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Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants.
Rubert, Diego P; Martinez, Fábio V; Stoye, Jens; Doerr, Daniel.
Afiliação
  • Rubert DP; Faculdade de Computação - FACOM, Universidade Federal de Mato Grosso do Sul - UFMS, Campo Grande, Brazil.
  • Martinez FV; Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
  • Stoye J; Faculdade de Computação - FACOM, Universidade Federal de Mato Grosso do Sul - UFMS, Campo Grande, Brazil.
  • Doerr D; Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
BMC Genomics ; 21(Suppl 2): 273, 2020 Apr 16.
Article em En | MEDLINE | ID: mdl-32299356
BACKGROUND: Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants. RESULTS: Our work relies on an established workflow in the reconstruction of ancestral plants, but improves several steps of this process. Instead of using gene annotations for inferring the genome content of the ancestral sequence, we identify genomic markers through a process called genome segmentation. This enables us to reconstruct the ancestral genome from hundreds of thousands of markers rather than the tens of thousands of annotated genes. We also introduce the concept of local genome rearrangement, through which we refine syntenic blocks before they are used in the reconstruction of contiguous ancestral regions. With the enhanced workflow at hand, we reconstruct the ancestral genome of eudicots, a major sub-clade of flowering plants, using whole genome sequences of five modern plants. CONCLUSIONS: Our reconstructed genome is highly detailed, yet its layout agrees well with that reported in Badouin et al. (2017). Using local genome rearrangement, not only the marker-based, but also the gene-based reconstruction of the eudicot ancestor exhibited increased genome content, evidencing the power of this novel concept.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Mapeamento Cromossômico / Magnoliopsida / Genômica Idioma: En Revista: BMC Genomics Assunto da revista: GENETICA Ano de publicação: 2020 Tipo de documento: Article País de afiliação: Brasil País de publicação: Reino Unido

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Mapeamento Cromossômico / Magnoliopsida / Genômica Idioma: En Revista: BMC Genomics Assunto da revista: GENETICA Ano de publicação: 2020 Tipo de documento: Article País de afiliação: Brasil País de publicação: Reino Unido