diff --git a/augur/data/schema-annotations.json b/augur/data/schema-annotations.json
index 7e09b9b0e..406978991 100644
--- a/augur/data/schema-annotations.json
+++ b/augur/data/schema-annotations.json
@@ -6,21 +6,47 @@
         "nuc": {
             "type": "object",
             "allOf": [{ "$ref": "#/$defs/startend" }],
+            "properties": {
+                "strand": {
+                    "type": "string",
+                    "not": {"enum":["-"]},
+                    "$comment": "Auspice assumes +ve strand for 'nuc', but will not proceed if you specify '-'"
+                }
+            },
             "additionalProperties": true,
-            "$comment": "All other properties are unused by Auspice. Strand is always considered to be positive."
+            "$comment": "All other properties are unused by Auspice."
         }
     },
     "required": ["nuc"],
     "patternProperties": {
-        "^[a-zA-Z0-9*_-]+$": {
+        "^(?!nuc)[a-zA-Z0-9*_-]+$": {
+            "$comment": "Each object here defines a single CDS",
             "type": "object",
-            "allOf": [{ "$ref": "#/$defs/startend" }],
+            "oneOf": [{ "$ref": "#/$defs/startend" }, { "$ref": "#/$defs/segments" }],
             "additionalProperties": true,
+            "required": ["strand"],
             "properties": {
+                "gene": {
+                    "type": "string",
+                    "description": "The name of the gene the CDS is from. Optional.",
+                    "$comment": "Shown in on-hover infobox & influences default CDS colors"
+                },
                 "strand": {
-                    "description": "Is the gene on the positive ('+') or negative ('-') strand.",
+                    "description": "Is the CDS on the positive ('+') or negative ('-') strand.",
                     "$comment": "Auspice assumes positive strand unless strand is '-'",
                     "type": "string"
+                },
+                "color": {
+                    "type": "string",
+                    "description": "A CSS color or a color hex code. Optional."
+                },
+                "display_name": {
+                    "type": "string",
+                    "$comment": "Shown in the on-hover info box"
+                },
+                "description": {
+                    "type": "string",
+                    "$comment": "Shown in the on-hover info box"
                 }
             }
         }
@@ -41,6 +67,25 @@
                     "description": "End position (one-based, following GFF format). This value _must_ be greater than the start."
                 }
             }
+        },
+        "segments": {
+            "type": "object",
+            "required": ["segments"],
+            "properties": {
+                "segments": {
+                    "type": "array",
+                    "items": {
+                        "type": "object",
+                        "allOf": [{ "$ref": "#/$defs/startend" }],
+                        "properties": {
+                            "name": {
+                                "type": "string",
+                                "$comment": "Displayed for the individual CDS segment"
+                            }
+                        }
+                    }
+                }
+            }
         }
     }
 }