Three new cephalopod genomes have been published
April 6, 2019
There's been a lot of developments in the world of cephalopod genomics, with three new genomes out recently! One for the bobtail squid Euprymna scolopes, one for Octopus vulgaris, and one for the long-arm octopus Octopus minor!
New paper on cephalopod RNA editing, and its evolutionary costs
April 6, 2017
New paper on cephalopod RNA editing, and its evolutionary costs
April 6, 2017
New paper out today in Cell, reporting on the extensive RNA editing seen in coleiod cephalopods. Liscovitch-Brauer et al. found that behaviorally complex cephalopods diversify their neural proteome, at the cost of slowing down their genomic evolution. Find out more about these exciting findings, here!
Octopus bimaculoides genomic and transcriptomic data live, and more!
August 17, 2015
Oleg Simakov, one of the authors of the recent paper announcing the sequenced genome and multiple transcriptomes of O. bimaculoides, has released a new site containing the raw data files generated in the initial processing of the sequences. It includes not only a gene browser, but further information on synteny dynamics, phylogenetic analyses, and cephalopod novel genes. Explore it by clicking here.
The first sequenced cephalopod
genome is published!
August 12, 2015
The sequenced and assembled genome and transcriptomes of the California two-spot Octopus bimaculoides have been published! Researchers describe massive expansions of a number of gene families, including the protocadherins and the C2H2 zinc-finger transcription factors, as well as massive rearrangements in the architecture of the genome. Read about it in Nature.
Loligo pealeii transcriptomes
and draft genome released!
February 17, 2014
CephSeq members Joshua Rosenthal and C. Titus Brown have just released a wealth of data from their work on squid transcriptomes and genomes, in an effort to aide other researchers in their pursuits. Titus's description of the project, as well as links to the data, can be found on his blog.
New study documents extensive
RNA editing in squid
January 8, 2015
Using next-generation sequencing of the long fin inshore squid (Doryteuthis pealeii), researchers find unprecidented levels of RNA editing in the squid nervous system. Many of the edits identified in this study result in recoding of protein sequences. Read about it in eLIFE.
Idea: Crowdsourced -omic analysis with data privacy sunset?
March 25, 2013
Titus Brown has ideas about how you might get your large cephalopod sequence datasets analyzed. There is a catch, but it is a very reasonable one. Read about it on his web site.
Tom Abrams: Comparative Molluscan Gene Expression Links
March 25, 2013
Tom Abrams at the University of Maryland School of Medicine has been spearheading the development of Aplysia transcriptomics for the Aplysia community in response to how difficult the Aplysia genome assembly has become (blame all those SSRs). He provides the links below for cephalopod researchers interested in comparative molluscan gene expression.
There is a website for BLAST searches, as well as a forum website. The combined Ac_All.fasta combines all of the Broad assembly. The Ac_CNS IGS transcripts contain the recent pilot assembly for CNS.
You can write to Tom to exchange ideas and compare notes at tabrams@umaryland.edu. Tom is very interested in the development of cephalopod genomics.
Pharyngula Approves the
CephSeq Plan
October 29, 2012
Pharyngula has approved and summarized the plan of the Cephalopod Sequencing Consortium. Read about it here.
The White Paper has been
Published!
October 22, 2012
As many of our members and followers know, the white paper has recently been published by Standards in Genomic Sciences. The paper is titled “Cephalopod Genomics: A Plan of Strategies and Organization, authored by: Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert J. Freeman, Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J.C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, and Clifton W. Ragsdale.
This white paper discusses the conclusions and recommendations that resulted from the meeting of The Cephalopod Sequencing Consortium (CephSeq Consortium), which was established at the NESCent Catalysis Group Meeting titled “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” which was held in Durham, North Carolina, USA from May 24 through May 27 of 2012. The group of individuals present included cephalopod biologists, neuroscientists, developmental and evolutionary biologists, bioinformaticians, and researchers.
To read the full paper, click here.
Titus Brown has blogged on the
NEScent CephSeq Meeting
May 28, 2012
C. Titus Brown has posted a great blog entry on his experience at the NESCent CephSeq Meeting. Please read and share!
New paper out today in Cell, reporting on the extensive RNA editing seen in coleiod cephalopods. Liscovitch-Brauer et al. found that behaviorally complex cephalopods diversify their neural proteome, at the cost of slowing down their genomic evolution. Find out more about these exciting findings, here!