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<p>As genome sequencing becomes more accessible to non-model species, it is key to ensure high-quality genome annotations exist. These efforts include the re-annotation of important genomes when newer data and software are available. Here, we present a re-annotation of the ‘Bartlett’ doubled haploid (DH) genome, which has served as the reference genome for European pear research. We employed a newly developed annotation pipeline that incorporated a polished version of the DH genome, an Iso-Seq RNA-seq dataset developed by sampling eleven different tissue types from adult trees and in vitro treelets, and RNA-seq evidence from nine publicly available transcriptomes encompassing ten tissue types. The resulting re-annotation exhibited improved BUSCO and OMArk scores, increased gene capture, and improved gene model accuracy. Further, we saw increases in the number of orthogroups represented, as well as improved completeness of those orthogroups, based on Core Orthogroup similarity to recent high-quality pome annotations. Together, the improvements generated from this annotation will enable efficient use for molecular biology, genetic evolution studies, and other downstream applications.</p>

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Long-read Iso-Seq re-annotation of the Pyrus communis ‘Bartlett’ doubled haploid genome

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月1日

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  • Jon Eilers,
  • Huiting Zhang,
  • Christopher Gottschalk,
  • Melissa Williams,
  • Jane Grimwood,
  • Alex Harkess,
  • Loren Honaas,
  • Jessica M. Waite

摘要

As genome sequencing becomes more accessible to non-model species, it is key to ensure high-quality genome annotations exist. These efforts include the re-annotation of important genomes when newer data and software are available. Here, we present a re-annotation of the ‘Bartlett’ doubled haploid (DH) genome, which has served as the reference genome for European pear research. We employed a newly developed annotation pipeline that incorporated a polished version of the DH genome, an Iso-Seq RNA-seq dataset developed by sampling eleven different tissue types from adult trees and in vitro treelets, and RNA-seq evidence from nine publicly available transcriptomes encompassing ten tissue types. The resulting re-annotation exhibited improved BUSCO and OMArk scores, increased gene capture, and improved gene model accuracy. Further, we saw increases in the number of orthogroups represented, as well as improved completeness of those orthogroups, based on Core Orthogroup similarity to recent high-quality pome annotations. Together, the improvements generated from this annotation will enable efficient use for molecular biology, genetic evolution studies, and other downstream applications.