Corylus heterophylla Fisch. is a species of the Betulaceae family native to China. As an economically and ecologically important nut tree, C. heterophylla can survive in extremely low temperatures (–30 to –40 °C). To deepen our knowledge of the Betulaceae species and facilitate the use of C. heterophylla for breeding and its genetic improvement, we have sequenced the whole genome of C. heterophylla. Based on >64.99 Gb (∼175.30×) of Nanopore long reads, we assembled a 370.75-Mb C. heterophylla genome with contig N50 and scaffold N50 sizes of 2.07 and 31.33 Mb, respectively, accounting for 99.23% of the estimated genome size (373.61 Mb). Furthermore, 361.90 Mb contigs were anchored to 11 chromosomes using Hi-C link data, representing 97.61% of the assembled genome sequences. Transcriptomes representing 4 different tissues were sequenced to assist protein-coding gene prediction. A total of 27,591 protein-coding genes were identified, of which 92.02% (25,389) were functionally annotated. The phylogenetic analysis showed that C. heterophylla is close to Ostrya japonica, and they diverged from their common ancestor ∼52.79 million years ago. We generated a high-quality chromosome-level genome of C. heterophylla. This genome resource will promote research on the molecular mechanisms of how the hazelnut responds to environmental stresses and serves as an important resource for genome-assisted improvement in cold and drought resistance of the Corylus genus.

Corylus heterophylla and Corylus kweichowensis are economically and ecologically important nut-producing woody shrubs that are distributed across northern and southern regions of China. However, few studies have examined the genetic diversity and genetic relationships between C. heterophylla and C. kweichowensis , and their taxonomic relationships have been questioned. In this study, 796 individuals collected from 34 natural populations (21 C. heterophylla and 13 C. kweichowensis populations) were investigated to assess the genetic diversity and population structure using 11 microsatellite loci. Analysis of molecular variance revealed that genetic differentiation of C. heterophylla and C. kweichowensis within populations accounted for 93.57% and 88.91% of total variation, respectively. The C. heterophylla and C. kweichowensis populations as a whole group were analyzed by multiple programs, which showed that the 34 populations were divided into two genetic clusters. One cluster included 21 C. heterophylla populations, and the second cluster contained 13 C. kweichowensis populations. We conclude from these results that C. heterophylla and C. kweichowensis are distinct species. The Mantel test showed that the genetic distance was significantly correlated with the geographic distance ( r = 0.580, P < 0.001). The populations of C. heterophylla [e.g., populations WC (Weichang), MS (Mishan), and WA (Wu’an)] and C. kweichowensis [e.g., populations YX (Yuexi), ZP (Zhenping), LA (Lin’an), and TB (Taibai)] with high allelic richness are considered suitable for in situ conservation. Our study provides valuable information for breeding and conservation of genetic resources of C. heterophylla , C. kweichowensis , and related species.