Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

Abstract

Aim 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. Methods and results 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. Conclusion and Perspective 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.

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions

“…The clean reads were further trimmed using Trimmomatic and trimmed reads shorter than 50 bp were discarded. The trimmed reads mapped to the pear genomes, including P. bretschneideri , ( 30 , 85 ), P. betuleafolia ( 86 ), and P. pyrifolia ( 87 ) were identified and removed by Bowtie2 software ( 88 ), resulting in a total of 100 GB clean reads. Kraken2 and Bracken were used for annotation and abundance assessment of microbial species, resulting in archaea (93,666), bacteria (17,032,193), phage (459), and plants and fungi (77,964) categories.…”

Genome-Wide Identification of the 1-Aminocyclopropane-1-carboxylic Acid Synthase (ACS) Genes and Their Possible Role in Sand Pear (Pyrus pyrifolia) Fruit Ripening

“…Although two ACSs have been found in sand pear [4], there are likely to be unidentified ACS genes in the pear genome, and their relationship with ripening behavior is unknown. Currently, the full-length genome of sand pear (P. pyrifolia) has been sequenced, providing valuable gene resources for further functional genomics study [30]. In this study, a total of 13 ACS genes were found in the genome of sand pear, and the number is the same as that identified in P. ussuriensis [34].…”

“…2' in three ripening stages, including 1 (pre-ripening, 30 days before harvest), 2 (at harvest) and 3 (fruit senescence, 10 days after harvest). Over 89.2% of clean reads were uniquely mapped to the sand pear genome [30]. Expression of 13 PpyACSs in the pear genome was detected.…”

The Identification of SQS/SQE/OSC Gene Families in Regulating the Biosynthesis of Triterpenes in Potentilla anserina

“…The sequenced and annotated genome data of Potentilla anserina (Pan) [ 16 ], Potentilla micrantha (Pmi) [ 31 ], Fragaria vesca (Fve) [ 32 ], Rosa rugosa (Rru) [ 22 ], and Pyrus pyrifolia (Ppy) [ 33 ] of Rosaceae were requested from the Genome Database for Rosaceae (GDR) ( , accessed on 14 March 2023), while the sequence of Vitis vinifera (Vvi) [ 20 ] was downloaded from the National Center for Biotechnology Information (NCBI) database. Oryza sativa (Osa) and Arabidopsis thaliana (Ath), serving as outgroups, were also downloaded from the NCBI.…”