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 RGBNet). 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
Paulo Célio Alves
Rita Casadio
CIBIO, University of
Porto
University of Bologna
Pier Luigi Martelli
University of Bologna
Ettore Randi
ISPRA
Ian Streeter
EBI-EMBL
Nizar Drou
TGAC
Cristiano Vernesi
Fondazione E. Mach
Antonio Lavazza
IZSLER
José Melo Ferreira
CIBIO, University of
Porto
Universidad Nacional
Autonoma de Mexico
Fernando A.
Cervantes
Zissis Mamuris
Office National de la
Chasse et de la Faune
Sauvage
University of Thessaly
Mihajla Djan
University of Novi Sad
Carl-Gustaf Thulin
Nevena Velickovic
Swedish Agricultural
University
University of Novi Sad
Vlatka Cubric
University of Zagreb
Katie Andrea Solari
Stanford University
Chiara Angelone
University of Rome 3
Enrico D'Alessandro
University of Messina
Giuseppina Schiavo
University of Bologna
Francesca Bertolini
University of Bologna
Anisa Ribani
University of Bologna
Jerome Letty
Italy
luca.fontanesi@unibo.it
Portugal
pcalves@fc.up.pt
Italy
rita.casadio@unibo.it
Italy
gigi@biocomp.unibo.it
Italy
ettore.randi@isprambiente.it
UK
streeter@ebi.ac.uk
UK
Nizar.Drou@tgac.ac.uk
Italy
cristiano.vernesi@fmach.it
Italy
antonio.lavazza@izsler.it
Portugal
jmeloferreira@cibio.up.pt
Mexico
fac@ibunam2.ibiologia.una
m.mx
France
jerome.letty@oncfs.gouv.fr
Greece
zmamuris@gmail.com
Serbia
mihajla.djan@dbe.uns.ac.rs
Sweden
Carl-Gustaf.Thulin@slu.se
Serbia
nevena.velickovic@dbe.uns.
ac.rs
Croatia
vcubric@agr.hr
USA
ksolari@stanford.edu
Italy
chiara.angelone@uniroma3.it
Italy
enrico.dalessandro@unime.it
Italy
pippi@biocomp.unibo.it
Italy
Italy
francesca.bertolini2@studio.
unibo.it
anisa.rib@hotmail.it
Valerio Joe Utzeri
University of Bologna
Stefania Dall'Olio
University of Bologna
Emilio Scotti
University of Bologna
Antonia Bianca
Samorè
Federica Di Palma*
University of
Bologna/Milan
Broad Institute
U. S. Geological Survey,
Leetown Science Center,
Aquatic Ecology Branch
Tim L. King*
* On conference call
Italy
va.joe6@gmail.com
Italy
stefania.dallolio@unibo.it
Italy
emilio.scotti3@unibo.it
Italy
antonia.samore@unimi.it
USA
fdipalma@broadinstitute.org
USA
tlking@usgs.gov
Appendix 2:
List of scientists supporting this initiative that could not attend the Bologna meeting
Andrew T. Smith
Nuno Ferrand de
Almeida
Miguel Carneiro
Pedro J. Esteves
Joana Abrantes
Franz Suchentrunk
Klaus Hackländer
Paul Flicek
Stefane
Marchandeau
Michael Russello
Rajeev Patnaik
Zelalem Gebre
Mariam
Mahmoud Mohamed
Paolo Tizzani
Rudy Boonstra
Terence J. Robinson
Narayan Pd Koju
Nishma Dahal
Chair, IUCN/SSC
Lagomorph Specialist
Group, Arizona State
University
CIBIO, University of
Porto
CIBIO, University of
Porto
CIBIO, University of
Porto
CIBIO, University of
Porto
Research Institute of
Wildlife Ecology,
University of Veterinary
Medicine Vienna
University of Natural
Resources and Life
Sciences, Vienna
(BOKU)
EBI-EMBL
Office National de la
Chasse et de la Faune
Sauvage
The University of British
Columbia
Centre of Advanced
Study in Geology,
Panjab University
USA
a.smith@asu.edu
Portugal
nmferran@fc.up.pt
Portugal
miguel.carneiro@cibio.up.pt
Portugal
pjesteves@cibio.up.pt
Portugal
jabrantes@cibio.up.pt
Austria
Franz.Suchentrunk@vuwien.ac.at
Austria
klaus.hacklaender@boku.ac.at
UK
France
flicek@ebi.ac.uk
stephane.marchandeau@oncfs.
gouv.fr
Canada
michael.russello@ubc.ca
India
rajeevpatnaik@gmail.com
Ethiopia
aslnp2000@yahoo.com
Suez Canal University
Egypt
Department of Veterinary
Sciences
Parasitology Section
University of Torino
Centre for the
Neurobiology of Stress
& Department of
Biological Sciences,
University of Toronto
Scarborough
Stellenbosch University
Tribhuvan University
National Centre for
Biological Sciences
Italy
ghaffar_mahmoud@yahoo.co
m
paolo.tizzani@unito.it
Canada
boonstra@utsc.utoronto.ca
South Africa
Nepal
India
tjr@sun.ac.za
npkoju.2003@gmail.com
Nishmad@ncbs.res.in
Hung Sun Koh
Joerns Fickel
Adrienne Kovach
Thomas J.
McGreevy
Thomas Husband
Anthony Tur
Lindsey Edwards
Bangalore
Chungbuk University
Leibniz Institute for Zoo
and Wildlife Research
University of New
Hampshire
University of Rhode
Island
University of Rhode
Island
USFWS
South Korea
Germany
syskoss@chungbuk.ac.kr
fickel@izw-berlin.de
USA
adrienne.kovach@unh.edu
USA
tjmcg@my.uri.edu
USA
tom@uri.edu
USA
Ireland
Anthony_Tur@fws.gov
l_edwards@online.ie
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
Lepus 18
L. timidus (20x)
Sylvilagus 7
S. floridanus
Ochotona 4
O. curzoniae
L. europaeus
L. corsicanus
L. granatensis
(>20x)
L. castroviejoi
S. audubonii
S. cunicularius
S. brasiliensis
O. macrotis
O. princeps (>7x)
O. thibetana
L. capensis
L. saxatilis
L. tolai
L. nigricolis
L. coreanus
S. mansuetus
S. bachmani
S. nuttallii
Others 5
Prolagus sardus (Ext,
bones)
Romerolagus diazi
Pronolagus rupestris
Bunolagus monticularis
Pentalagus furnessi
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