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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 the corresponding headers of the FASTA file in the second column of the file:
    GH27_QRW17738.1_taxa.txt
    Rhizoctonia solani    >GH27_QRW17738.1|RHISO@456999@016906535_1|XP_043177975.1|1
Aspergillus oryzae    >GH27_QRW17738.1|ASPOR@510516@000184455_2|XP_001820370.1|1
Trichomonas vaginalis    >GH27_QRW17738.1|TRIVA@412133@000002825_2|XP_001315888.1|1
Cordyceps militaris    >GH27_QRW17738.1|CORMI@983644@000225605_1|XP_006673409.1|1
Bradysia coprophila    >GH27_QRW17738.1|BRACO@38358@014529535_1|XP_037033872.1|1
Hydra vulgaris    >GH27_QRW17738.1|HYDVU@6087@000004095_1|XP_002159485.2|1
Notolabrus celidotus    >GH27_QRW17738.1|NOTCE@1203425@009762535_1|XP_034555657.1|1
Homo sapiens    >GH27_QRW17738.1|HUMAN@9606@000001405_39|NP_000160.1|1
  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    >GH28_QRW23661.1|SPOLI@69820@002706865_1|XP_022836218.1|1
Rhizoctonia solani    >GH28_QRW23661.1|RHISO@456999@016906535_1|XP_043183898.1|1
Rhagoletis zephyria    >GH28_QRW23661.1|RHAZE@28612@001687245_1|XP_017491101.1|1
Bradysia coprophila    >GH28_QRW26843.1|BRACO@38358@014529535_1|XP_037032572.1|1
Protomyces lactucae-debilis    >GH28_QRW23661.1|PROLA@2754530@002105105_1|XP_040722516.1|1
Pyricularia oryzae 70-15    >GH28_QRW23661.1|PYROR@242507@000002495_2|XP_003719232.1|1
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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