compgenomics:modul5

Biodiverse genome assemblies

How do we explain the sporadic presence of orthologs in a clade?

Assumption: All detected genes are encoded in the genome of the respective species

Analysis

In this module, we will analyse the orthologs of the GH28 glycosyl hydrolase in the two invertebrates Bradysia coprophila and Spodoptera litura in more detail.

Task 1: Spodoptera litura

Find the NCBI accession ID of the GH28_QRW23661.1 in Spodoptera litura using the interactive webviewer

Spoiler

Spoiler

XP_022836218.1
Perform a BLASTp search against the “Non-redundant protein sequences (nr)” database
Take a look at the list of best hits. Which taxonomic clade do they represent?

Task 2: Bradysia coprophila

Repeat the analysis with the GH28_QRW23661.1 ortholog in Bradysia coprophila

Spoiler

Spoiler

https://www.ncbi.nlm.nih.gov/protein/XP_037031340.1

Summary and Discussion

Note down your observation and discuss with the group

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