Trifolium repens (DRAFT) White Clover

We try to follow a historical path regarding white clover, which was introduced by settlers in the 17th century and is now widespread throughout the USA. What happens when comparing genomes nowadays? What is the genomic difference between a plant in West London and a plant growing in Gainesville, Florida, in the USA?

Both genomes are > 98% identical. But we can identify an editing pattern in the promoter region of an RNA polymerase to illustrate what could be functionally different.

On this 38 kb DNA strand of Chromosome, four protein-coding genes are aligned. We first have an RNA polymerase, followed by a growth regulator factor, an RNA polymerase II subunit, and finally an R2R3MYB14-like factor. A few mutations are observed when comparing the two strands across these 38 kilobases (A). The ultimate exception lies in the promoter region of the RNA polymerase. On a short strand of 451 base pairs (B), an enlargement of STRs under (A), six STRs are apparent: polyA, polyT, polyCT, polyAT, polyATG, which differ in length, indicating that a regulatory event has taken place with respect to the introduced plants in the USA. Furthermore, we realize that these genomes have dynamic properties that reach their own steady state over time.

Upon reviewing the slides, one might see that these STRs (T.repens) vary widely in length and that there is no clear correlation between their lengths and geographic coordinates. It looks like a regulatory code independent of regular inheritance. We also note that this 38 kb strand is located on chromosome 8, 15, or 16, depending on the sample taken. It seems that chromosomes are just containers for information, but their load and arrangement can change quickly! We also added reads from 3 T. pratense genomes covering the same locus, along with others.

 (rolfy April-'26)