Cephalopod genomics

15 Pages·2012·0.4 MB·English

Cephalopod genomics: A plan of strategies and
organization
Citation
Albertin, Caroline B., Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. da
Fonseca, Carlo Di Cristo, Brian P. Dilkes, et al. 2012. Cephalopod genomics: a plan of strategies
and organization. Standards in Genomic Sciences 7(1): 175-188.
Published Version
doi:10.4056/sigs.3136559
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Standards in Genomic Sciences (2012) 7:175-188 DOI:10.4056/sigs.3136559
Cephalopod genomics: A plan of strategies and
organization
Caroline B. Albertin1, Laure Bonnaud2, C. Titus Brown3, Wendy J. Crookes-Goodson4, Rute
R. da Fonseca5, Carlo Di Cristo6, Brian P. Dilkes7, Eric Edsinger-Gonzales8, Robert M.
Freeman, Jr.9, Roger T. Hanlon10, Kristen M. Koenig11, Annie R. Lindgren12, Mark Q.
Martindale13, Patrick Minx14, Leonid L. Moroz15, Marie-Therese Nödl16, Spencer V.
Nyholm17, Atsushi Ogura18, Judit R. Pungor19, Joshua J. C. Rosenthal20, Erich M. Schwarz21,
Shuichi Shigeno22, Jan M. Strugnell23, Tim Wollesen24, Guojie Zhang25, Clifton W.
Ragsdale,1,26*
1Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
2Muséum National d'Histoire Naturelle, Université Paris Diderot, Sorbonne Paris Cité,
Paris, France
3Departments of Computer Science and Engineering, and Microbiology and Molecular
Genetics, Michigan State University, East Lansing, MI, USA
4Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force
Research Laboratory, Wright-Patterson AFB, OH, USA
5Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
6Department of Biological, Geological and Environmental Sciences, University of Sannio,
Benevento, Italy
7Department of Horticulture and Landscape Architecture, Purdue University, West
Lafayette, IN, USA
8Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley,
CA, USA
9Department of Systems Biology, Harvard Medical School, Boston, MA, USA
10Marine Biological Laboratory, Woods Hole, MA, USA
11Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
12Department of Biology, Portland State University, Portland, OR, USA
13Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI, USA
14The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
15Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
16Department of Theoretical Biology, University of Vienna, Vienna, Austria
17Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
18Institute for Genome Research, University of Tokushima, Tokushima, Japan
19Hopkins Marine Station of Stanford University, Pacific Grove, CA, USA
20Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan,
PR, USA
21Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
22Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
23Department of Genetics, La Trobe University, Bundoora, Victoria, Australia
24Department of Integrative Zoology, University of Vienna, Vienna, Austria
25 BGI-Shenzhen, Shenzhen, China
26Department of Neurobiology, University of Chicago, Chicago, IL, USA
*Corresponding author: Clifton W. Ragsdale ([email protected])
The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Cataly-
sis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in
Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine coun-
tries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the
pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod
biologists, neuroscientists, developmental and evolutionary biologists, materials scientists,
bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed
on a set of cephalopod species of particular importance for initial sequencing and developed strategies
and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recom-
mendations of this meeting are described in this white paper.
The Genomic Standards Consortium
Cephalopod genomics
Cephalopods
Nautilus
Cephalopod biological research has a long history
involving a wide range of experimental para-
Cephalopods (octopus, squid, cuttlefish, )
digms, the best known of which is the work on
have captured the imagination of scientists and
squid giant axon physiology that led to Nobel
the general public since Aristotle. These predato-
Prize awards for Alan Hodgkin and Andrew Hux-
ry creatures are an ancient group, known from at
ley. Also prominent are the extensive investiga-
least the Late Cambrian and today comprising
tions by J.Z. Young, Brian Boycott, Martin Wells
more than 700 species [1,2]. Cephalopods range
and colleagues into cephalopod brain and behav-
in size from the pygmy squids (thumbnail-sized
ior, with a particular focus on the sophisticated
adults) to the colossal and giant squids (18 me-
learning and memory systems of the octopus [9].
ters in total length), which are the largest known
Cephalopod biology has recently become rele-
invertebrates. Cephalopods are believed to be
vant to the field of biomimetic research, particu-
among the most “advanced” invertebrates, hav-
larly for robotics and materials science [10,11].
ing evolved large, highly differentiated brains, a
There are likely to be many new areas of cepha-
sophisticated set of sensory organs that includes
lopod-based research. For example, cephalopods
vertebrate-like eyes, and fast jet-propelled loco-
immobilize prey organisms withtoxins, some of
motion [3]. The neuroendocrine and heart-blood
which are very poisonous to humans [1]. Study of
vascular systems of cephalopods have long been
such toxins may serve to identify new
recognized for their complexity and similarity to
biomedically valuable reagents [12].
those found in vertebrates [4-6]. A particularly
striking trait of cephalopods is that they are mas-
Cephalopods are mollusks, which show a greater
ters of rapid adaptive coloration, having the abil-
variety of forms than do any other extant animal
ity to change quickly the texture, pattern, color
phylum. Even within the Mollusca, cephalopods
and brightness of their skin. Dynamic camouflage
display a remarkable level of modification in
helps the animals evade detection by predators
body plan organization. Particularly notable
and approach prey with stealth; the same sys-
among the soft-bodied (coleoid) cephalopods are
tems produce signals for communication with
the reduction or loss of the shell, the adaptation
conspecifics [3]. The remarkable morphological
of the mantle for locomotion and respiration, and
and physiological innovations of cephalopods
the modification of the ventral molluscan foot
provide the scientific community with a tremen-
into arms [2]. These innovations are undoubtedly
dous opportunity for insight into mechanisms of
tightly linked to the selective pressures from the
evolutionary convergence and innovation in
loss of the shell and the development of a “high-
structure and function.
performance” nervous system. The cephalopod
lineage, and its origins from a monoplacophoran-
Cephalopods have diversified to inhabit all
like molluscan ancestor [2,13], thus represents a
oceans of the world, from benthic to pelagic
deeply attractive model for understanding the
zones, from intertidal areas to the deep sea, and
acquisition of novelty through evolutionary time.
from the polar regions to the tropics. They share
the “behavioral space” in their many marine hab-
All of these areas of cephalopod biology, from
itats with teleost fishes and marine mammals [7],
neuronal function at the cellular and systems
placing them in some of the most competitive
levels to cephalopod population dynamics to the
ecohabitats on Earth. Cephalopods are ecologi-
evolution of gene regulatory elements mediating
cally important for the central position they play
body plan variation, would benefit greatly from
in trophic predator-prey relationships; they are a
the molecular insight that high-quality cephalo-
primary food source for marine mammals and for
pod genomics would provide. Indeed, it is aston-
many harvested fish species. Their importance in
ishing that, in 2012, with the explosion of ge-
the food web is often underestimated, but they
nome resources for so many life forms, there is
constitute a crucial element in coastal ecosystem
not yet available a single assembled cephalopod
equilibrium. Moreover, cephalopods themselves
genome. The goal of the NESCent meeting and
are the target of large commercial fisheries
this white paper is to provide organizational
worldwide, with an annual harvest of two million
mechanisms for cephalopod biology to move
metric tons of squid alone [8].
from the pre-genomic to the post-genomic age.
176 Standards in Genomic Sciences
Albertin et al.
Genomics
phenomena at the level of gene function and regu-
lation impossible. Sequencing of cephalopods
Genomic and transcriptomic sequencing will
would do more than expand our knowledge of ge-
greatly aid the biological study of cephalopods. A
nome organization within lophotrochozoans. With
sequenced genome produces a comprehensive list
genomic data, researchers currently studying mo-
of genes, and contains the regulatory blueprint
lecular evolution of complex metazoans would be
dictating their expression [14]. Sequenced
able to investigate cephalopods as a new, inde-
transcriptomes reveal the expression levels of
pendent instance of such evolution.
gene sets for different cells, tissues and organs at
different developmental stages and under differ- The genomes of cephalopods are known to be
ent physiological states [15,16]. Resequencing in- larger and more repeat-rich than many previously
dividuals of a genome-enabled species offers un- sequenced metazoan genomes [30]. With newly
precedented datasets that can be applied to long- developed methods for sequencing and assembly
standing questions in population genetiac sp, rdioisreiase, [31,32], these genomes are now more tractable
and the characterization of species of commercial than they would have been even a few years ago.
importance where there may be little ge- Indeed, the likely challenges of cephalopod ge-
netic knowledge [17,18]. Comparative genomics nomics will prove an important test of these
has revolutionized and stabilized our understand- emerging technologies.
ing of the evolutionary relationships among or- Genomic data will allow analyses of cephalopod
ganisms throughout the Tree of Life, both living molecular biology that have, until now, not been
and recently extinct [19,20]. Sequence data have considered by the cephalopod community. De-
also advanced novel areas of research, such as tailed studies of the genomes of mammals, flies,
nanotechnology, biomaterials and synthetic biolo- and nematodes have revealed unanticipated
gy [21-23]. mechanisms of gene regulation: microRNAs-first
The most obvious benefit of cephalopod genomics characterized through nematode genetics and
will be to individual laboratories already studying then shown to bDer uobsoiqpuhiitloaus [33]; epigenetic mod-
cephalopod biology. With a full inventory and ification of the genome-first documented through
complete sequences for known genes of interest, the genetics of position-effect variega-
laboratories can study gene function much more tion and then mechanistically clarified by studies
rapidly and thoroughly. In addition, with a near- in many speXcisiets,H i1n9c)luding mammals [34,35]; and
complete inventory of protein-coding and non- long non-coding RNAs-initially identified in
coding RNA genes, these researchers can assess a mammals ( , and flies (BX-C) and subse-
much larger set of candidate genes for function in quently found to be pervasive [36,37]. The extent
their biological processes of interest. to which gene and protein expression in mollusks
is regulated by the mechanisms identified in
The greater benefits may come, however, to bio-
mouse, fruit fly, and nematode is unknown, but
logical researchers outside the existing cephalo-
one striking example is provided by RNA editing.
pod field. Until very recently, genome-scale anal-
This regulatory process for protein diversification
yses of biological processes have favored the se-
was initially described in mammals, but now ap-
quencing of two out of the three major divisions of
pears to be much more widely employed in cepha-
bilateral animals [24]: deuterostomes (primarily
lopods than in vertebrates [38,39]. It is possible
vertebrates, with an expanding study of other
that deeper genomic studies of mollusks, and in
chordates and selected non-chordaDteros ssoupchhil aas m seela-
particular cephalopods, will reveal additional, as
aunrcohgiansst erand hCeameniochrhoardbdatiteiss) e leagnadn secdysozoans
yet undiscovered mechanisms of animal gene reg-
(from which the model organisms
ulation.
and both come).
In contrast, there has been far less genomic analy- Another promising arena of research that may
sis of lophotrochozoans, with genomes published benefit from cephalopod genomics is the global
for only a handful of organisms, including three analysis of protein-coding gene families [40],
trematode parasitic worms and one oyster [25- which has to date been strongly biased towards
29]. The genes and gene networks regulating the deuterostomes and ecdysozoans. Proteins in these
independent evolution of the host of highly de- two groups feature extremely well characterized
rived features displayed in cephalopods are un- domains as well as domains that remain complete-
khtntpo:w//snta, nmdaarkdsiningg ecnoommpicasr.oartgiv e analyses of these ly obscure and are typically described as "Dom1a7i7n
Cephalopod genomics
Hapalochlaena maculosa
of Unknown Function" [41]. Cephalopod genomics The deadly venom of blue-ringed octopus
can be expected to enrich our knowledge of such makes this species of in-
protein domain modules. Moreover, study of terest for study of the evolution and regulation of
cephalopods will also almost undoubtedly expand toxicity within octopods [1].
the pool of protein domains, as it has already done
Comparative studies of these octopus species
in the identification of the reflectin protein family
would illuminate the bases of both their shared
C[1h1o].i ces of cephalopod species for genomic characteristics as well as those of their divergent
sequencing features. Additionally, these species have essential-
ly non-overlapping geographic distributions,
providing animal accessibility to cephalopod re-
Sepia Loligo
Within the Mollusca, cephalopods diverged from a searchers globally.
Sepia officinalis
monoplacophorNaanu-ltiiklues ancestorA ollvoenra u5t0il0u smillion Within the decapodiforms, and are the
years ago, later branching into the extant clades
most studied genera. Historically, S.
Nautiloidea ( and ) and
hofafsic ibneaelnis a key cephalopod for neurobiological re-
Coleoidea (squid, cuttlefish and octopus) [2,42-44].
search, and is a critical species in global fisheries.
The CephSeq Consortium has come together with
possesses a complex chromatophore
the intention of using strategic genomic and
network for countershading, camouflage and com-
transcriptomic sequencing of key cephalopod spe-
munication [3,52,53]. Its internal calcified shell
cies to address previously unanswerable questions
supplies buoyancy andS. tohfefi ceinffaelcits of global climate
about this group. Taking into account the challeng-
changes on this structure has become a focus of
es of cephalopod genome sequencing, as well as the
recent study [54,55]. is emSe.r ogfifnicgi naasl ias
necessity to address nodal taxa, we have identified
particularly versatile model organism in eco-evo-
a set of species on which to focus our initial efforts.
devo studies [56]. As a practical matter,
Selected species have been chosen based on the
eggs are voluminouSs., oaffnicdi neaalissily collected, main-
curiosity of their biological features as well as the
tained and reared in the laboratory [57]. The mor-
possible advantages of their practical use. These
phological events in embryogenesis are
Loligo
species also cover ecologically diverse life histories,
well described in the literature [58-61].
representing benthic, nectobenthic and nectonic
, and particularly its giant fiber system, has
animals.
served as the fundamental basis for our under-
Cephalopods are animals with advanced cognitive
standing of nerve impulse conduction. The giant
skills and a complex repertoire of behavioral abili-
Lsyonliagpose system has recently been employed as a
ties [3,45]. Their brains are comparable both in size
biomedical model of neurological disease [62].
and complexity with those of vertebrates, and have
Loligo pise aoleniei of the most important groups for
been the focus of a number of studies on the neu-
cephalopod fisheries in the North Atlantic [8].
robiology of behavior [46]. In particular, they have
is the premier experimental species
Osecrtvoepdu sa sv umlgoadreisls for the cellular and systems cir- of the loliginids, with not only an extensive publica-
cuitry of learning and memory [4,9]. Historically,
tion base [63], but also annual availability at the
Euprymna scolopes
has been a key species for this
Marine Biological Laboratory (Woods Hole, MA).
work through studies of anatomy [9O], bveuhlgaavrioisr fol-
is a unique cephalopod mViobdrieol
lowing lesions and brain stimulation [3,4,47] and
foirscghaenriism because of its well-described symbiotic
cellular neurophysiology [48,49]. . has
relationship with the luminescent bacterium
also served as an attractive model for neuroendo-
Octopus bimaculoides . This important biomedical model has been
crine studies in invertebrates [5,50].
employed to study the mechanisms of host coloni-
Recently, (California TwoO-. Ezautpiorynm annad sscyomlobpieosnt specificity, host/microbe cell-
bspimota cOucltooidpeuss) has emerged as a model system for cell signaling, and innate immunity [64-67].
cephalopod biology. The large size of
’ short life cycle and small egVg.
eggs grants unique access to early
fsiiszceh earlsio make it an attractive choice for develop-
embryonic stages, making this species a prime can-
mental studies in culture [68,69]. In 2005, the
didate for future genetic and develoOpmbiemnatcaul lsotiuddes- genome was sequenced [70]; having access
ies. The hardiness, ready availability in the United
to the host genome would allow this field to ad-
States and easy husbandry of adult .
vance rapidly.
1[5718] add to the appeal of this model species. Standards in Genomic Sciences
Albertin et al.
Idiosepius
Pygmy squids ( ) have one of the smallest mixture of high read coverage derived from short
genomes among cephalopods (2.1 Gb), making insert libraries (300-2000 bp) and high clone-
them strong candidates for assembly and annota- coverage of longer insert (5-10 kb) and fosmid
tion [30]. Their small body size and exceptionally jump libraries (or mate-pair libraries). In this ap-
short life cycle also distinguish these cephalopods proach, approximately 45× coverage from the
Architeuthis dux
as possible model organisms [71]. smaller insert libraries and 45× coverage from a
The giant squidA rchiteuthis Archit esuetrhviess to repre- 5-kb insert library would be produced for each
sent deep-sea cephalopods. Little is known about taxon. In addition, 5× read coverage would be
the species of . is globally generated for 10-kb insert size libraries. For in-
distributed and a recent analysis of the complete creasing genomic contiguity and long-range scaf-
mitogenomes of multiple giant squid worldwide folding, 40-kb fosmid jump libraries at 1× genomic
showed no detectable phylogenetic structure on coverage should be added for the ten pioneer
the mitochondrial level and an exceptionally low cephalopod genomes (see Table 1). These meth-
level of nucleotide diversityA, rscuhgitgeeustthiinsg that there oded sn hoavvoe been tested and were successful in the
is only one global species of giant squid [72]. A nu- sequencing of the 2.4 Gb giant panda [74] and the
clear reference genome for would clar- assembly of the 3.2 Gb human genome
ify the population genetics of this species and pro- with ALLPATHS-LG [75]. Additional approaches,
vide critical information for comparative studies such as sequence-based genetic mapping to bridge
Nautilus
across cephalopods. the gap between scaffolds and chromosomes and
emerging long-read single molecule technologies
, the cephalopod “livingN afoustsiliul”s, is a repre-
(PacBio RS), could also be employed.
sentative of a phylogenetically unique branch of the
cephalopods, the nautiloids. possesses InAiptilyasl iaef, foBritosm inp hcaelpahriaal,o pLoodt tgiaenomics, as well as
many presumably ancestral anatomical features more mature efforts in other molluscan genomes
not shared with other cephalopods, including pin- ( ), have identified
hole eyes, rhinophores for odor detection, an ex- many challenges in generating useful genomic as-
ternal shNealul, tialunsd numerous tentacles, all without semblies. Many specific taxa were discussed at the
suckers [73]. Comparative genomic studies em- NEOSCcteonptu ms eeting, and several collaborative pro-
ploying would highlight the genetic bases jects have been initiated. For example, two species
oSfe tqheusee ndcivienrgge nstt rfeaatteugreys . of will soon have genomic sequence gen-
erated,I daionsde ptiwuso groups plan to sequence the
smallest known cephalopod genomesS, ethpioaseL oofl itghoe
genusE uprymna (2.1 Gb). There was broad sup-
Cephalopod genomes are large, complex and full
port at the meeting for sequencing , ,
of repeats. Sequencing and assembly may be tech-
and , based on biological significSaenpciea,
nically very challenging. Below we recommend
oreffsiecianraclhis comEumpurynmityn as izesc oalnodp epshylHogaepnaeloticch lpaoensia-
what, with the current state of hardware and
tmioanc.u lLoismaitAerdc hgietenuotmhies dsueqxuenceN aduattialu fsr opomm pilius
software, would be excellent approaches to tack-
, ,
ling cephalopod genomes. Researchers in the
, and
CephSeq Consortium will undoubtedly choose
are or will soon be available. Integration of these
varying combinations of approaches for their spe-
sequence data will assist with Naanuntoiltuastion and
cific projects. In any event, with rapid changes in
gene detection by sampling broadly across the
the underlying technologies for sequencing, as-
phylogeny of cephalopods, with provid-
sembly and annotation, this series of technical
ing an important outgroup for the coleoid cepha-
recommendations will need to be revisited on a
lopods. Interpretation of cephalopod-specific ge-
regular basis, and should be viewed as the snap-
netic novelty and the innovations involved in
shot it is of a particular moment (May 2012) in a
nervous system specialization would be further
rapidly advancing field.
assisted by the sequencing of an outgroup such as
Our recommendation for the initial approach to
one from the Monoplacophora. While contiguous
genome sequencing of cephalopods is to use a
and annotated genomes are our ultimate goal, the
proven low-cost short-read sequencing approach
strong sense of the community is that intermedi-
(Illumin≥a HiSeq with long-insert mate pairs). The ate assemblies and transcriptome sequencing
current best practices for initial assembly of com-
would be immensely helpful, and ideally would be
http://standardsingenomics.org 179
plex ( 1 Gb) eukaryotic genomes involve a
exchanged prior to publication.
Cephalopod genomics
Table 1. Cephalopod species proposed for initial sequencing efforts.
Current
Estimated genome sequencing Geographic Lifestyle
Species size (Gb) coverage distribution juvenile/adult Research importance
classic model for brain
planktonic/
O. vulgaris 2.5-5 46× world-wide and behavior, fisheries
benthic
science
emerging model for de-
O. bimaculoides 3.2 50× California, Mexico benthic velopment and behavior,
fisheries science
H. maculosa 4.5 10× Indo-Pacific benthic Toxicity
classic model for behav-
East Atlantic-
S. officinalis 4.5 - nectobenthic ior and development,
Mediterranean
fisheries science
cellular neurobiology,
L. pealeii 2.7 - Northwest Atlantic nectonic
fisheries science
animal-bacterial symbio-
E. scolopes 3.7 - Hawaii nectobenthic sis, model for develop-
ment
model for development,
I. paradoxus 2.1 80× Japan nectobenthic
small genome size
model for development,
I. notoides - 50× Australia nectobenthic
small genome size
A. dux 4.5 60× world-wide nectonic largest body size
“living fossil”, outgroup
N. pompilius 2.8-4.2 10× Indo-Pacific nectonic
to coleoid cephalopods

It must be emphasized that all the projects de- resources to assist and train automated gene de-
scribed above are in their infancy and are ex- tection programs. Of primary importance will be
pected to benefit from the formation of the the generation of transcript inventories to identify
CephSeq Consortium. Indeed, representatives genes, refine gene models, detect start points and
from each of these cephalopod sequencing efforts intron-exon boundaries, and train automated gene
participated in the NESCent meeting and agreed to identification algorithms. Transcriptome data
the formation of the Consortium. such as those from RNAseq are quick and relative-
ly inexpensive to generate, and will be immensely
Annotation of novel genomes is a complex prob- useful. Systematic sequencing of nervous system
lem [76]. Efforts at automated annotation of tissues and embryonic stages can be combined
molluscan genomic sequences have demonstrated with relatiOvecltyo peuasrly-stage assOe.m bvulilegsa rtois generatOe.
the challenge facing the future annotation of ceph- gbeimnea cumlooiddeelss and Iedxioonse psitursuctures. InI . andodtiotiidoens,
alopod genomes. Long branch lengths within the pairsI . poaf radoxus species ( and
phylum, the taxonomic distances to well annotat- ) and species (
ed animal genomes, and the relatively low quanti- and ), through comparative sequence
ty of previous molecular and genetic work in the analysis, may be critical for annotation.
180 Standards in Genomic Sciences
Mollusca will demand the generation of additional
Albertin et al.
Annotation efforts are labor-intensive but also offer defined cephalopod community, while protecting
an opportunity to grow the cephalopod research the interests of those generating the data.
community and attract outside expertise. For exam-
We therefore propose to adopt a liberal opt-in da-
ple, domain experts of particular gene families or
ta sharing policy, modeled in part on the JGI data
pathways can be recruited to assist in the descrip-
usage policy [78], which will support the rapid
tion of likely protein function. Bioinformatics re-
sharing of sequence data, subject to significant
searchers interested in the problems of annotation
restrictions on certain types of usage. Community
across long phylogenetic distances, the assessment
members will be encouraged to submit their data,
of unique gene families and the evolution of bio-
but not required to do so. We plan to provide in-
chemical novelty, and the likely challenges of exten-
centives for this private data sharing by (1) devel-
sively RNA-edited transcriptomes, will also be en-
oping a community data and analysis site with a
listed. Finally, annotation provides an outreach op-
simple set of automated analyses such as contig
portunity to involve young scientists and K-12 class-
assembly and RNAseq transcript assembly; (2)
rooms in cutting-edge scientific discovery on these
offering pre-computed analyses such as homology
fDasacitnaa tsinhga orrignagni spmlas.n search across the entire database; and (3) sup-
porting simple investigative analyses such as
BLAST and HMMER. We also plan to provide bulk
An important goal of the CephSeq Consortium is to download services in support of analysis and re-
share data rapidly and effectively both within and analysis of the entire dataset upon mutual agree-
beyond the Consortium. Data sharing is necessary ment between the requesting scientist and the
to foster the broadest possible impact of our se- CephSeq Consortium Steering Committee (see be-
quencing and annotation efforts. This sharing will low), who will represent the depositing scientists.
prove critically important for the cephalopod Collectively, these policies would provide for
community. We expect sequence homology within community engagement and participation with
the taxon to be an important foundation for col- the CephSeq Consortium while protecting the in-
laboration within the field because cephalopods terests of individual contributors, both scientifi-
have evolved many new and unique character fea- cally and with respect to the Convention on Bio-
tures. Sharing data prior to publication could sig- logical Diversity [79]. Policy details will need to be
nificantly accelerate cephalopod research. How- specified and implementation is subject to fund-
ever, data sharing policies must also recognize ing. Our intent is to build an international com-
that there is significant publication, funding, and munity by putting the fewest barriers between the
career recognition risks involved in making data data and potential researchers, while still protect-
available before publication: often the first to pub- iTnhg eth Ce deaptah gSeenqer Catoorns.s ortium: Mission
lish a particular observation garners the most
statement and organization
recognition.
Mission Statement:
Broad data-sharing agreements such as the Ft.
Lauderdale agreement [77] have already been
The vision of the Cephalopod
adopted by the international genomics communi-
Sequencing Consortium is rapid advancement of
ty, and, most significantly, by many large sequenc-
cephalopod science into the genomics era, one
ing centers. However, as the sequencing capacity
employing the most modern and efficient methods
of small collaborations has increased, this type of
available and engaging broad international partic-
agreement is an increasingly poor fit for the data
ipation by the entire cephalopod scientific com-
being generated. Moreover, for a federated com-
munity. This vision entails communication and
munity such as the CephSeq Consortium, with sig-
active promotion of sequencing technologies and
nificant international participation by many small
findings to researchers across a great diversity of
groups, enforcement of any agreement is challeng-
fields. Bioinformatics experts initially outside of
ing. We believe that an explicit policy should be
cephalopod biology will participate with cephalo-
adopted to protect data generators while creating
pod researchers in this effort. The Consortium will
incentives for the earliest possible sharing of data.
help facei.lgit.ate funding endeavors by individuals
An effective policy should also encourage use of
and groups by providing basic summary docu-
cephalopod sequence data beyond the currently
ments ( , white papers, letters of support) that
http://standardsingenomics.org describe the current state and consensus goal1s8 o1f
Cephalopod genomics
cephalopod genomics efforts worldwide. In addi- on an international scale. One likely venue for
tion to promoting and accelerating scientific pro- such workshops would be society meetings, such
gress, the CephSeq Consortium aims to translate as the annual meeting of the Society for Integra-
The Steering Committee urges scientists
the contributions of cephalopod science to society tive and Comparative Biology (SICB).
who support the goals of this white paper
at large by encouraging applied science in fields as
to join the consortium by signing the
diverse as fisheries science, materials science and
biomedical research. Education and outreach will white paper and participating in the ac-
be emphasized for broad dissemination of pro- tivities of the consortium.
gress in cephalopod genomics at multiple levels,
including K-12, undergraduate and graduate stu- Broader impacts
Organizational Structure:
dents, and the public at large.
Establishment of a
Steering Committee was agreed upon at the May A specific recommendation of this white paper is
2012 NESCent Catalysis Group Meeting. The com- to compete for a Research Coordination Network
position of the committee was initially set at seven (RCN) grant from the NSF. A Cephalopod RCN
members, with broad international representation would facilitate annotation of the cephalopod ge-
of cephalopod biologists, genomicists and nomes being produced worldwide, mediate the
bioinformaticians. The Committee will initially exchange of emerging technologies that will bene-
meet every 4 months, either in person, or remote- fit from genomic resources and accelerate the ad-
ly, or both. The Steering Committee is charged vent of new areas of research made possible by
with providing international oversight of the cephalopod genomics. It would also serve to ex-
community’s activities, fostering the free-flow of pand the next generation of cephalopod research-
information among CephSeq Consortium mem- ers. Consequently, a central element of a Cephalo-
bers (see Data Sharing Plan), promoting collabora- pod RCN would be short-term laboratory ex-
tions, and ensuring that the CephSeq Consortium changes for undergraduate and graduate students
remains focused on the Mission Statement objec- to aid in genome annotation and analysis, to pro-
tives set forth above. The Steering Committee will mote education in bioinformatics and cephalopod
also work to facilitate community-wide efforts to biology and to foster new collaborations across
annotate assembled genomes. the cephalopod community.
The tenure of the Committee will initially be two Cephalopods are important to science, including
years, and any and all cephalopod researchers are the fields of cellular neurobiology, learning and
encouraged to contact the Committee about the memory, neuroethology, biomaterial engineering,
changing needs of the community. The inaugural animal-microbe interactions, developmental biol-
members are: Laure Bonnaud (Univ. Paris, ogy, and fundamental molecular biology such as
France), C. Titus Brown (Michigan State Univ., RNA editing. Access to genomic information will
USA), Roger Hanlon (Marine Biological Laborato- greatly facilitate this ongoing research, particular-
ry, USA), Atsushi Ogura (Ochanomizu Univ., Ja- ly through gene discovery. Cephalopod genomics
pan), Clifton Ragsdale/Chair (Univ. Chicago, USA), will also drive the creation of new areas of inves-
Jan Strugnell (La Trobe Univ., Australia) and tigation, including such biomedically important
Guojie Zhang (BGI, China). topics as regeneration and aging [83,84]. Other
examples of promising post-genomic cephalopod
A web site [80] will serve as a point of contact for
research include study of the unknown chemosen-
the worldwide community. An auxiliary site for
sory systems by which cephalopods monitor their
sharing cephalopod genomic and transcriptomic
marine environments, and the isolation of cepha-
data is to be established within the next six
lopod neurotoxins, which could lead to novel rea-
months (see Data Sharing Plan). The CephSeq
gents for research and drug-based therapies [12].
Consortium will coordinate internationally with
Cephalopod genomics will also be important for
the Cephalopod International Advisory Council
evolutionary biology, particularly for understand-
(CIAC) [81] and with the newly established
ing the great diversity and genomic complexity of
CephRes-Associazione Cephalopod Research-
the whole molluscan phylum and for probing the
ONLUS [82], which is based in Europe.
emergence of the evolutionary innovations that
Workshops will be organized annually to ensure
are represented by cephalopod eyes, large brains
182 Standards in Genomic Sciences
coordinated and cooperative progress in genomics
and prehensile arms.
Albertin et al.
Cephalopods are a critical component of marine help monitor cephalopod overfishing and improve
Nauti-
ecology, are important commercially to the fisher- cephalopod aquaculture.
lus
ies industry and are an emerging aquaculture tax-
People are fascinated by cephalopods, from
on. The effects of global warming and marine acid-
to the octopus to the giant squid. The coupling
ification and hypoxification on cephalopod health
of genomics to cephalopod biology represents a
and viability are unknown and can only be fully
fusion of two areas of great interest and excite-
assessed with improved species delineation and a
ment for the public. This fusion presents a tre-
deeper understanding of population dynamics.
mendous educational platform, particularly for K-
Specifically, cephalopod genomics will aid our
12 students, who can be engaged in the classroom
ability to track population migrations and monitor
and through the public media. Public outreach
demographic expansions and contractions. This
about cephalopod genomics will help build sup-
information will in turn directly inform efforts to
port for basic scientific research, including study
assess the effects of climate change on cephalopod
of marine fauna and ecology, and will add to the
stocks [85]. Cephalopods are a critical food source
public’s understanding of global changes in the
and genomic resources can also be expected to
Acknowledgements biosphere.
We thank Drs. Carlos Canchaya and David Glanzman Foundation through the National Evolutionary Synthe-
who were unable to attend the full meeting but con- sis Center (NESCent) under grant number NSF #EF-
tributed to our discussions and decisions. The Catalysis 0905606.
Group Meeting was supported by the National Science
Scientists who have written in support of the
white paper
Tom Abrams, University of Maryland School of Med-
Euan R. Brown, Heriot-Watt University, Edinburgh,
icine, Baltimore, MD, USA
UK
Shelley Adamo, Dalhousie University, Halifax, Nova Bernd U. Budelmann, Galveston, TX, USA
Scotia, Canada
Roy Caldwell, University of California, Berkeley, CA,
Louise Allcock, National University of Ireland, Gal- USA
way, Ireland
R. Andrew Cameron, California Institute of Technol-
Frank E. Anderson, Southern Illinois University, Car- ogy, Pasadena, CA, USA
bondale, IL, USA
David Carlini, American University, Washington, DC,
Paul Andrews, St George's, University of London, USA
London, UK
Sean Carroll, University of Wisconsin, Madison, WI,
George J. Augustine, Center for Functional USA
Connectomics, KIST, Seoul, Korea
Maria G. Castillo, New Mexico State University, Las
Yann Bassaglia, Univ. Paris-Est Creteil, Creteil, Cruces, NM, USA
France
Thomas W. Cronin, University of Maryland Balti-
Elaine L. Bearer, University of New Mexico Health more County, Baltimore, MD, USA
Sciences Center, Albuquerque, NM, USA
Joseph A. DeGiorgis, Providence College, Providence,
Francisco Bezanilla, University of Chicago, Chicago, RI, USA
IL, USA
Anna Di Cosmo, University of Naples "FedericoII",
Jean Geary Boal, Millersville University, Millersville, Naples, Italy
PA, USA
Ludovic Dickel, University of Caen Lower-
Sydney Brenner, Okinawa Institute of Science and Normandy, Caen, France
Technology, Okinawa, Japan
Casey Dunn, Brown University, Providence, RI, USA
http://standardsingenomics.org 183