Figure 7.
Functional conservation and divergence of gpa-5 regulation.
(A) Vista plots represent primary sequence conservation in the intergenic region upstream of gpa-5, relative to C. elegans. Window size = 20 bp, threshold: 70%. From top to bottom: C. briggsae, C. remanei, C. brenneri, C. japonica. (B) Expression patterns driven by the C. elegans (Cel), C. briggsae (Cbr), C. remanei (Cre), and C. brenneri (Cbn) CREs of gpa-5. For all cells, frequency of expression is indicated. For groups of multiple cells, percentages represent frequency of expression in at least one of these cells: AWAs (AWAL/R), MCs (MCL/R), PVNs (PVNL/R), PVQs (PVQL/R). Reductions of expression compared to the endogenous pattern are circled. Detailed data are shown in Table S8.
Figure 8.
Functional conservation and divergence of oig-1 regulation.
(A) Vista plots represent primary sequence conservation in the intergenic region upstream of oig-1, relative to C. elegans. Window size = 20 bp, threshold: 70%. From top to bottom: C. briggsae, C. remanei, C. brenneri, C. japonica. (B) Expression patterns driven by the C. elegans (Cel), C. briggsae (Cbr), C. remanei (Cre), C. brenneri (Cbn), and C. japonica (Cja) CREs of oig-1. For all cells, frequency of expression is indicated, except for D-type neurons for which the median number of expressing cells in shown. For groups of multiple cells, percentages represent frequency of expression in at least one of these cells: Head neurons (large cluster of head neurons, including ALAL/R, SMDVL/R, RMDVL/R, RIAL/R, AVAL/R, RIML/R, RMDDL/R and IL1s), PVCs (PVCL/R), ADEs (ADEL/R), HSNs (HSNL/R), PDEs (PDEL/R). Reductions and losses of expression compared to the endogenous pattern are circled. Detailed data are shown in Table S9.
Figure 9.
Functional conservation and divergence of mod-5 regulation.
(A) Vista plots represent primary sequence conservation in the intergenic region upstream of mod-5, relative to C. elegans. Window size = 20 bp, threshold: 70%. From top to bottom: C. briggsae, C. remanei, C. brenneri, C. japonica. (B) Expression patterns driven by the C. elegans (Cel), C. briggsae (Cbr), C. remanei (Cre), and C. brenneri (Cbn) CREs of mod-5. For all cells, frequency of expression is indicated. For groups of multiple cells, percentages represent frequency of expression in at least one of these cells: ADFs (ADFL/R), AIMs (AIML/R). Losses of expression compared to the endogenous pattern are circled. Detailed data are shown in Table S10.
Figure 10.
Recurrent “gains” of expression by different CREs.
CREs of acr-14 from C. brenneri (Figure 3B) and unc-47 from C. japonica (Figure 4B) drive expression in CEP neurons in the head. CREs of unc-46 from C. brenneri and C. japonica (Figure 2B) and oig-1 from C. briggsae, C. remanei and C. brenneri (Figure 8B) drive expression in HSN neurons in the mid-body. CREs of acr-14 from C. remanei (Figure 3B) and unc-47 from C. japonica (Figure 4B) drive expression in PVN neurons in the tail.