Below are four allelic DNA sequences from a species of domes

Below are four allelic DNA sequences from a species of domestic ungulate (family Bovidae). Nucleotide positions are numbered 1 to 40 (numbers are written vertically) above the sequences. For example, nucleotide position 7 has a substitution (G) in sequence 2 and 4, which is different from the \"t\" in reference sequence 1.

(a) Build a parsimony network (as in Figures 16.12 and 16.14a) by hand by connecting the sequences based on their similarity at polymorphic nucleotide sites (in bold and capitals). The two circles (connected by a line) below the sequences are to get you started drawing the network. Circles represent sequences 1 and 3 and the line connecting the circles show the one substitution at base pair position 23 that exists between the two sequences (haplotypes) 1 and 3.

(b) Conduct a BLAST search (at http://www.ncbi.nlm.nih.gov/BLAST/) with sequence number 1, and identify the gene and species of origin of the sequence. Follow the link below and click on the \"nucleotide blast\" link. Change the database to \"nucleotide collection\" (this may already be the default), paste the sequence below into the large box at the top and click the \"BLAST\" button at the bottom of the page. Scroll down below the colored bars - the top sequence is the best match. Here is a copy of sequence number 1 that you can copy and paste into your BLAST search:

gagtattata agggcgagtg tcatttcttc aacgggaccg

Base pair position (1-40) 12 3 4 567 891 1111111112 222 222 2223 33 33333334 0 1234567890 1 2 3 4 567 890 123 45 67890 1) gagtattata agggagagtg tcatttctt C acgggaCCg 2) gagtatGcta agagogagtg Ecatttotta a accggacgg 3 gagtattata agggcgagtg tCTtttct t C aacgggaCCg 4) gagt at agAgcgagtg toatt t Gttc aacgggacgg 23 13

Solution

b) gagtattata agggcgagtg tcatttcttc aacgggaccg

Gene: Ovis aries clone IM4189 MHC class II antigen (DRB1) mRNA, complete cds

gagtatgcta agagcgagtg tcatttcttc aaccggacgg

Gene: Ovis aries clone IM5628 MHC class II antigen (DRB1) mRNA, complete cds

gagtattata agggcgagtg tcttttcttc aacgggaccg

No significant gene sequence is found in NCBI blast

gagtatgcta agagcgagtg tcatttgttc aacgggacgg

no significant gene similarity found in NCBI blast