Review

Plant Molecular Biology

, Volume 80, Issue 6, pp 555-569

Towards decoding the conifer giga-genome

  • John MackayAffiliated withCenter for Forest Research, Institute for Integrative and Systems Biology, Université Laval, Québec
  • , Jeffrey F. D. DeanAffiliated withDepartment of Biochemistry and Molecular Biology, Warnell School of Forestry and Natural Resources, Davison Life Sciences, University of Georgia
  • , Christophe PlomionAffiliated withUMR BIOGECO, INRA
  • , Daniel G. PetersonAffiliated withInstitute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University
  • , Francisco M. CánovasAffiliated withDepartamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga
  • , Nathalie PavyAffiliated withCenter for Forest Research, Institute for Integrative and Systems Biology, Université Laval, Québec
  • , Pär K. IngvarssonAffiliated withDepartment of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University
  • , Outi SavolainenAffiliated withDepartment of Biology and Biocenter Oulu, University of Oulu
  • , M. Ángeles GuevaraAffiliated withGenomics and Forest Ecology, Forest Research Centre INIA-CIFOR, National Research Institute for Agricultural and Food Technology (INIA)
    • , Silvia FluchAffiliated withHealth and Environment Department, Platform for Integrated Clone Management (PICME), AIT Austrian Institute of Technology GmbH
    • , Barbara VincetiAffiliated withCenter for Forest Research, Institute for Integrative and Systems Biology, Université Laval, QuébecBioversity International
    • , Dolores AbarcaAffiliated withCenter for Forest Research, Institute for Integrative and Systems Biology, Université Laval, QuébecDepartment of Plant Biology, University of Alcalá
    • , Carmen Díaz-SalaAffiliated withCenter for Forest Research, Institute for Integrative and Systems Biology, Université Laval, QuébecDepartment of Plant Biology, University of Alcalá
    • , María-Teresa CerveraAffiliated withGenomics and Forest Ecology, Forest Research Centre INIA-CIFOR, National Research Institute for Agricultural and Food Technology (INIA) Email author 

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Abstract

Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world’s conifer forests.

Keywords

Conifers Giga-genome sequencing Functional genomics Comparative genomics Integrative studies