Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety 'Nijisseiki'.

Kenta Shirasawa,Sachiko Isobe,Akihiro Itai

doi:10.1093/dnares/dsab001

Kenta Shirasawa, Sachiko Isobe + Show 1 more

Open Access

https://doi.org/10.1093/dnares/dsab001

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Abstract

We analyzed the genome sequence of a Japanese pear (Pyrus pyrifolia) to facilitate its genetics and genomics as well as breeding programs, in which a variety 'Nijisseiki' with superior flesh texture has been used as a parent for most Japanese pear cultivars. De novo assembly of long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6 Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 high-confidence protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of genome-wide duplication was observed, consistent with related species. This is the first chromosome-scale genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

Highlights

Pear (Pyrus spp.) is a genus of the Malinae subtribe of the Rosaceae that includesEuropean pear (P. communis), Chinese white pear (P. × bretschneideri), Japanese pear (P. pyrifolia), and apple (Malus × domestica)
Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences
This is the first genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear

Summary

Introduction

Pear (Pyrus spp.) is a genus of the Malinae subtribe of the Rosaceae that includesEuropean pear (P. communis), Chinese white pear (P. × bretschneideri), Japanese pear (P. pyrifolia), and apple (Malus × domestica). European pear (P. communis), Chinese white pear × bretschneideri), Japanese pear (P. pyrifolia), and apple (Malus × domestica). In the Malinae, genome sequence data are publicly available for crop species such as apple[4], European pear[5], and Chinese white pear[6], as well as for some pear wild relatives (P. betuleafolia and (P. ussuriensis × communis) × spp.) that are used for root stocks[7,8]. To simplify genomic analysis, doubled-haploid lines were developed to reduce the genome complexities in materials used for genome sequencing[5,6]. Neither doubled-haploid lines nor genome sequence data are available for Japanese pear, despite the publication of transcriptome data[10] and genetic maps[11,12]

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