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Gene trees and homologues in Sus scrofa (Pig) breeds

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Gene trees and homologues in Sus scrofa (Pig) breeds

We are going to look at the PLAG1 gene in the pig reference (Sscrofa11.1) genome and explore its gene tree and homologues.

  1. Have orthologues been identified in any pig breeds? If so, which ones?

  2. Open the cDNA sequence alignment against the Tibetan breed. What does the asterisk (*) symbol mean in the alignment? What is the % identity (cDNA) and what does the number stand for?

  3. Let’s look at the PLAG1 breed gene tree. How many genes are depicted in the gene tree? According to the gene tree, which orthologue is the most closely related to the pig reference PLAG1 gene? What is the Ensembl ID of the orthologue and what strand is it located on?

  4. Export the gene tree in Newick format.

  1. Open the Gene tab for the PLAG1 gene (ENSSSCG00000006247) in the pig reference (Sscrofa11.1) genome. In the left-hand panel, click on Comparative Genomics: Breeds: Orthologues to explore orthologues in pig breeds.

    PLAG1 orthologues have been identified in all 12 available pig breeds: Bamei, Berkshire, Hampshire, Jinhua, Large white, Meishan, Pietrain, Rongchang, Tibetan, Wuzhishan and USMARC.

  2. Stay in the Comparative Genomics: Breeds: Orthologues page and look for the Pig - Tibetan entry in the Orthologues table. Click on View Sequence Alignments and select View cDNA Alignment in the pop-up menu. This will lead you to the sequence alignment between the pig reference PLAG1 gene and the orthologue in the Tibetan breed. Click on the ? icon above the alignment to open the corresponding help page and find a description of the data (including descriptions of the conservation codes and summary statistics).

    The alignment is in ClustalW format and the asterisk (*) is a conservation code that denotes the aligned nucleotides are identical in both sequences.

    In the **Type: 1-to-1 orthologues table, look for the column **% identity (cDNA).

    The % identity (cDNA) describes the number of identical nucleotides between the two sequences in the alignment. The % identity (cDNA) between the pig reference and the Tibetan breed is 99%, meaning 99% of the cDNA sequence alignment is identical.

  3. In the left-hand panel, click on Comparative Genomics: Breeds: Gene tree. Above the gene tree image, you can find some summary statistics.

    There are 16 genes in the gene tree.

    In the gene tree, look for PLAG1, Pig (coloured in red) in the tree and find the closest branch.

    The most closely related orthologue is the PLAG1 gene in the Berkshire breed. Clicking on PLAG1, Pig - Berkshire opens more details on the orthologue including the Ensembl ID (ENSSSCG00065079212) and strand (reverse).

  4. Click on the Export button at the top of the gene tree image. In the pop-up menu, select File format: Newick (you can find a preview of each file format underneath) and Preview the file on your browser.