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@ARTICLE{Hoopes:905938,
      author       = {Hoopes, Genevieve and Meng, Xiaoxi and Hamilton, John P.
                      and Achakkagari, Sai Reddy and de Alves Freitas Guesdes,
                      Fernanda and Bolger, Marie E. and Coombs, Joseph J. and
                      Esselink, Danny and Kaiser, Natalie R. and Kodde, Linda and
                      Kyriakidou, Maria and Lavrijssen, Brian and van Lieshout,
                      Natascha and Shereda, Rachel and Tuttle, Heather K. and
                      Vaillancourt, Brieanne and Wood, Joshua C. and de Boer, Jan
                      M. and Bornowski, Nolan and Bourke, Peter and Douches, David
                      and van Eck, Herman J. and Ellis, Dave and Feldman, Max J.
                      and Gardner, Kyle M. and Hopman, Johannes C. P. and Jiang,
                      Jiming and De Jong, Walter S. and Kuhl, Joseph C. and Novy,
                      Richard G. and Oome, Stan and Sathuvalli, Vidyasagar and
                      Tan, Ek Han and Ursum, Remco A. and Vales, M. Isabel and
                      Vining, Kelly and Visser, Richard G. F. and Vossen, Jack and
                      Yencho, G. Craig and Anglin, Noelle L. and Bachem, Christian
                      W. B. and Endelman, Jeffrey B. and Shannon, Laura M. and
                      Strömvik, Martina V. and Tai, Helen H. and Usadel, Björn
                      and Buell, C. Robin and Finkers, Richard},
      title        = {{P}hased, chromosome-scale genome assemblies of tetraploid
                      potato reveals a complex genome, transcriptome, and
                      predicted proteome landscape underpinning genetic diversity},
      journal      = {Molecular plant},
      volume       = {15},
      number       = {3},
      issn         = {1674-2052},
      address      = {Oxford},
      publisher    = {Oxford Univ. Press},
      reportid     = {FZJ-2022-01120},
      pages        = {520-536},
      year         = {2022},
      abstract     = {Cultivated potato is a clonally propagated autotetraploid
                      species with a highly heterogeneous genome. Phased
                      assemblies of six cultivars including two chromosome-scale
                      phased genome assemblies revealed extensive allelic
                      diversity, including altered coding and transcript
                      sequences, preferential allele expression, and structural
                      variation that collectively result in a highly complex
                      transcriptome and predicted proteome, which are distributed
                      across the homologous chromosomes. Wild species contribute
                      to the extensive allelic diversity in tetraploid cultivars,
                      demonstrating ancestral introgressions predating modern
                      breeding efforts. As a clonally propagated autotetraploid
                      that undergoes limited meiosis, dysfunctional and
                      deleterious alleles are not purged in tetraploid potato.
                      Nearly a quarter of the loci bore mutations are predicted to
                      have a high negative impact on protein function,
                      complicating breeder’s efforts to reduce genetic load. The
                      StCDF1 locus controls maturity, and analysis of six
                      tetraploid genomes revealed that 12 allelic variants of
                      StCDF1 are correlated with maturity in a dosage-dependent
                      manner. Knowledge of the complexity of the tetraploid potato
                      genome with its rampant structural variation and embedded
                      deleterious and dysfunctional alleles will be key not only
                      to implementing precision breeding of tetraploid cultivars
                      but also to the construction of homozygous, diploid potato
                      germplasm containing favorable alleles to capitalize on
                      heterosis in F1 hybrids.},
      cin          = {IBG-4},
      ddc          = {580},
      cid          = {I:(DE-Juel1)IBG-4-20200403},
      pnm          = {2171 - Biological and environmental resources for
                      sustainable use (POF4-217)},
      pid          = {G:(DE-HGF)POF4-2171},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:35026436},
      UT           = {WOS:000767562700006},
      doi          = {10.1016/j.molp.2022.01.003},
      url          = {https://juser.fz-juelich.de/record/905938},
}