LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.

The order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action "A Collaborative European Network on Rabbit Genome Biology-RGB-Net" and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration.

[1]  HL Atherton,et al.  A hidden history , 2016, Journal of intellectual disabilities : JOID.

[2]  Luis D. Verde Arregoitia,et al.  Diversity, extinction, and threat status in Lagomorphs , 2015 .

[3]  Russell E. Durrett,et al.  Assembly and diploid architecture of an individual human genome via single-molecule technologies , 2015, Nature Methods.

[4]  A. Cameron,et al.  Expertly Validated Models and Phylogenetically-Controlled Analysis Suggests Responses to Climate Change Are Related to Species Traits in the Order Lagomorpha , 2015, PloS one.

[5]  M. Carneiro,et al.  The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach. , 2015, Molecular phylogenetics and evolution.

[6]  A. Lavazza,et al.  Field and experimental data indicate that the eastern cottontail (Sylvilagus floridanus) is susceptible to infection with European brown hare syndrome (EBHS) virus and not with rabbit haemorrhagic disease (RHD) virus , 2015, Veterinary Research.

[7]  S. O’Brien,et al.  The Genome 10K Project: a way forward. , 2015, Annual review of animal biosciences.

[8]  Y. E. Chen,et al.  Rabbit models for the study of human atherosclerosis: from pathophysiological mechanisms to translational medicine. , 2015, Pharmacology & therapeutics.

[9]  A. Caroli,et al.  Detection of the new emerging rabbit haemorrhagic disease type 2 virus (RHDV2) in Sicily from rabbit (Oryctolagus cuniculus) and Italian hare (Lepus corsicanus). , 2014, Research in veterinary science.

[10]  E. Holmes,et al.  Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV). , 2014, Virology.

[11]  P. Alves,et al.  Detection of RHDV strains in the Iberian hare (Lepus granatensis): earliest evidence of rabbit lagovirus cross-species infection , 2014, Veterinary Research.

[12]  Patrick O. McGowan,et al.  Impact of high predation risk on genome-wide hippocampal gene expression in snowshoe hares , 2014, Oecologia.

[13]  P. Alves,et al.  The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation , 2014, Molecular ecology.

[14]  Eric S. Lander,et al.  Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication , 2014, Science.

[15]  H. Burbano,et al.  The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit , 2014, PLoS genetics.

[16]  P. Lukacs,et al.  Snowshoe hares display limited phenotypic plasticity to mismatch in seasonal camouflage , 2014, Proceedings of the Royal Society B: Biological Sciences.

[17]  A. Lissovsky.  Taxonomic revision of pikas Ochotona (Lagomorpha, Mammalia) at the species level , 2014 .

[18]  P. Boursot,et al.  The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression , 2014, Genome biology and evolution.

[19]  Jianglin Fan,et al.  Effective gene targeting in rabbits using RNA-guided Cas9 nucleases. , 2014, Journal of molecular cell biology.

[20]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[21]  P. Boursot,et al.  Home-loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing , 2013, Heredity.

[22]  C. Ligios,et al.  The new French 2010 Rabbit Hemorrhagic Disease Virus causes an RHD-like disease in the Sardinian Cape hare (Lepus capensis mediterraneus) , 2013, Veterinary Research.

[23]  G. Marion,et al.  High prevalence of paratuberculosis in rabbits is associated with difficulties in controlling the disease in cattle. , 2013, Veterinary journal.

[24]  M. Russello,et al.  Adaptive divergence along environmental gradients in a climate-change-sensitive mammal , 2013, Ecology and evolution.

[25]  M. Lemay,et al.  Novel genomic resources for a climate change sensitive mammal: characterization of the American pika transcriptome , 2013, BMC Genomics.

[26]  M. Nachman,et al.  Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit , 2013, Molecular ecology.

[27]  J. Abatzoglou,et al.  Camouflage mismatch in seasonal coat color due to decreased snow duration , 2013, Proceedings of the National Academy of Sciences.

[28]  Z. Wen,et al.  Evolutionary History of Lagomorphs in Response to Global Environmental Change , 2013, PloS one.

[29]  N. Galtier,et al.  Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap , 2013, PLoS genetics.

[30]  Daniel R. Richards,et al.  Genomic responses in mouse models poorly mimic human inflammatory diseases , 2013, Proceedings of the National Academy of Sciences.

[31]  Andrea L. Cirranello,et al.  The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals , 2013, Science.

[32]  M. Pop,et al.  Sequence assembly demystified , 2013, Nature Reviews Genetics.

[33]  Daniel W. A. Buchan,et al.  A large-scale evaluation of computational protein function prediction , 2013, Nature Methods.

[34]  Deacon J. Sweeney,et al.  Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus) , 2012, Nature Biotechnology.

[35]  The UniProt Consortium,et al.  Update on activities at the Universal Protein Resource (UniProt) in 2013 , 2012, Nucleic Acids Res..

[36]  M. Russello,et al.  Genetic Evidence for Restricted Dispersal along Continuous Altitudinal Gradients in a Climate Change-Sensitive Mammal: The American Pika , 2012, PloS one.

[37]  P. Boursot,et al.  Recurrent introgression of mitochondrial DNA among hares (Lepus spp.) revealed by species-tree inference and coalescent simulations. , 2012, Systematic biology.

[38]  P. Kerr.  Myxomatosis in Australia and Europe: a model for emerging infectious diseases. , 2012, Antiviral research.

[39]  J. Le Pendu,et al.  Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review , 2012, Veterinary Research.

[40]  Sonja Althammer,et al.  Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data , 2011, Bioinform..

[41]  Albert J. Vilella,et al.  A high-resolution map of human evolutionary constraint using 29 mammals , 2011, Nature.

[42]  A. Dell,et al.  Histo-Blood Group Antigens Act as Attachment Factors of Rabbit Hemorrhagic Disease Virus Infection in a Virus Strain-Dependent Manner , 2011, PLoS pathogens.

[43]  P. Boursot,et al.  INTERSPECIFIC X‐CHROMOSOME AND MITOCHONDRIAL DNA INTROGRESSION IN THE IBERIAN HARE: SELECTION OR ALLELE SURFING? , 2011, Evolution; international journal of organic evolution.

[44]  Damiano Piovesan,et al.  BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences , 2011, Nucleic Acids Res..

[45]  P. Alves,et al.  Molecular bases of genetic diversity and evolution of the immunoglobulin heavy chain variable region (IGHV) gene locus in leporids , 2011, Immunogenetics.

[46]  C. N. Slobodchikoff,et al.  The paradox of keystone species persecuted as pests: A call for the conservation of abundant small mammals in their native range , 2011 .

[47]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[48]  L. Rossi,et al.  First report of Obeliscoides cuniculi in European brown hare (Lepus europaeus) , 2011, Parasitology Research.

[49]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[50]  N. Friedman,et al.  Comprehensive comparative analysis of strand-specific RNA sequencing methods , 2010, Nature Methods.

[51]  Joshua M. Stuart,et al.  Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. , 2009, The Journal of heredity.

[52]  L. Olson,et al.  Inferring divergence times within pikas (Ochotona spp.) using mtDNA and relaxed molecular dating techniques. , 2009, Molecular phylogenetics and evolution.

[53]  P. Ferreras,et al.  Key Role of European Rabbits in the Conservation of the Western Mediterranean Basin Hotspot , 2008, Conservation biology : the journal of the Society for Conservation Biology.

[54]  P. Boursot,et al.  The ubiquitous mountain hare mitochondria: multiple introgressive hybridization in hares, genus Lepus , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[55]  N. L. Martínez,et al.  Evolution of Prolagus sardus (Ochotonidae, Lagomorpha) in the Quaternary of Sardinia Island (Italy) , 2008 .

[56]  H. Wada,et al.  Genome duplications of early vertebrates as a possible chronicle of the evolutionary history of the neural crest , 2006, International journal of biological sciences.

[57]  H. Tegelström,et al.  Species assignment and hybrid identification among Scandinavian hares Lepus europaeus and L. timidus , 2006 .

[58]  P. Boursot,et al.  Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia , 2005, Molecular ecology.

[59]  T. J. Robinson,et al.  A molecular supermatrix of the rabbits and hares (Leporidae) allows for the identification of five intercontinental exchanges during the Miocene. , 2004, Systematic biology.

[60]  T. Andrews,et al.  The Ensembl automatic gene annotation system. , 2004, Genome research.

[61]  Jianglin Fan,et al.  Transgenic rabbits as therapeutic protein bioreactors and human disease models. , 2003, Pharmacology & therapeutics.

[62]  G. Yohe,et al.  A globally coherent fingerprint of climate change impacts across natural systems , 2003, Nature.

[63]  I. Landau,et al.  Parasitic pattern of rodent Plasmodium in blood from mouse tail and from Anopheles blood meal. , 2002, Parassitologia.

[64]  R. Mittermeier,et al.  Biodiversity hotspots for conservation priorities , 2000, Nature.

[65]  D. Chasey,et al.  Rabbit haemorrhagic disease , 1994, Veterinary Record.

[66]  Andrew T. Smith.  The Distribution and Dispersal of Pikas: Influences of Behavior and Climate , 1974 .

[67]  L. Wang,et al.  Behavioral thermoregulation in the pika Ochotona princeps: a field study using radiotelemetry. , 1974, Canadian journal of zoology.

[68]  A. Sgoifo,et al.  Animal Models of Psychogenic Cardiovascular Disorders , 2015 .

[69]  Kun Huang,et al.  Injury, Large-Scale Collaborative Research Program , 2015 .

[70]  E. Nalivaiko.  Frontiers In Research Review: Stress and Hypertension Animal models of psychogenic cardiovascular disorders: what we can learn from them and what we cannot , 2011 .

[71]  Michael J Meaney,et al.  Epigenetics and the environmental regulation of the genome and its function. , 2010, Annual review of psychology.

[72]  J. Tash,et al.  Testing Multiple Hypotheses to Identify Causes of the Decline of a Lagomorph Species: The New England Cottontail as a Case Study , 2008 .

[73]  Andrew T. Smith.  Conservation of Endangered Lagomorphs , 2008 .

[74]  Imadeldin E. Aradaib,et al.  Molecular Biology Laboratory , 2003 .

[75]  N. L. Martínez.  Paleobiogeographical history of Prolagus,an European ochotonid (Lagomorpha) , 2001 .

[76]  C. Krebs,et al.  What Drives the 10-year Cycle of Snowshoe Hares? , 2001 .

[77]  J. A. Chapman,et al.  Rabbits, Hares, and Pikas: Status Survey And Conservation Action Plan , 1991 .

[78]  L C Wang,et al.  Physiology of thermoregulation in the pika, Ochotona princeps. , 1973, Canadian journal of zoology.

[79]  S. Française.  Bulletin de la Société préhistorique française , 1911 .

[80]  Lagomorphs , 2022, Zoo and Wild Animal Dentistry.