Do apes and humans share 99% of DNA or 99% of genes? What is the difference?

Question

I made an answer on the Scifi.SE that can be read here. It is about how the characters in the story Jurassic Park might have gotten DNA for all the species shown.

In my answer, I said this:

Apes and Humans, for example, share over 99% of their genes. That means the difference between our species is less than 1% of our genes. In fact, all life on Earth shares about 50% of it's genes.

but in the original posting (before someone edited it) I chose to use the word DNA instead of genes.

He left this comment in the section to explain the edit:

Sorry, I'm a biologist, I can't help it. Humans and apes share 99% similarity in the coding sequences of their DNA, the ~5% that codes for genes, not on all the DNA. I simplified this to genes for the answer.

I have a basic high school understanding of DNA and genes, so I'm afraid I fail to see the difference between using "DNA" or using "genes" in my statement. I understand that genes are specific sequences of DNA that are used by the cell in some way. I understand that DNA is more generic, including all of the strands, whether they are used or not, whether they seem to code for something or not.

So is it wrong then to say that apes and humans share 99% of their DNA or is it equally correct to say "genes"?

Answer 1

So, a quick molecular biology lesson.

• Proteins are the things that make up a good percentage of our cells (which make up a good percentage of us), and are the things that do the work of the cells - many are catalysts and are known as "enzymes".

• Proteins are encoded by genes - while the statement that one gene codes for one protein is not quite correct (one gene can code for different variations of the same basic protein), it's a good way to think about things in this context.

• Genes are made up of DNA, a polymeric molecule that constitutes our chromosomes, the informational portion of which resides four “letters” (chemical bases).

• However, now we get to the key part — although all genes are made of DNA, not all the DNA of chromosomes makes up genes. In fact, as @terdon mentioned in a comment, only about 5% (or less) of the 4 billion letters in the total DNA — the genome — constitute genes - those sequences that
  directly code for protein.

• The function of the rest of the genome is not entirely clear. Some is regulatory, some may be structural, and may be “junk DNA”. However it’s stuck around for millions of years, so it we assume it must have some purpose. This non-coding DNA differs between species to a greater extent than the genes themselves do, so perhaps it somehow contributes to the differences between organisms.

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From AndroidPenguin

Here are the links to a paper about the function of "junk" DNA from 2013.

1. Summary in NY Times

2. Abstract in Nature

3. ENCODE threads on nature.com

Answer 2

Since it was my edit of your question that started all this, I may as well weigh in. I will give a simplified version of genes and gene transcription, there are various details that make the process much more complicated than what I will describe but they are not relevant to the basic question here.

First of all, as others have mentioned, genes are specific sequences of DNA. A gene's job is to "code for" a protein (first big simplification). However, not all of the gene codes for protein, only those parts of it called exons (image modified slightly from here):

The take home message from the image above is that the red bits (the introns) are removed and do not affect the final protein product. So, only part of the gene codes for the protein. Introns tend to be far less conserved between different species than exons.

Not only does the entire gene not code for protein but most of the genome does not contain genes. In fact, in humans, genes represent ~5% of the total DNA and exons represent ~2%.

Another confounding factor are the sequences called repetitive elements. These are various types of usually shortish sequences that exist in many copies in genomes, In the human genome ~41% consists of repetitive elements of various types, and ~10% represents copies of a single such element (Alu), that's twice as many as genes. Such repetitive elements are usually not considered when calculating whole genome similarity rates.

In terms of their entire genome, human and chimp are very very similar. However, the exact percentages vary (I've seen estimates from ~85 to ~90something) depending on the way the sequences are studied. To be on the safe side, you should say that they share 99% similarity at the gene level and leave it at that.

Answer 3

Just to clarify definitions, your genome is made up of sequences of DNA. DNA is constructed pairs of four nucleic acids, or nucleotides (A,G,T,C). That DNA has many loci within it, each codes for a gene. Loci are given gene names such as SHH (sonic hedgehog) which is part of a discipline called gene nomenclature. Humans have two versions of each gene, one from each parent. These genes, such as SHH, have different variants called alleles. This is where you may have heard the terms homozygote and heterozygote, when a person has two copies of the same allele or two different ones respectively. You may remember talking about sickle cell anemia in high school.

So is it wrong then to say that apes and humans share 99% of their DNA or is it equally correct to say "genes"?

Well the similarity between humans and chimps in terms of known DNA sequence is about 98.8%, there is fairly low sequence divergence, so in my opinion you are right to say that they share 99% of their DNA. This means that in 100 nucleotides there is roughly one difference e.g. (showing 90 bases, made using random sample of four letters in R):

Human DNA strand:

atgactgtagcccatga t gtaaacgtaccaagcctcctcggctgtcccgaaatagatacgcctggtagacgtattaatagtgagtaa...cgt

Chimpanzee:

atgactgtagcccatga c gtaaacgtaccaagcctcctcggctgtcccgaaatagatacgcctggtagacgtattaatagtgagtaa...cgt

Having said that, given that there is >3,000,000,000 base pairs in the human genome (the sequence of 4 nucleotides that make up the DNA) that equates to ~36,000,000 different base pairs (bnetween humans and chimps) which likely equates to a large difference. Sometimes even a single nucleotide polymorphism (SNP, pronounced snip), a change in just one base pair, can bring about quantifiable changes:

a single base mutation in the APOE (apolipoprotein E) gene is associated with a higher risk for Alzheimer disease.

Here is a little reading on the humans vs chimp. You may also wish to see this similar post on biology SE.

But the editor of your original post is right... only the Euchromatic region has been sequenced.

"Humans and apes share 99% similarity in the coding sequences of their DNA"

The euchromatic region is often thought of as the protein coding part of the DNA, and makes up 92% of the genome (I think this is perhaps 92% of genes, but only a small part of the physical DNA).

The rest, the heterochromatin, contains non-sequenced information and could harbour some of the DNA variation between the two species. Some work has suggested that the heterochromatin, previously labelled as Junk DNA, actually has some effect on traits. For example in Drosophila there has been studies which show effects of the Y chromosome on traits despite the Y chromosome being mainly heterochromatic.

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Further: I think a common source of confusion comes from the use of the word gene. It is often used interchangeably to mean either Allele or Genetic Locus. When someone says that humans and apes share 99% of their genes they mean they share 99% of their genetic loci. When someone says that a person shares 50% of their genes with a parent they mean that they share half of their alleles with that parent (it is only roughly half due to recombination and mutation). An individual has all (barring genetic defects such as deletions) the same loci as their parent.

Answer 4

Most of the answers here focus on the difference between the concepts of 'DNA' and 'genes' very well. However, the sequence identity between humans and chimpanzees is not covered as rigorously and remains unclear from what has been answered. Therefore, I will elaborate on that, so that the first part of the question is also covered.

Humans and chimpanzees differ approximately every 100 nucleotides in their total DNA sequence. This is does not mean that 98.5% of the genes are shared. It means that humans have about 98.5% (more precisely about 98.8%, The Chimpanzee Sequencing and Analysis Consortium, 2005) sequence identity with chimpanzees, disregarding indels. They treated indels and nucleotide differences separately and "calculate[d] the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%" which includes intergenic regions and introns - so obviously also non-genic regions. Sequence identity at the gene level is presumably way bigger.

The Chimpanzee Sequencing and Analysis Consortium also gives information how this divergence is structured. The main part (about 85% of the 30 - 35 Mio. different nucleotides) comes from fixed differences: a fixed difference is a position in the haploid genome in which every human has, say, a G and every chimpanzee has a T. Accordingly, the site is different between the two species for every individual of the respective species. The smaller part (about 15%) comes from sites that are either variable (SNP) in humans or variable in chimpanzees, or in both (there is even a small number of very old variants, i.e. shared alleles between humans and chimpanzees, e.g. see Azevedo et al., 2015). Note that the estimates get better the more individuals of the respective species are sequenced and compared.

Answer 5

I just read a article that says even the 99% stat is not technically correct. To get to that number they had to ignore 25% of the human DNA and I think 18% of the chimp DNA. I am also assuming the stat was only including the coded DNA. Because if the what they used to refer to as junk DNA is not the same, then the 99% stat from 2005 starts to look less and less accurate and bit misleading. https://futurism.com/watch-do-we-really-share-99-our-dna-chimps/

Answer 6

Humans and chimpanzees differ approximately every 100 nucleotides in their total DNA sequence.This is does not mean that 98.5% of the genes are shared.It means that human have about 98.5% (more precisely about 98.8%,The Chimpanzee Sequence and Analysis Consortium,2005) sequence identity with chimpanzees,disregarding indels.They treated indels and nucleotide differences separately and "calculate[d] the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%" which includes intergenic regions and introns-so obviously also non-genic regions.Sequence identity at the gene level is presumably way bigger.