De novo assembly of a wild pear (Pyrus betuleafolia) genome

Abstract

SummaryChina is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia‐Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi‐C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein‐coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide‐binding site (NBS)‐type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR‐NBS‐LRR (TNL)‐type genes, which represented the greatest number of TNL‐type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism‐related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high‐quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.

The genome of kenaf (Hibiscus cannabinus L.) provides insights into bast fibre and leaf shape biogenesis

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Mining downy mildew susceptibility genes: a diversity study in grapevine

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Molecular karyotypes of loquat (Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity

“…The studies that produced these maps allow the possibility of constructing complete molecular karyotypes for these species. Whole-genome sequences of apple [93,94], pear [95,96], strawberry [97], peach [98], Prunus mume [99], sweet orange [100], jujube [101], pineapple [102], and kiwifruit [103], as well as those of rice, maize, wheat, soybean [104], have been published; therefore, we can obtain large numbers of conserved SSR markers located in the centromeres and telomeres from these whole-genome sequences. Therefore, molecular karyotyping using SSR markers and qPCR is a very useful tool for basic genetic research and accurate breeding.…”