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Back to BACs: Conifer Genome Exploration with Bacterial Artificial Chromosomes

  • Kermit RitlandEmail author
  • Nima Farzaneh
  • Claire Cullis
  • Agnes Yuen
  • Michelle Tang
  • Joël Fillon
  • Sarah Chao
  • Daniel G. Peterson
  • Carol Ritland
Chapter
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Part of the Compendium of Plant Genomes book series (CPG)

Abstract

We sought to ascertain the structure of spruce and pine genomes via sequencing of randomly selected bacterial artificial chromosomes (BACs) from both white spruce and loblolly pine. In the first genomic comparison of spruce and pine for its time, using 454 sequencing, we compared 96 random BACs from each species. Thirty-three (spruce) and 24 (pine) genes were found in the BACs that spanned 8.7 MB (spruce) and 10.3 MB (pine), respectively; greater numbers of pseudogenes were also found. The gene numbers found in BACs gives conflicting estimates about the true numbers of genes in the genome (46K in pine, 75K in spruce). There were ten times as many retrotransposons as genes, and clustering of inverted repeats showed transposition may have peaked in both species about 50 million years ago. Dotplots of BACs show interesting repeat structures in these conifers. A phylogeny of retrotransposons shows recent periods of expansion in both species, and a general peak of activity ca. 50 million years ago. Besides providing a snapshot of conifer genome structure and evolution, BACs can aid in the assembly of conifer genomes.

Keywords

Bacterial artificial chromosome BAC Transposons Transposition Conifer genome 

Notes

Acknowledgments

This work was primarily funded by a Science Opportunity Fund grant “Exploration of conifer genomes” from Genome British Columbia to KR. Our co-investigators from Arborea (Genome Quebec) and Mississippi Genome Exploration Laboratory (MGEL) assisted with our objectives. The Genome Quebec project, “Pilot studies and resource development for Conifer Genome Sequencing; genome characterization and gene space,” served as our co-funding and their study had complementary activities.

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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Kermit Ritland
    • 1
    Email author
  • Nima Farzaneh
    • 1
  • Claire Cullis
    • 1
  • Agnes Yuen
    • 1
  • Michelle Tang
    • 1
  • Joël Fillon
    • 1
  • Sarah Chao
    • 1
  • Daniel G. Peterson
    • 2
  • Carol Ritland
    • 1
  1. 1.Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverCanada
  2. 2.Institute for Genomics, Biocomputing & BiotechnologyMississippi State UniversityStarkvilleUSA

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