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Cephalopod genomes
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RonO
May 8, 2022, 9:41:15 AM5/8/22
to talk-o...@moderators.isc.org
https://www.mbl.edu/news/squid-and-octopus-genome-studies-reveal-how-cephalopods-unique-traits-evolved
https://www.nature.com/articles/s41467-022-29694-7#citeas
They have made assemblies of multiple cephalopod genomes and found some
weird stuff. They have reorganized their genomes a lot more than other
lineages, and have expanded some gene families in their lineage that
haven't seen such gene expansion in other lineages. What is wackiest of
all is that they do a lot of RNA editing. They change the sequence of
the mRNA to make the final coding sequence.
When I was a graduate student some protozoans were known to do this for
their mitochondrial genomes. It seems crazy that you would want to
modify an encoded sequence because it is just another level of
complexity, but the protozoans seem to be using the system to fix
messups in the original gene. They would add bases to fix frame shifts
and complete codons. It could be a way to increase the genetic
variation and number of transcripts with different functional
characteristics, but it ended up as a system to restore the original
function of a gene that had obviously lost that function. Certain genes
became dependent on it and likely kept losing bits that were replaced
upon editing until over 20% of the gene sequence had to be altered. It
may be needed, but it isn't a good way to do things because of the
errors that can happen along the way. How many functional transcripts
are produced?
Cephalopods seem to be using RNA editing to change the coding sequence
and expand their sequence variation. It is freaky to think, but
neurological genes are edited, and it may be the way that cephalopids
have created such efficient brains. They may have been able to
experiment with a lot of different variants of certain proteins to see
what they get.
If we hadn't evolved what would cephalopods have become in another
hundred million years.
Ron Okimoto
https://www.nature.com/articles/s41467-022-29694-7#citeas
They have made assemblies of multiple cephalopod genomes and found some
weird stuff. They have reorganized their genomes a lot more than other
lineages, and have expanded some gene families in their lineage that
haven't seen such gene expansion in other lineages. What is wackiest of
all is that they do a lot of RNA editing. They change the sequence of
the mRNA to make the final coding sequence.
When I was a graduate student some protozoans were known to do this for
their mitochondrial genomes. It seems crazy that you would want to
modify an encoded sequence because it is just another level of
complexity, but the protozoans seem to be using the system to fix
messups in the original gene. They would add bases to fix frame shifts
and complete codons. It could be a way to increase the genetic
variation and number of transcripts with different functional
characteristics, but it ended up as a system to restore the original
function of a gene that had obviously lost that function. Certain genes
became dependent on it and likely kept losing bits that were replaced
upon editing until over 20% of the gene sequence had to be altered. It
may be needed, but it isn't a good way to do things because of the
errors that can happen along the way. How many functional transcripts
are produced?
Cephalopods seem to be using RNA editing to change the coding sequence
and expand their sequence variation. It is freaky to think, but
neurological genes are edited, and it may be the way that cephalopids
have created such efficient brains. They may have been able to
experiment with a lot of different variants of certain proteins to see
what they get.
If we hadn't evolved what would cephalopods have become in another
hundred million years.
Ron Okimoto
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