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

Authors: EILERS, JON - Former ARS Employee; ZHANG, HUITING - Washington State University; Gottschalk, Christopher; WILLIAMS, MELISSA - Hudsonalpha Institute For Biotechnology; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; HARKESS, ALEX - Hudsonalpha Institute For Biotechnology; Honaas, Loren; Waite, Jessica

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2026
Publication Date: 4/1/2026
Citation: Eilers, J., Zhang, H., Gottschalk, C.C., Williams, M., Grimwood, J., Harkess, A., Honaas, L.A., Waite, J.M. 2026. Long-read Iso-Seq re-annotation of the Pyrus communis ‘Bartlett’ doubled haploid genome. Tree Genetics and Genomes. 22. Article 8. https://doi.org/10.1007/s11295-026-01734-z.
DOI: https://doi.org/10.1007/s11295-026-01734-z

Interpretive Summary: Genome sequencing has greatly increased in recent years, due to lowered costs and improved technologies. However, a lot of the information from that genome needs to be annotated in a way that is usable before it can be used for further studies. For example, if a biologist wants to study how a specific gene affects root growth in a pear, they would need to know information like: where the gene is located within the genome, the sequence of the gene and the RNA encoded by the gene (which includes beginning, end, and splicing information), and how many other relatives, or homologs, that gene has in the genome. These can be crucial data points for understanding gene function. In European pears, the genome assembly of Bartlett has many genes that are poorly annotated, partially due to limited availability of RNA-seq evidence when it was sequenced. Here, we use a newly developed genome annotation pipeline, as well as updated RNA-seq evidence to improve the Bartlett genome annotation to make it more usable for functional studies in pears.

Technical Abstract: As genome sequencing becomes more accessible to non-model species, it is key to ensure quality genome annotations, including reannotation of important genomes when newer data and software are available. Here we present a reannotation of the Bartlett doubled haploid (DH) genome, which has served as an important genome for European pear research. We employ a newly developed annotation software to incorporate 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 reannotation shows 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, improvement of this annotation will aid efficiency in its use for molecular biology, genetic evolution studies, and other downstream applications.