Brent Cornell

    
The number of genes present in an organism will differ between species and is not a valid indicator of biological complexity

The number of genes in a genome is usually predicted by identifying sequences common to genes

• These identifying regions may include expressed sequence tags (ESTs) or sequences that are homologous to known genes
• The presence of pseudogenes and transposons make accurate counts of unique gene numbers very difficult

As scientists may use different approaches to predicting gene numbers, final estimations can vary significantly 

• For instance, the number of genes in rice (Oryza sativa) is estimated as being between 32,000 – 50,000
• The number of genes in humans is estimated as being between 19,000 – 25,000

Gene Comparisons Between Different Species

    
Gene sequences from different species can be identified and then compared using two online resources:

• GenBank – a genetic database that serves as an annotated collection of DNA sequences
• Clustal Omega – an alignment program that compares multiple sequences of DNA

Identifying Gene Sequences

GenBank can be used to identify the DNA sequence for a gene in a number of different species

To identify a specific gene sequence:

• Change the search parameter from nucleotide to gene and type in the name of the gene of interest
• Choose the species of interest and click on the link (under ‘Name / Gene ID’)
• Scroll to the ‘Genomic regions, transcripts and products’ section and click on the ‘FASTA’ link

Below are examples of different genes that may be searched for:

• HBB  –  Haemoglobin beta gene
• COX1  –  Cytochrome oxidase 1 gene
• F8  –  Coagulation factor VIII gene
• IGF1R  –  Insulin growth factor 1 receptor gene

Comparing Gene Sequences

Clustal Omega aligns multiple gene sequences to allow for the determination of differences in the base sequence

To construct a multiple alignment:

• Change the input sequence type to DNA and paste the relevant FASTA sequences into the provided space
• Before each sequence designate a species name preceded by a forward arrow (e.g. '>Human’ or ‘>Chimpanzee’)
• Alternatively, sequences can be saved as a document in plain text format (.txt) and then uploaded
• When all sequences have been included, click ‘Submit’ (under step 3)

Clustal Omega possesses several useful features that are absent in alternative tools like BLASTN:

• Multiple (more than two) sequences can be compared at once
• Sequence consensus is colour coded in a Jalview applet found under ‘Result Summary’ (requires Java)
• Branched phylograms can be generated to show evolutionary relationships (under ‘Phylogenetic Tree’)

Below is a plain text file that can be uploaded to compare gene sequence fragments from different species:

• CHRNE  –  Cholinergic receptor epsilon (nicotinic) for various species

Sequence Alignment of DNA from Two Species