MONOCULUS Copepod Newsletter - World Association of ...

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development of a communications strategy and associatednetwork in order to keep interested parties informed ofprogress. One major hurdle in the process described above isthe establishment of a consensus concerning the best initialcopepod(s) species to be sequenced. Perhaps the bestapproach to such a problem is the establishment of anindependent committee supported by experts from withinand external to the copepodology community who maymake a balanced and informed decision on the community’sbehalf.Given the extended timescale of a full-genomesequencing project, no given copepod species can currentlybe considered to be substantially ahead of the field in termsof the availability of genomic resources or progress towardsa funded genome project, although some species do possessgenomic resources that may help to form the basis forprospective genome projects. For this reason the authorswould be delighted to receive comments, suggestions ornotes of interest from members of the community or toanswer questions relating to the establishment of or use ofgenomics or proteomic resources (no hate-mail please).― James BronUniversity of Stirling, Scotland (jeb1@stir.ac.uk)Grace WyngaardJames Madison University, U.S.A.(wyngaaga@jmu.edu)andStewart JohnsonNational Research Council of Canada(Stewart.Johnson@nrc-cnrc.gc.ca)ReferencesGregory, T.R. 2006. Animal Genome Size Database.http://www.genomesize.comHumes, A.G. 1994. How many copepods? In: Ferrari, F.D.& B.P. Bradley (eds.). Ecology and Morphology ofCopepods. Proceedings of the Fifth InternationalConference on Copepoda. Hydrobiologia 292/293:1-7.————Dear Colleagues,In their letter, James Bron, Grace Wyngaard and StewartJohnson advocate the need for a dialogue for building thegenomics resources for copepod research. They alsoeloquently describe the criteria that should be used forselecting species for comprehensive genome and ESTsequencing projects. These include factors such as genomesize and complexity, wide geographic distributions tomaximize accessibility to investigators worldwide, andability to generate inbred lines. In addition to these criteria,we should also consider the specific questions or problemsthat we would like to address. Advances in functional8genomics are enabling us to move fairly quickly fromdescriptive genome sequencing to identifying the functionsand interactions of genes, conferring the ability to addressproblems across a wide array of disciplines in biology at amechanistic level.In this letter, we would like to share with you our plansfor sequencing the genome of the calanoid copepodEurytemora affinis. We first discuss why we chose thisspecies as a model organism, then we describe how thiscopepod genome project will facilitate future copepodgenome sequencing projects, and finally, we makerecommendations on how to build a community ofresearchers that could utilize genomic tools to address avariety of questions in copepodology. We highly encouragethe copepod community to begin discussing what othergenomic resources would benefit research in copepodbiology. Insights into morphology, ecology, and evolutionon copepods will be greatly enriched by having genomicresources for multiple copepod species.The copepod Eurytemora affinis serves as an excellentmodel for addressing fundamental questions in ecology andevolutionary biology, including those regarding adaptation,speciation, morphological stasis, niche evolution, biologicalinvasions, and host-pathogen coevolution. Eurytemoraaffinis is a key component of subtropical and temperateestuaries throughout the Northern Hemisphere. This copepodis a major grazer of algae and serves as a food source formany important fisheries. Within the past century, E. affinishas invaded freshwater lakes and reservoirs multiple timesindependently 1 . For example, E. affinis entered the GreatLakes ca. 1958, probably through dumping of ship ballastwater 2, 3 . These invasions have serious implications fordisease transmission, because E. affinis hosts a variety ofpotential disease agents, such as the pathogen Vibriocholerae.Because of the association between E. affinis and V.cholerae, The Institute for Genome Research (TIGR), aDivision of the J. Craig Venter Institute, is interested insequencing the genome of E. affinis. This sequencing projectwill probably begin in 2007. The copepod E. affinis is amain host of Vibrio cholerae 4-6 , but the nature of theassociation is not well understood. The riverine andestuarine bacterium V. cholerae causes cholera, an acute,diarrheal illness. In general, models of vector borne diseaseshave not been well developed in aquatic systems. Complexinteractions between E. affinis and V. cholerae might affectvirulence of V. cholerae. For example, chitin induces naturalcompetence in V. cholerae, allowing the bacteria to take upDNA from their environment and acquire genes necessaryfor virulence 7 . In addition, growth on chitin induces theproduction of toxin-coregulated pilus (TCP) by V. cholerae 8 ,which is critical for virulence. Also, the ability of V.cholerae to enter or exit dormancy might be related to the
association of V. cholerae with E. affinis, particularly whenthe copepods are in diapause. A comprehensive genomesequence and annotation of E. affinis would greatly facilitateidentifying genes and pathways that encode the mostrelevant traits, such as those associated with copepodphysiology and virulence. Because TIGR has alreadysequenced the genomes of several serovars of V. cholerae,we will be able to use entire genome sequences of both hostand pathogen to understand genetic responses of hostpathogeninteractions and the dynamics of this disease.Aside from host-pathogen dynamics, there are otherimportant questions that could be addressed using E. affinisas a model. For example, E. affinis provides an exceptionalmodel for exploring mechanisms of niche evolution.Phylogenetic analyses have revealed that freshwaterinvasions have occurred multiple times independently fromgenetically distinct saline sources 1 . Most notably, someclades have given rise to invasive populations, while othershave not 1 . Direct comparisons of source and invadingpopulations have revealed evolutionary adaptations that areassociated with habitat transitions 9, 10 . Analysis of multipleindependent invasions is beginning to offer insights intorepeatability of evolutionary pathways and parallel evolutionacross independent invasion events 1, 10 . Finally, comparinginvasive and noninvasive populations is allowing us todetermine properties that are exclusive to successfulinvaders 10, 11 . The use of cDNA microarrays has allowed theLee Lab to analyze functional categories of genes associatedwith freshwater invasions by E. affinis 10 . A comprehensivegenome would allow us to determine the actual targets ofnatural selection during these invasions.Finally, E. affinis provides an excellent model forexploring patterns of speciation in copepods. Speciesconcepts are difficult to define among copepods, with manystudies showing lack of correlation between morphologicaltraits, genetic distance, and reproductive isolation 12-16 . Thus,the field could benefit greatly from integrating genetics anddevelopment underlying morphological traits with thegenomics of reproductive isolation. Like many copepods, E.affinis forms a species complex that displays jagged andidiosyncratic patterns of speciation 14, 15 . Patterns ofmolecular evolution, morphological evolution andreproductive isolation are completely uncorrelated anddiscordant 15 . Despite the extremely high levels of geneticdivergence among clades (up to 20% at COI), there is a highdegree of morphological stasis 15 . Moreover, there isreproductive isolation between genetically andmorphologically proximate populations 14 . Eurytemoraaffinis offers an excellent model for the genomic study ofspeciation because they are easy to cross in the lab forstudies of reproductive isolation and possess a well-definedclade structure.9From a practical standpoint, E. affinis is one of the bestcandidates with which to begin a copepod genomesequencing project. It is tractable as a genomic model, andhas among the smallest copepod genomes (1C = 300 MB) 17 .The small genome greatly lowers sequencing costs andcomplexity of the assembly process, possibly allowing fullclosure and completion of the project to a ‘gold standard’level. This species does not possess chromatin diminution 17 ,a feature in some copepods where large fragments of thegenome are discarded from the presomatic line duringdevelopment. Extensive work has been devoted todeveloping culture techniques for this species, and as aconsequence it is readily cultured in a laboratory setting.Inbred lines of E. affinis can easily be generated, avoidingproblems associated with heterozygosity, which often plaguethe assembly phase of genome sequencing projects.Currently, inbred lines are being reared in the Lee Lab inpreparation for the genome sequencing project.In short, E. affinis provides an excellent candidate for acomprehensive genome project from multiple perspectives.However, if we want the entire field of copepodology toadvance and take full advantage of genomic resources, weshould not stop here. We describe the utility of choosing E.affinis as a model organism in order to illustrate the types ofquestions that we plan to address in a mechanistic fashion,using genomics tools. The availability of this genomesequence will make subsequent copepod genome projectsmuch faster and cheaper by providing the template forassembly and annotation. We hope that this example inspiresothers in the field of copepodology to think about theirquestions and about the best species that could be used toaddress those questions.As a community, we should begin discussing howgenomic tools could be used to address the most vexing andinteresting problems in copepod biology. For example,comparative genomics across multiple species could help usunderstand morphological evolution and elucidate problemsin morphological taxonomy. It has been demonstratedmultiple times that morphological characteristics areinadequate for defining many copepod species. In somecases, single gene phylogenies are inadequate, as well. Weneed to integrate our traditional methods with frameworksthat more accurately reflect the evolutionary history ofcopepod groups.The copepod community lags behind other communities(e.g., Daphnia, decapods) in employing genomicsapproaches. How do we train our community in this newarea? The copepod community needs a plan. GAW wouldlike to prepare a grant proposal to fund a training workshopand major symposium on a range of genomics topics toadvance the field of copepodology to be held at the 10thICOC in Thailand in 2008. We would like to hear from youabout your interest in participating in or attending such a
Page 1 and 2: MONOCULUS Copepod NewsletterThe New
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Page 5 and 6: A Copepod Genome Project:Opening Di
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Page 14 and 15: BooksPublications of R.V. GottoGott
Page 16 and 17: New Books and Websites: ReviewsMari
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Page 20 and 21: News from or about MembersMark Gryg
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