6 ms·

Timeline: Organisms that have had their genomes sequenced

99 points by lelf 10y ago

jamessb 10y ago
Note that this a very incomplete list. For more complete overviews, see the Quick Guide to Sequenced Genomes [1], the NCBI's list of genome sequences [2], or the wikipedia lists of sequenced bacterial [3] and eukaryotic [4] genomes (and their related lists). [1]: http://www.genomenewsnetwork.org/resources/sequenced_genomes/genome_guide_p1.shtml http://www.genomenewsnetwork.org/resources/sequenced_genomes... [2]: https://www.ncbi.nlm.nih.gov/genome/browse/ https://www.ncbi.nlm.nih.gov/genome/browse/ [3]: https://en.wikipedia.org/wiki/List_of_sequenced_bacterial_genomes https://en.wikipedia.org/wiki/List_of_sequenced_bacterial_ge... [4]: https://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomes https://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_g...
BioGeek 10y ago
This list highlights the most import organisms that have their genome sequenced, but look at [1] to see the full list of 22244 organisms that are currently sequenced. Most human pathogens, like Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Salmonella enterica, Mycobacterium tuberculosis, ... have several thousand assemblies each. [1] https://www.ncbi.nlm.nih.gov/genome/browse/ https://www.ncbi.nlm.nih.gov/genome/browse/
- fatboy93 10y ago
  Many are just deconvolutions of microbiomes. Not that I'm against it as I'm very much into metagenomics, but many of these genome assemblies can barely qualify as draft genomes. Also yet another important point here is the strain level resolution, which the depth of sequencing had afforded us. For eg, if one were to look at staph or any other human pathogen, you'll find at the bare minimum more than tens of those.
vijayr 10y ago
What determines the complexity of sequencing these? The number of pairs?
- dekhn 10y ago
  The other big complexity is the self-similarity of the genome. To sequence, the genome is duplicated, then sharded physically into many overlapping tiles around an average length, each tile starting at a different position. Each sequence is determined in parallel, and then the shards have to be reassembled computationally (really, this is a post-sequencing process, but is critical to being able to call the result a "sequence" rather than a bag of reads). If the genome in question contains a lot of regions that are similar to each other, the algorithms that do the assembly will get confused.
- niels_olson 10y ago
  There are regions with sparse coverage due to higher concentrations of C-G bases. This can make alignment results less reliable. Plasmids may interfere with alignment or need to be isolated out before or during library prep. And you want to detect and discard any members of the population with any evidence of cancer, genetic disease, etc. And you need good population coverage. What's a normal variant? Newer methods propose a graph alignment instead of just trying to build a single sequence reference genome.
- cixin 10y ago
  Yes mostly the number of base pairs. Large repeats can also cause issues finishing a genome.
- Ovah 10y ago
  Today there exists a multitude of different genome sequencing techniques, and distinct complexities are associated with each method. However, the number of pairs is today seldomly the main complexity. Sanger sequencing was one of the first methods of sequencing, and employs linear sequencing: the synthesis of strands with increasing length. With the advent of the Human Genome Project, Celera instead came up with the idea of fragmenting the genome, amplifying the fragments, sequence the fragments, and match them together using bioinformatics. The complexity here lies in that much of the DNA is repeated (such as microsatellites) or no, which makes it hard to 'phase' the genome. As such, a short 20 nucleotide sequence may be present in may parts of the genome which makes it hard to generate a 100% complete connected genome. Today, Illumina sequencing is the major sequencing platform (~85% of market share). It relies of the fragmentation of DNA into ~300 bp fragments. By synthesising the complementary strand of each fragment with fluorescent nucleotides, we may employ lasers to detect (sequence) the nucleotides of the fragments. Here we have the same problem as with shotgun sequencing: that we have many repeats in the DNA sequence. To remedy this, error-prone sequencing methods with long read lengths such as IonTorrent/PacBio/etc. may be employed to. These long reads may then act as a map for stiching together the more precise short reads. This is called 'hybrid' sequencing. Other sequencing methods, such as Pyrosequencing, has the inherent problem of not being able to discern too many (5) of the same nucleotide in a row. Other methods are primer based (i.e. need to know a short subsequence of the DNA beforehand). This is problematic if we want to perform a de-novo whole genome sequence. Note: Illumina does not rely on primers, and may be deployed directly on unknown sequences, unlike Pyrosequencing/Sanger sequencing.
major505 10y ago
You missed Xylella fastidiosa. It was sequenced in 2000's
roadnottaken 10y ago
Would be nice to list the approximate number of genes, too.
- alextheparrot 10y ago
  Most non-plant organisms I can think of are around 15,000 - 25,000 genes.
  - liberalsurfer 10y ago
    Not true. Majority of bacterial cells have far less genes than 15,000.
- liberalsurfer 10y ago
  Agreed, number of bases gives little information about the complexity of an organism. Genes is a better metric.
  - 08-15 10y ago
    "Number of characters gives little information about the complexity of a program. Functions is a better metric." When the human genome was sequences (it was a ten year project), lots of pseudo-philosophers predicted the number of genes that would be found, with numbers ranging from thousands to millions. The genome in hand, we found about 25000 genes, which make up a few percent (1.5-3%) of the genome. We then looked more closely, and now we can't even agree on the defintion of "gene" anymore, which is one reason why I can't give an exact percentage. It turns out that one gene can produce more than one protein, or sometimes less. There are lots of genes whose only function (assuming "function" is even well defined) is to regulate other genes, a bit like a program could have functions of higher order. We're slowly grasping the fact that we have no idea how complex the genome and the machine interpreting it really are. Number of genes really is no metric at all.
mrtron 10y ago
2016 Beaver [1]. [1] https://www.utoronto.ca/news/happy-150th-canada-u-t-researchers-first-world-sequence-beaver-s-genome https://www.utoronto.ca/news/happy-150th-canada-u-t-research...
supersan 10y ago
This is super interesting for someone who has no knowledge of the field. Has my interest piqued as to how they do it, what is number of bases, why do mice have more bases than us, etc. Very nice presentation wise, even if it is incomplete (as other comments state).
- alextheparrot 10y ago
  I can address some of these. Sequencing today is done mostly using computational methods. Think of DNA as a couple long strings (Number of bases is effectively the character count of those strings, each string is a "chromosome" in higher organisms), so the problem is how do we read these long, physical strings. It turns out that parallel processing is way more effective, so we break the really long strings into much, much smaller strings that overlap (Millions of characters long to hundreds often). Because the strings overlap, we can construct a good portion of the actual sequence computationaly by exploiting this overlapping feature of our small strings. The physical way they do this is by using machines (Think GPU vs CPU) that are effectively a bunch of parallel microscopes specialized to read those short strings and by "attaching" colors to each of the characters (DNA bases). Initial DNA sequencing methods lacked both the computational and physical devices to do this, so they were done by hand. The move from doing sequencing by hand to doing it computationally is why we see the significant increase in characters read (Number of bases). Your last comment I think is the most interesting, as it effectively asks "Why do mice have a larger string size than us, which means they contain more information on an absolute level?". The answer is just because. The number of bases, or even the number of blocks of information that produce proteins (These blocks are called genes, and a protein is another chemical construct that mainly focuses on doing actions in the cell), is not strongly correlated with the complexity of the organism. The key is how those bases interact, not necessarily in how many there are. If you have any more questions or need some clarification I'd love to address them, it is a wonderful time to be alive.
  - valine 10y ago
    This is really interesting. For someone who knows nothing about the subject, how were DNA strands physically read at a low level before computational methods? I was under the impression DNA is too small to see without an electron microscope. You mention reading dna by hand, and I'm really interested in how that is done.
deathanatos 10y ago
When we say that we've "sequenced a genome" — what does that mean, exactly? Just that we've scanned/digitized the DNA sequence of a single member of that species? (Since of course the DNA of all members of a species isn't the same, otherwise, we'd all look alike.) Do we ever sample more than one member of a species? How many members of various species have we sampled? (While I'd expect them to be similar, of course, I'd also expect the interesting things to be in the differences.)
- inetknght 10y ago
  https://en.wikipedia.org/wiki/Human_Genome_Project https://en.wikipedia.org/wiki/Human_Genome_Project "The genome published by the HGP does not represent the sequence of every individual's genome. It is the combined mosaic of a small number of anonymous donors, all of European origin." I work at a for-profit DNA company which sequences humans for genealogical purposes. The human reference, as we call it, has been through several 'revisions'. My company uses anywhere from "build 36" to "build 38", depending on the specific sequencing product purchased. It's an ongoing effort to upgrade older products to use the newer sequencing version: each revision may change, add, or remove genomic locations of specific named variants. That can wreak havoc, of course, when trying to translate older data to the newer revision. Customers would of course notice right away if their genome data were to change on them! It creates rather a conundrum to solve.
- 08-15 10y ago
  > "sequenced a genome" — what does that mean, exactly? It means we got the sequence of As, Cs, Gs and Ts; but in practice, we don't even achieve that. The human genome has approximately 3 billion nucleotides in 23 chromosomes. So you would think a "sequenced genome" is 23 strings over the alphabet {A,C,G,T} with a length of 130 million or so each. However, it is only possible to sequence a few hundred nucleotides at a time. So you end up with a jigsaw puzzle of tiny pieces, some containing errors, some missing, some exact duplicates of each other. Putting these back together corectly isn't even possible, doing it approximately is still difficult. So in practice, a sequenced genome is a sequence of medium size strings, arranged in the mostly correct order, with many small and a few large gaps, so they form a good chunk of the long strings that would really be a genome. And even if all of that was completely correct, we still wouldn't know what most of these nucleotides mean. The first "draft" of a genome is usually even worse. If you simply dump DNA fragments from a mammal onto a modern day sequencer (Illumina HiSeq), and run software to kind-of solve the jigsaw puzzle, you end up with a million pieces, each about 2000 nucleotides in length, in no particular order. Since most genes by far are longer than that, I'd say it's fraudulent to call something like that a genome, but it's being done all the time. > Do we ever sample more than one member of a species? Yes, but not in the same way. Instead of (approximately) solving the impossible jigsaw puzzle again (that's called de-novo assembly), we tend to compare the puzzle pieces from a new individual against the big picture we got from the first genome (that's called mapping). This way, we can see small differences (single substitutitions, small insertions and deletions), which is most of the variation present in a species. What we can't see is large scale variation, like duplicated genes, or rearrangements of large pieces of the genome, or insertions of retroviruses. We know these exist, it's just more expensive to look for them. (All of this changing as sequencing is becoming cheaper.) Multiple individuals of a species get sequenced when there is interest. Probably tens of thousands of humans have been sequenced by now. For model organisms, the number is much lower. For pathogens, where everything is much easier anyway, the number could easily be higher.
Aardwolf 10y ago
Does anyone know how expensive it is to fully sequence your own genome today (not genotyping but full sequencing)? And how complete is it, would every bit be correct?

99 points by lelf 10y ago

Note that this a very incomplete list. For more complete overviews, see the Quick Guide to Sequenced Genomes [1], the NCBI's list of genome sequences [2], or the wikipedia lists of sequenced bacterial [3] and eukaryotic [4] genomes (and their related lists). [1]: http://www.genomenewsnetwork.org/resources/sequenced_genomes/genome_guide_p1.shtml http://www.genomenewsnetwork.org/resources/sequenced_genomes... [2]: https://www.ncbi.nlm.nih.gov/genome/browse/ https://www.ncbi.nlm.nih.gov/genome/browse/ [3]: https://en.wikipedia.org/wiki/List_of_sequenced_bacterial_genomes https://en.wikipedia.org/wiki/List_of_sequenced_bacterial_ge... [4]: https://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomes https://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_g...

BioGeek 10y ago

This list highlights the most import organisms that have their genome sequenced, but look at [1] to see the full list of 22244 organisms that are currently sequenced. Most human pathogens, like Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Salmonella enterica, Mycobacterium tuberculosis, ... have several thousand assemblies each. [1] https://www.ncbi.nlm.nih.gov/genome/browse/ https://www.ncbi.nlm.nih.gov/genome/browse/

fatboy93 10y ago
Many are just deconvolutions of microbiomes. Not that I'm against it as I'm very much into metagenomics, but many of these genome assemblies can barely qualify as draft genomes. Also yet another important point here is the strain level resolution, which the depth of sequencing had afforded us. For eg, if one were to look at staph or any other human pathogen, you'll find at the bare minimum more than tens of those.

vijayr 10y ago

What determines the complexity of sequencing these? The number of pairs?

dekhn 10y ago
The other big complexity is the self-similarity of the genome. To sequence, the genome is duplicated, then sharded physically into many overlapping tiles around an average length, each tile starting at a different position. Each sequence is determined in parallel, and then the shards have to be reassembled computationally (really, this is a post-sequencing process, but is critical to being able to call the result a "sequence" rather than a bag of reads). If the genome in question contains a lot of regions that are similar to each other, the algorithms that do the assembly will get confused.
niels_olson 10y ago
There are regions with sparse coverage due to higher concentrations of C-G bases. This can make alignment results less reliable. Plasmids may interfere with alignment or need to be isolated out before or during library prep. And you want to detect and discard any members of the population with any evidence of cancer, genetic disease, etc. And you need good population coverage. What's a normal variant? Newer methods propose a graph alignment instead of just trying to build a single sequence reference genome.
cixin 10y ago
Yes mostly the number of base pairs. Large repeats can also cause issues finishing a genome.
Ovah 10y ago
Today there exists a multitude of different genome sequencing techniques, and distinct complexities are associated with each method. However, the number of pairs is today seldomly the main complexity. Sanger sequencing was one of the first methods of sequencing, and employs linear sequencing: the synthesis of strands with increasing length. With the advent of the Human Genome Project, Celera instead came up with the idea of fragmenting the genome, amplifying the fragments, sequence the fragments, and match them together using bioinformatics. The complexity here lies in that much of the DNA is repeated (such as microsatellites) or no, which makes it hard to 'phase' the genome. As such, a short 20 nucleotide sequence may be present in may parts of the genome which makes it hard to generate a 100% complete connected genome. Today, Illumina sequencing is the major sequencing platform (~85% of market share). It relies of the fragmentation of DNA into ~300 bp fragments. By synthesising the complementary strand of each fragment with fluorescent nucleotides, we may employ lasers to detect (sequence) the nucleotides of the fragments. Here we have the same problem as with shotgun sequencing: that we have many repeats in the DNA sequence. To remedy this, error-prone sequencing methods with long read lengths such as IonTorrent/PacBio/etc. may be employed to. These long reads may then act as a map for stiching together the more precise short reads. This is called 'hybrid' sequencing. Other sequencing methods, such as Pyrosequencing, has the inherent problem of not being able to discern too many (5) of the same nucleotide in a row. Other methods are primer based (i.e. need to know a short subsequence of the DNA beforehand). This is problematic if we want to perform a de-novo whole genome sequence. Note: Illumina does not rely on primers, and may be deployed directly on unknown sequences, unlike Pyrosequencing/Sanger sequencing.

major505 10y ago

You missed Xylella fastidiosa. It was sequenced in 2000's

roadnottaken 10y ago

Would be nice to list the approximate number of genes, too.

alextheparrot 10y ago
Most non-plant organisms I can think of are around 15,000 - 25,000 genes.
- liberalsurfer 10y ago
  Not true. Majority of bacterial cells have far less genes than 15,000.
liberalsurfer 10y ago
Agreed, number of bases gives little information about the complexity of an organism. Genes is a better metric.
- 08-15 10y ago
  "Number of characters gives little information about the complexity of a program. Functions is a better metric." When the human genome was sequences (it was a ten year project), lots of pseudo-philosophers predicted the number of genes that would be found, with numbers ranging from thousands to millions. The genome in hand, we found about 25000 genes, which make up a few percent (1.5-3%) of the genome. We then looked more closely, and now we can't even agree on the defintion of "gene" anymore, which is one reason why I can't give an exact percentage. It turns out that one gene can produce more than one protein, or sometimes less. There are lots of genes whose only function (assuming "function" is even well defined) is to regulate other genes, a bit like a program could have functions of higher order. We're slowly grasping the fact that we have no idea how complex the genome and the machine interpreting it really are. Number of genes really is no metric at all.

mrtron 10y ago

2016 Beaver [1]. [1] https://www.utoronto.ca/news/happy-150th-canada-u-t-researchers-first-world-sequence-beaver-s-genome https://www.utoronto.ca/news/happy-150th-canada-u-t-research...

supersan 10y ago

This is super interesting for someone who has no knowledge of the field. Has my interest piqued as to how they do it, what is number of bases, why do mice have more bases than us, etc. Very nice presentation wise, even if it is incomplete (as other comments state).

alextheparrot 10y ago
I can address some of these. Sequencing today is done mostly using computational methods. Think of DNA as a couple long strings (Number of bases is effectively the character count of those strings, each string is a "chromosome" in higher organisms), so the problem is how do we read these long, physical strings. It turns out that parallel processing is way more effective, so we break the really long strings into much, much smaller strings that overlap (Millions of characters long to hundreds often). Because the strings overlap, we can construct a good portion of the actual sequence computationaly by exploiting this overlapping feature of our small strings. The physical way they do this is by using machines (Think GPU vs CPU) that are effectively a bunch of parallel microscopes specialized to read those short strings and by "attaching" colors to each of the characters (DNA bases). Initial DNA sequencing methods lacked both the computational and physical devices to do this, so they were done by hand. The move from doing sequencing by hand to doing it computationally is why we see the significant increase in characters read (Number of bases). Your last comment I think is the most interesting, as it effectively asks "Why do mice have a larger string size than us, which means they contain more information on an absolute level?". The answer is just because. The number of bases, or even the number of blocks of information that produce proteins (These blocks are called genes, and a protein is another chemical construct that mainly focuses on doing actions in the cell), is not strongly correlated with the complexity of the organism. The key is how those bases interact, not necessarily in how many there are. If you have any more questions or need some clarification I'd love to address them, it is a wonderful time to be alive.
- valine 10y ago
  This is really interesting. For someone who knows nothing about the subject, how were DNA strands physically read at a low level before computational methods? I was under the impression DNA is too small to see without an electron microscope. You mention reading dna by hand, and I'm really interested in how that is done.

deathanatos 10y ago

When we say that we've "sequenced a genome" — what does that mean, exactly? Just that we've scanned/digitized the DNA sequence of a single member of that species? (Since of course the DNA of all members of a species isn't the same, otherwise, we'd all look alike.) Do we ever sample more than one member of a species? How many members of various species have we sampled? (While I'd expect them to be similar, of course, I'd also expect the interesting things to be in the differences.)

inetknght 10y ago
https://en.wikipedia.org/wiki/Human_Genome_Project https://en.wikipedia.org/wiki/Human_Genome_Project "The genome published by the HGP does not represent the sequence of every individual's genome. It is the combined mosaic of a small number of anonymous donors, all of European origin." I work at a for-profit DNA company which sequences humans for genealogical purposes. The human reference, as we call it, has been through several 'revisions'. My company uses anywhere from "build 36" to "build 38", depending on the specific sequencing product purchased. It's an ongoing effort to upgrade older products to use the newer sequencing version: each revision may change, add, or remove genomic locations of specific named variants. That can wreak havoc, of course, when trying to translate older data to the newer revision. Customers would of course notice right away if their genome data were to change on them! It creates rather a conundrum to solve.
08-15 10y ago
> "sequenced a genome" — what does that mean, exactly? It means we got the sequence of As, Cs, Gs and Ts; but in practice, we don't even achieve that. The human genome has approximately 3 billion nucleotides in 23 chromosomes. So you would think a "sequenced genome" is 23 strings over the alphabet {A,C,G,T} with a length of 130 million or so each. However, it is only possible to sequence a few hundred nucleotides at a time. So you end up with a jigsaw puzzle of tiny pieces, some containing errors, some missing, some exact duplicates of each other. Putting these back together corectly isn't even possible, doing it approximately is still difficult. So in practice, a sequenced genome is a sequence of medium size strings, arranged in the mostly correct order, with many small and a few large gaps, so they form a good chunk of the long strings that would really be a genome. And even if all of that was completely correct, we still wouldn't know what most of these nucleotides mean. The first "draft" of a genome is usually even worse. If you simply dump DNA fragments from a mammal onto a modern day sequencer (Illumina HiSeq), and run software to kind-of solve the jigsaw puzzle, you end up with a million pieces, each about 2000 nucleotides in length, in no particular order. Since most genes by far are longer than that, I'd say it's fraudulent to call something like that a genome, but it's being done all the time. > Do we ever sample more than one member of a species? Yes, but not in the same way. Instead of (approximately) solving the impossible jigsaw puzzle again (that's called de-novo assembly), we tend to compare the puzzle pieces from a new individual against the big picture we got from the first genome (that's called mapping). This way, we can see small differences (single substitutitions, small insertions and deletions), which is most of the variation present in a species. What we can't see is large scale variation, like duplicated genes, or rearrangements of large pieces of the genome, or insertions of retroviruses. We know these exist, it's just more expensive to look for them. (All of this changing as sequencing is becoming cheaper.) Multiple individuals of a species get sequenced when there is interest. Probably tens of thousands of humans have been sequenced by now. For model organisms, the number is much lower. For pathogens, where everything is much easier anyway, the number could easily be higher.

Aardwolf 10y ago

Does anyone know how expensive it is to fully sequence your own genome today (not genotyping but full sequencing)? And how complete is it, would every bit be correct?