Summary Report of the first LaGomiCs meeting_v3

Summary report of the first Lagomorph Genomics Meeting, 18-19 February 2013,Bologna, Italy Hosted by the Department of Agricultural and Food Sciences of the University of Bologna The mee

Summary report of the first Lagomorph Genomics Meeting, 18-19 February 2013,

Bologna, Italy

Hosted by the Department of Agricultural and Food Sciences of the University of Bologna

The meeting was organized by RGB-Net (COST Action “A Collaborative European Network on Rabbit Genome Biology – RGB-Net”) in collaboration with the World Lagomorph Society (WLS)

It was attended by 30 people from 10 countries (please see Appendix 1 for a list of all participants) Other scientists, who could not attend the Bologna meeting (listed in Appendix 2), expressed their

interests and support this initiative, guaranteeing different levels of contributions/cooperation (collection of samples, sequencing, etc.)

The meeting was held in two days according to the programme in the Appendix 3.

The main aim of the meeting was to establish an international collaborative consortium for sequencing the genome of all species of the order Lagomorpha (around 90 species), in a timeframe

of 5 years (as estimated now)

All participants agreed to name the consortium “Lagomorph Genomics Consortium: LaGomiCs”

Following the organization of the meeting, the Consortium was born from a joint initiative of the World Lagomorph Society and RGB-Net, and all participants agreed to participate However, the consortium is open to all future contributors Apart the individual contributions, institutional participations are welcome and desired (the Memorandum of Understanding – MoU - should be signed by representatives of the institutions) J Melo-Ferreira and Paulo Alves, announced that CIBIO/University of Porto wants to participate in the consortium, and offer special conditions for genome sequencing and data analysis in CIBIO’s genomic platform and for funding the genome sequencing of two lagomorph species University of Bologna wants to participate and offers next generation sequencing platforms of its Centre for Genome Biology and bioinformatics expertises, including the possibility to sequence a few lagomorph species Also other institutions represented

by members attending the meeting expressed interest in participating in the consortium A list of institutions willing to participate will be updated in next documents

Main decisions that have been taken:

1) Prepare a “White Paper” reporting the reasons for sequencing all Lagomorph genomes, resources available and how to proceed on this aim The structure of this document has been

already drafted with the following sections: i) Introduction (what Lagomorphs are, special

features of the Lagomorphs, state of the art, from rabbit and pika genomes to all lagomorphs

genomes); ii) research potential of Lagomorph genomics values and impacts (speciation and

hybridization; rapid radiation, phylogeny and taxonomy; conservation and ecology; biological invasions; ecosystems services; zoonosis - bioindicators and reservoirs; mechanisms of genome evolution; local adaptation and climate change (including altitude adaptation, animal models; host-parasite coevolution; ancient DNA and paleontology;

economic value and impact); iii) sampling and storage of biological material; sequencing methods and analyse; v) data storage and ownership/release policies; resources/sequencing already available; vi) science outreach and education The writing of the White Paper will be

coordinated by Paulo Alves (President of the WLS) and by Luca Fontanesi (Chair of RGB-Net) Several contributors have been already identified within the attendees and agreed to write paragraphs or topics related to their expertises A few other experts will be contacted

A draft of the white paper should be ready within two months

2) Based on the White Paper draft, a brief introductoria paper will be produced to send to

scientific journals

3) A review on lagomorph genomics will be prepared (identified journal: Mammal Review?)

It will be useful for PhD students to contribute to the writing to this paper as an introduction for their thesis

4) A Web page will be prepared and hosted by the University of Bologna It will include a

summary of the white paper, list of people and research institutions joining the LaGomiCs consortium The LaGomiCs webpage will have links on the following existing webpages:

World Lagomorph Society, RGB, departments from the participants, ???

5) A Memorandum of Understanding (MoU) will be produced to regulate sharing of samples, data and resources, and to establish the rules This document will be prepared just after the White Paper (or in parallel if needed by the activities of consortium’s members)

6) The next LaGomiCs appointment will be based on an electronic conference call that should

take place during may

7) The next LaGomiCs meeting will be held in 2014 (probably Zagreb, Croatia, in April as a

satellite meeting of the COST Action RGB-Net meeting)

8) The Consortium established a priority list of species to be sequenced and exchanged it with the Broad Institute to avoid overlapping and complement resources (this list is included in

Appendix 4).

9) A repository information for biological samples available within the consortium will be based on the Biosamples database already established at EMBL (http://www.ebi.ac.uk/biosamples/index.html) An example file to be filled will be distributed among the participants

10) A pilot RAD-seq project has been proposed in Lepus sp by Cristiano Vernesi and Ettore

Randi A few groups have already agreed to contribute

During the meeting we had a conference call with the Broad Institute (Federica Di Palma), but also including a call with Tim L King, Leetown Science Center, USA) The main topic discussed was the possibility to combine efforts as the Broad Institute already decided to sequence other mammals, including a few lagomorphs species During the conference call, it was decided to share a list of priority list of species to be sequenced This list has been already sent to the Broad Institute

(see Appendix 4) It was also discussed how to participate to the 10XGenome project Federica will

introduce the LaGomiCs initiative to the direction board of the 10XGenome.

A complete report with detailed minutes of the discussions and decisions carried out during the meeting will follow shortly

A framework of the White Paper with possible contributors will be sent around in a few days This text will be the basis to write a first draft

Appendix 1:

List of participants

Luca Fontanesi University of Bologna Italy luca.fontanesi@unibo.it Paulo Célio Alves CIBIO, University of

Rita Casadio University of Bologna Italy rita.casadio@unibo.it Pier Luigi Martelli University of Bologna

Italy gigi@biocomp.unibo.it

UK Nizar.Drou@tgac.ac.uk Cristiano Vernesi Fondazione E Mach Italy cristiano.vernesi@fmach.it

Italy antonio.lavazza@izsler.it José Melo Ferreira CIBIO, University of

Fernando A

Cervantes

Universidad Nacional Autonoma de Mexico Mexico fac@ibunam2.ibiologia.unam.mx

Jerome Letty Office National de la

Chasse et de la Faune Sauvage

France jerome.letty@oncfs.gouv.fr Zissis Mamuris University of Thessaly

Mihajla Djan University of Novi Sad Serbia mihajla.djan@dbe.uns.ac.rs Carl-Gustaf Thulin Swedish Agricultural

University Sweden Carl-Gustaf.Thulin@slu.se Nevena Velickovic University of Novi Sad

Serbia nevena.velickovic@dbe.uns.ac.rs Vlatka Cubric University of Zagreb Croatia vcubric@agr.hr Katie Andrea Solari Stanford University

USA ksolari@stanford.edu Chiara Angelone University of Rome 3 Italy chiara.angelone@uniroma3.it Enrico D'Alessandro University of Messina Italy enrico.dalessandro@unime.it Giuseppina Schiavo University of Bologna

Italy pippi@biocomp.unibo.it Francesca Bertolini University of Bologna Italy francesca.bertolini2@studio

unibo.it Anisa Ribani University of Bologna Italy anisa.rib@hotmail.it

Valerio Joe Utzeri University of Bologna Italy va.joe6@gmail.com Stefania Dall'Olio University of Bologna

Italy stefania.dallolio@unibo.it Emilio Scotti University of Bologna Italy emilio.scotti3@unibo.it Antonia Bianca

Samorè

University of

Federica Di Palma* Broad Institute USA fdipalma@broadinstitute.org

Tim L King*

U S Geological Survey, Leetown Science Center,

* On conference call

Appendix 2:

List of scientists supporting this initiative that could not attend the Bologna meeting

Andrew T Smith Chair, IUCN/SSC

Lagomorph Specialist Group, Arizona State University

USA a.smith@asu.edu

Nuno Ferrand de

Almeida

CIBIO, University of Porto

Portugal nmferran@fc.up.pt

Miguel Carneiro CIBIO, University of

Porto

Portugal miguel.carneiro@cibio.up.pt

Pedro J Esteves CIBIO, University of

Joana Abrantes CIBIO, University of

Franz Suchentrunk Research Institute of

Wildlife Ecology, University of Veterinary Medicine Vienna

Austria

Franz.Suchentrunk@vu-wien.ac.at

Klaus Hackländer University of Natural

Resources and Life Sciences, Vienna (BOKU)

Austria klaus.hacklaender@boku.ac.at

Stefane

Marchandeau

Office National de la Chasse et de la Faune Sauvage

France stephane.marchandeau@oncfs

gouv.fr

Michael Russello The University of British

Columbia

Canada michael.russello@ubc.ca

Rajeev Patnaik Centre of Advanced

Study in Geology, Panjab University

India rajeevpatnaik@gmail.com

Zelalem Gebre

Mariam

Ethiopia aslnp2000@yahoo.com Mahmoud Mohamed Suez Canal University Egypt ghaffar_mahmoud@yahoo.com Paolo Tizzani Department of Veterinary

Sciences Parasitology Section University of Torino

Italy paolo.tizzani@unito.it

Rudy Boonstra Centre for the

Neurobiology of Stress

& Department of Biological Sciences, University of Toronto Scarborough

Canada boonstra@utsc.utoronto.ca

Terence J Robinson Stellenbosch University South Africa tjr@sun.ac.za

Narayan Pd Koju Tribhuvan University Nepal npkoju.2003@gmail.com Nishma Dahal National Centre for

Biological Sciences Bangalore

India Nishmad@ncbs.res.in

Hung Sun Koh Chungbuk University South Korea syskoss@chungbuk.ac.kr Joerns Fickel Leibniz Institute for Zoo

and Wildlife Research

Germany fickel@izw-berlin.de

Adrienne Kovach University of New

Thomas J

McGreevy University of Rhode Island USA tjmcg@my.uri.edu

Thomas Husband University of Rhode

Island

Appendix 3:

Programme of the meeting

18 February

9.00-10.00 Arrival

10.00-10.30 Introduction of the initiative - presentation of RGB-Net and WLS: Fontanesi L., Alves P 10.30-11.00 An overview on Lagomorph biology: Alves P.

11.00-11.45 Round table of presentation of the participants (4-5 slides for each group)

11.45-12.00 Coffee break

12.00-12.30 RAD-sequencing project

12.30-13.30 Definition of the aims of the consortium, preparation of a white paper (ideas and

preliminary draft of the content), rules, roles, funds

13.30-14.30 Lunch

14.30-16.00 Databases, discussion about the visibility of the initiative (web-site, preparation of a paper/review to be submitted to a scientific journal, press communications, etc.)

16.00-16.30 Coffee break

16.30-18.00 Conference call with the Broad Institute (Federica Di Palma) and other groups around the world: Presentation of the discussion and ideas produced in the morning, presentation of the research programmes of the groups connected - additional ideas

18.00-18.30 Summary and closure of the first day (how this initiative could join the 10K genome project)

20.30 Dinner together

19 February

9.30-10.00 Constitution of working groups: a) fund raising, b) catalogue of research activities in lagomorphs related to this initiative, c) technology exploitation - sequencing strategies/data analysis, d) identification of priorities (species, etc.), including extinct species (aDNA)

10.00-11.00 Working group activities

11.00-11.30 Coffee break

11.30-12.30 Presentation of working group activities and discussion

12.30-13.30 Assignment of duties - Summary - Next meeting/conference call

13.30 Lunch

14.00 Departure

Appendix 4

Priority List for genome Sequencing (existing samples) – preliminary list

L timidus (20x) S floridanus O curzoniae Prolagus sardus (Ext,

bones)

L europaeus S audubonii O macrotis Romerolagus diazi

L corsicanus S cunicularius O princeps (>7x) Pronolagus rupestris

L granatensis

(>20x)

S brasiliensis O thibetana Bunolagus monticularis

S bachmani

L capensis S nuttallii

L saxatilis

L tolai

L nigricolis

L coreanus

L callotis

L flavigularis

L insularis

L californicus

L townsendii

L americanus (10x

+ 20x)

L othus

L arcticus

Ongoing Priority Already sequenced at high coverage by the Broad Institute