Overview

Pears (Pyrsus spp.) are one of the important fruit crops in temperate regions. The Rosaceae family contains antioxidant fruits, such as apples, plum, berry’s and cherries. Pyrus pyrifolia cultivar ‘Wonwhang (WH)’ (BioSample SAMN05196235)genome sequencing were conducted a nuclear, chloroplast (KX450876), mitochondria (KY563276). The nuclear genome size is estimated to be 535 Mb by K-mer analysis. The nucleotide genome assembly characteristics included high detection of 97% with 2,221 scaffolds, 649kb of N50 and 517Mbp. Three genetic maps in inter and intra cross populations were constructed with SNPs polymorphisms by genotype by sequencing (GBS). Owing to recent WGD in Pyreae, there are more than two loci in different homologous chromosomes in genetic maps. Follows on Hi-C mapping mainly, we could decide to pseudomolecule on 17 chromosomes with 440.3Mb and 964 scaffolds with 85.23% coverage to the assemble genome in WH.

SSR-containing genome sequences were subjected to categories of function putative genes with homology search, 510 SSR markers selected in this study. Of these, 70 markers were distributed across 17 chromosomes with more than one locus. We conducted QTL analysis with several breeding traits of fruit ripening with sweetness, acid, and texture. Catching four QTLs in one population (P. prifoilia and P. communis, inter cross) in sweetness, two SSR markers were decided in this population. Expected benefits of the pear genome sequencing will include identifying genes and utilizing them to develop new varieties to increase the market value of the fruit.

Statistics

Genome

Approximately 517Mbp Mb is assembled in 17 chromosomes, with 440.3Mb and 964 scaffolds with 85.23% coverage

Scaffold N50 = 649Kb, scaffold no. 2,221

Contig N50 = 256Kb, contig no.9,926

Loci

43,553 (Gene with isoforms, 1,623) protein-coding genes have been predicted

Organelle genomes

The complete chloroplast genome of P. pyrifolia is 159,922 bp in size (Accession no. KX450876). The chloroplast genome harbors 132 annotated genes, including 93 protein-coding genes, 31 tRNA genes, and eight rRNA genes. The complete mitochondrial genome of P. pyrifolia is 458,873 bp in length (Accession no. KY563276). A total of 65 genes are annotated including 39 protein-coding genes, 23 tRNA genes, and three rRNA genes.

References

H Y Chung, S Y Won, Y-K Kim, J S Kim* (2019) Development of the chloroplast genome-based InDel markers in Niitaka (Pyrus pyrifolia) and its application, Plant Biotechnology Reports11816-018-00513-0

P Soundararajan, S Y Won, J S Kim* (2019) Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective, BioMed Research International volume Article ID 7519687

J Y Lee, M-S seo, S Y Won, K A Lim, I S Sin, D S Choi, J S Kim* (2018) Construction of a Genetic Map using the SSR Markers Derived from “Wonwhang” of Pyrus pyrifolia, Korean J. Breed. Sci. 50(4):434-441

H Y Chung, T-H Lee, Y-K Kim, J S Kim* (2017) Complete chloroplast genome sequences of Wonwhang (Pyrus pryrifolia) and its phylogenetic analysis, Mitochondirial DNA Part B:resources VOL 2 No1, 325-326

H Y Chung, S Y Won, S-H Kang, S-H Sohn, J S Kim* (2017) Complete chloroplast genome sequences of Wonwhang (Pyrus pryrifolia) and its phylogenetic analysis, Mitochondirial DNA Part B:resources VOL 2 No1, 325-326