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
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Lineage specific genes (LSG) are isolated as potenital sources of lineage-specific evolutoon, formation of new genes or increased evoltuionary rate.
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The length of proteins produced is isolated. If LSG are much shorter than non-lineage speciifc genes they may be βnewβ genes.
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The distnace of LSG to the nearest ATrich repeat region is measured to determine potential of gene production.
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Quantification of genes is carried out in datasets with RNAseq data ( amarillans ) to determine expression of LSG.
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Gene ID, lineage specificity, length, TPM, and distance to AT regions is tabulated.
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GO functional annotation of LSG is carried out and displayed in a seperate table to confer potential functions of new or altered genes.
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Data is statsitically and graphically analysed.
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This project has huge opportunity for further study.