PEG10 (paternally expressed gene 10) is a paternally expressed gene (meaning only the paternal allele is expressed) that has an essential role in the formation of the placenta of the mouse. In the mouse genome, the PEG10 gene is flanked by the SGCE and PPP1R9A genes. To study the origin of PEG10, you examine syntenic regions spanning the SGCE and PPP1R9A loci in the genomes of several vertebrates, and you note that the PEG10 gene is present in the genomes of placental and marsupial mammals but not in the platypus, chicken, or fugu genomes.
The green bars in the figure indicate the exons of each gene. The gray bars represent LINEs and SINEs, and the blue bars represent long terminal repeat (LTR) elements of retrotransposons. Solid black diagonal lines link introns, and dashed black lines connect orthologous exons. Arrowheads indicate the direction of transcription.
Using the predicted protein sequence of PEG10, you perform a tblastn search for homologous genes and find that the most similar sequences are in a class of retrotransposons (the sushi-ichi retrotransposons). Propose an evolutionary scenario for the origin of the PEG10 gene, and relate its origin to its biological function.

Question

PEG10 (paternally expressed gene 10) is a paternally expressed gene (meaning only the paternal allele is expressed) that has an essential role in the formation of the placenta of the mouse. In the mouse genome, the PEG10 gene is flanked by the SGCE and PPP1R9A genes. To study the origin of PEG10, you examine syntenic regions spanning the SGCE and PPP1R9A loci in the genomes of several vertebrates, and you note that the PEG10 gene is present in the genomes of placental and marsupial mammals but not in the platypus, chicken, or fugu genomes.

The green bars in the figure indicate the exons of each gene. The gray bars represent LINEs and SINEs, and the blue bars represent long terminal repeat (LTR) elements of retrotransposons. Solid black diagonal lines link introns, and dashed black lines connect orthologous exons. Arrowheads indicate the direction of transcription.

Using the predicted protein sequence of PEG10, you perform a tblastn search for homologous genes and find that the most similar sequences are in a class of retrotransposons (the sushi-ichi retrotransposons). Propose an evolutionary scenario for the origin of the PEG10 gene, and relate its origin to its biological function.

Comparative genomics illustration showing PEG10 gene location and synteny across various vertebrate genomes.

Accepted Answer

Hi, everybody. Let's look at the next question. Suppose you want to investigate a specific locus and the region of similarities in the DNA between genomes of two different species. If your information is protein sequences, which basic local alignment, search tool blast. Should you use a T blast? N B blast, X C nucleotide blast or D protein blast. So we're talking about a search tool blast, basic local alignment, search tool. And this is a tool available that allows you to find regions of local similarity between DNA or protein sequences by comparing them to sequence databases from all different species and calculating the statistical significance of the similarity. So being able to compare from these large databases and say is this similarity between the protein sequence or DNA sequence of these two different species statistically significant. And you can start with a protein sequence, start with a DNA sequence. You can compare it to the same thing or the search tool will convert your DNA sequence into a protein sequence and compare it to a protein sequences in its database or vice versa. So we know in our question, we are starting with protein sequences and we're looking at the genomes. So we're starting with protein and we want to compare it to DNA sequences. So we can go ahead and eliminate from our answer choices, choice C nucleotide blast. Because that involves comparing a nucleotide sequence to a database of nucleotide sequences. And likewise, we can eliminate choice D protein blast because that involves comparing protein sequence to protein sequence. So we just need to decide between A and B and what we are looking for here is choice A T blast N because that starts with T translated protein and compares it to a database of nucleotide sequences. Choice B blast X is the reverse. So blast X would involve starting with a nucleotide sequence and comparing it to a database of protein sequences. So if we are starting with protein sequence information, looking to compare genomes of two different species, then and we, if we want to use this blast tool, we would use choice A T blast and see you in the next video.

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Key Concepts

Paternally Expressed Genes

Synteny

Retrotransposons