Editing Cephalopod (section)

=== Genetics ===
The sequencing of a full cephalopod genome has remained challenging to researchers due to the length and repetition of their DNA.<ref name="O'Brien 700">{{Cite journal |last1=O'Brien |first1=Caitlin E. |last2=Roumbedakis|first2=Katina |last3=Winkelmann |first3=Inger E. |date=2018-06-06 |title=The Current State of Cephalopod Science and Perspectives on the Most Critical Challenges Ahead From Three Early-Career Researchers|journal=Frontiers in Physiology|volume=9|pages=700 |doi=10.3389/fphys.2018.00700 |pmid=29962956 |pmc=6014164 |issn=1664-042X |doi-access=free}}</ref> The characteristics of cephalopod genomes were initially hypothesized to be the result of entire [[Gene duplication|genome duplications]]. Following the full sequencing of a [[California two-spot octopus]], the genome showed similar patterns to other marine invertebrates with significant additions to the genome assumed to be unique to cephalopods. No evidence of full genome duplication was found.<ref name="Albertin 220–224">{{Cite journal|last1=Albertin |first1=Caroline B. |last2=Simakov |first2=Oleg|last3=Mitros|first3=Therese |last4=Wang |first4=Z. Yan |last5=Pungor |first5=Judit R. |last6=Edsinger-Gonzales |first6=Eric |last7=Brenner |first7=Sydney |last8=Ragsdale |first8=Clifton W. |last9=Rokhsar |first9=Daniel S. |date=August 2015 |title=The octopus genome and the evolution of cephalopod neural and morphological novelties |journal=Nature|language=en |volume=524|issue=7564 |pages=220–224 |doi=10.1038/nature14668 |pmid=26268193|pmc=4795812|bibcode=2015Natur.524..220A |issn=0028-0836}}</ref>

Within the California two-spot octopus genome there are substantial replications of two gene families. Significantly, the expanded gene families were only previously known to exhibit replicative behaviour within vertebrates.<ref name="Albertin 220–224"/> The first gene family was identified as the [[protocadherin]]s which are attributed to neuron development. Protocadherins function as cell adhesion molecules, essential for [[Synaptogenesis|synaptic specificity]]. The mechanism for protocadherin gene family replication in vertebrates is attributed to complex splicing, or cutting and pasting, from a locus. Following the sequencing of the California two-spot octopus, researchers found that the protocadherin gene family in cephalopods has expanded in the genome due to [[Tandem exon duplication|tandem gene duplication]]. The different replication mechanisms for protocadherin genes indicate an independent evolution of protocadherin gene expansion in vertebrates and invertebrates.<ref name="Albertin 220–224"/> Analysis of individual cephalopod protocadherin genes indicate independent evolution between species of cephalopod. A species of shore squid ''[[Longfin inshore squid|Doryteuthis pealeii]]'' with expanded protocadherin gene families differ significantly from those of the California two-spot octopus suggesting gene expansion did not occur before [[speciation]] within cephalopods. Despite different mechanisms for gene expansion, the two-spot octopus protocadherin genes were more similar to vertebrates than squid, suggesting a [[convergent evolution]] mechanism. The second gene family known as {{chem2|C2H2}} are small proteins that function as [[Zinc finger transcription factor|zinc transcription factors]]. {{chem2|C2H2}} are understood to moderate DNA, RNA and protein functions within the cell.<ref name="O'Brien 700"/>

The sequenced California two spot octopus genome also showed a significant presence of [[transposable element]]s as well as transposon expression. Although the role of transposable elements in marine vertebrates is still relatively unknown, significant expression of transposons in nervous system tissues have been observed.<ref name="Gehring 117–142">{{cite book |last=Gehring |first=Mary A. |chapter=Imprinted Gene Expression and the Contribution of Transposable Elements |date=2013-02-04 |title=Plant Transposons and Genome Dynamics in Evolution |pages=117–142 |publisher=Wiley-Blackwell |doi=10.1002/9781118500156.ch7 |isbn=978-1-118-50015-6}}</ref> In a study conducted on vertebrates, the expression of transposons during development in the fruitfly ''[[Drosophila melanogaster]]'' activated genomic diversity between neurons.<ref>{{Cite journal|last1=Erwin|first1=Jennifer A. |last2=Marchetto |first2=Maria C. |last3=Gage |first3=Fred H. |date=August 2014 |title=Mobile DNA elements in the generation of diversity and complexity in the brain |journal=Nature Reviews Neuroscience|language=en |volume=15|issue=8 |pages=497–506 |doi=10.1038/nrn3730 |pmid=25005482 |pmc=4443810 |issn=1471-003X}}</ref> This diversity has been linked to increased memory and learning in mammals. The connection between transposons and increased neuron capability may provide insight into the observed intelligence, memory and function of cephalopods.<ref name="Gehring 117–142"/>

Using long-read sequencing, researchers have decoded the cephalopod genomes and discovered they have been churned and scrambled. The genes were compared to those of thousands of other species and while blocks of three or more genes co-occurred between squid and octopus, the blocks of genes were not found together in any other animals'. Many of the groupings were in the nervous tissue, suggesting the course they adapted their intelligence.<ref>{{Cite journal|last1=Albertin |first1=Caroline B. |last2=Medina-Ruiz |first2=Sofia |last3=Mitros |first3=Therese |last4=Schmidbaur |first4=Hannah |last5=Sanchez |first5=Gustavo |last6=Wang|first6=Z. Yan|last7=Grimwood |first7=Jane |last8=Rosenthal |first8=Joshua J. C. |last9=Ragsdale |first9=Clifton W. |last10=Simakov |first10=Oleg |last11=Rokhsar |first11=Daniel S. |date=2022-05-04 |title=Genome and transcriptome mechanisms driving cephalopod evolution |journal=Nature Communications |language=en |volume=13|issue=1 |pages=2427 |doi=10.1038/s41467-022-29748-w|pmid=35508532 |pmc=9068888 |bibcode=2022NatCo..13.2427A |hdl=1912/29234|hdl-access=free }}</ref><ref>{{Cite journal|last1=Schmidbaur |first1=Hannah |last2=Kawaguchi |first2=Akane |last3=Clarence |first3=Tereza |last4=Fu |first4=Xiao |last5=Hoang |first5=Oi Pui |last6=Zimmermann |first6=Bob|last7=Ritschard |first7=Elena A. |last8=Weissenbacher |first8=Anton |last9=Foster |first9=Jamie S. |last10=Nyholm |first10=Spencer V. |last11=Bates |first11=Paul A. |last12=Albertin |first12=Caroline B. |last13=Tanaka|first13=Elly |last14=Simakov |first14=Oleg |date=2022-04-21 |title=Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization |journal=Nature Communications|language=en|volume=13|issue=1 |pages=2172 |doi=10.1038/s41467-022-29694-7|pmid=35449136 |pmc=9023564 |bibcode=2022NatCo..13.2172S |hdl=1912/29187 |hdl-access=free}}</ref>