Scripts, manuscript and results from extension of Summer Scholarship work on Epichloe. Utilising Epichloe Amarillans and Epichloe Bromicola data, analysing lineage specific genes. See R manuscript for description of results and full code with annotation

1. Lineage specific genes (LSG) are isolated as potenital sources of lineage-specific evolutoon, formation of new genes or increased evoltuionary rate.

2. The length of proteins produced is isolated. If LSG are much shorter than non-lineage speciifc genes they may be ‘new’ genes.

3. The distnace of LSG to the nearest ATrich repeat region is measured to determine potential of gene production.

4. Quantification of genes is carried out in datasets with RNAseq data ( amarillans ) to determine expression of LSG.

5. Gene ID, lineage specificity, length, TPM, and distance to AT regions is tabulated.

6. GO functional annotation of LSG is carried out and displayed in a seperate table to confer potential functions of new or altered genes.

7. Data is statsitically and graphically analysed.

8. This project has huge opportunity for further study.