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Reconstructing evolutionary history

Can I infer the past from present day observations?

Assumption 1: Genes are passed on vertically from ancestor to offspring

Assumption 2: A gene is not invented twice

Analysis

In this exercise, we will extract the sequences of a subset of orthologs for two PCD gene families from our interactive webtool. We will align these sequences and calculate a phylogenetic tree. This tree will then help us to better understand the evolutionary history of the gene family

Task 1: GH27_QRW17738.1

  1. Download the data from the interactive webviewer using this link: https://applbio.biologie.uni-frankfurt.de/download/cellulase_pp_data.tar.gz
  2. Unpack the data using tar -zxvf cellulase_pp_data.tar.gz
  3. You will find the sequences in the file cell_wall.extended.fa in the extracted data directory
  4. Extract the sequences of GH27_QRW17738.1 orthologs for the following taxa. You find their five letter codes in the header of the Fasta file:
    GH27_QRW17738.1_taxa.txt
    Rhizoctonia solani|RHISO
Aspergillus oryzae|ASPOR
Trichomonas vaginalis|TRIVA
Cordyceps militaris|CORMI
Bradysia coprophila|BRACO
Hydra vulgaris|HYDVU
Notolabrus celidotus|NOTCE
Homo sapiens|HUMAN
  5. Align the sequences using ClustalOmega
  6. Inspect the distance tree generated by ClustalOmega. What can you learn?

Task 2: GH28_QRW23661.1

  1. Repeat the analysis using GH28_QRW23661.1 and the following taxon set:
    GH28_QRW23661.1_taxa.txt
    Spodoptera litura
Rhizoctonia solani
Rhagoletis zephyria
Bradysia coprophila (XP_037032572.1)
Protomyces lactucae-debilis
Pyricularia oryzae 70-15
Arcicela rosea (WP_367284634.1)

Summary and Discussion

  • Why are there plant cell wall degrading enzymes in animals?
  • Why is GH28 of Spodoptera litura identical to a bacterial sequence? What are the consequences given the assumptions stated above?

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