diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/variant/Variant.java b/biodata-models/src/main/java/org/opencb/biodata/models/variant/Variant.java
index <HASH>..<HASH> 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/variant/Variant.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/variant/Variant.java
@@ -174,7 +174,14 @@ public class Variant {
         if (chromosome == null || chromosome.length() == 0) {
             throw new IllegalArgumentException("Chromosome must not be empty");
         }
-        this.chromosome = chromosome.replaceAll("chrom|chrm|chr|ch", "");
+        // Replace "chr" references only at the beginning of the chromosome name
+        // For instance, tomato has SL2.40ch00 and that should be kept that way
+        if (chromosome.startsWith("chrom") || chromosome.startsWith("chrm")
+                || chromosome.startsWith("chr") || chromosome.startsWith("ch")) {
+            this.chromosome = chromosome.replaceFirst("chrom|chrm|chr|ch", "");
+        } else {
+            this.chromosome = chromosome;
+        }
     }
 
     public int getStart() {
Replace 'chr' and derivatives only when they are at the beginning of the chromosome name