Abstract
Corylus heterophylla (2n = 22) is the most widely distributed, unique, and economically important nut species in China. Chromosome-level genomes of C. avellana, C. heterophylla, and C. mandshurica have been published in 2021, but a satisfactory hazelnut genome database is absent. Northeast China is the main distribution and cultivation area of C. heterophylla, and the mechanism underlying the adaptation of C. heterophylla to extremely low temperature in this area remains unclear. Using single-molecule real-time sequencing and the chromosomal conformational capture (Hi-C) assisted genome assembly strategy, we obtained a high-quality chromosome-scale genome sequence of C. heterophylla, with a total length of 343 Mb and scaffold N50 of 32.88 Mb. A total of 94.72% of the test genes from the assembled genome could be aligned to the Embryophyta_odb9 database. In total, 22,319 protein-coding genes were predicted, and 21,056 (94.34%) were annotated in the assembled genome. A HazelOmics online database (HOD) containing the assembled genome, gene-coding sequences, protein sequences, and various types of annotation information was constructed. This database has a user-friendly and straightforward interface. In total, 439 contracted genes and 3,810 expanded genes were identified through genome evolution analysis, and 17 expanded genes were significantly enriched in the unsaturated fatty acid biosynthesis pathway (ko01040). Transcriptome analysis results showed that FAD (Cor0058010.1), SAD (Cor0141290.1), and KAT (Cor0122500.1) with high expression abundance were upregulated at the ovule maturity stage. We deduced that the expansion of these genes may promote high unsaturated fatty acid content in the kernels and improve the adaptability of C. heterophylla to the cold climate of Northeast China. The reference genome and database will be beneficial for future molecular breeding and gene function studies in this nut species, as well as for evolutionary research on species of the order Fagales.
Highlights
Hazelnut (Corylus spp.) belongs to the subfamily Coryloidae and is the most widely distributed and economically important genus in the Betulaceae family (Helmstetter et al, 2019)
The reads were 19,675 bp in length, with N50 of 30,570 bp. These results suggested that single molecule real-time (SMRT) sequencing is reliable and can produce long reads (Vaser et al, 2017; Vasanthan and Yasubumi, 2019)
The transcriptome data were aligned to our assembled genome, and the results showed that 81.48–84.79% reads could be aligned to the genome, indicating that our genome assembly is of good quality and can be used as a reference genome to meet the needs of information analysis (Supplementary Table 18)
Summary
Hazelnut (Corylus spp.) belongs to the subfamily Coryloidae and is the most widely distributed and economically important genus in the Betulaceae family (Helmstetter et al, 2019). Corylus heterophylla is the most widely distributed and economically important nut species in China. The area of C. heterophylla forests in China covers more than 1.0 million hectares, and this species is the main source of hazelnut in the Chinese market even though the yield of hybrid hazelnut (C. heterophylla × C. avellana) has increased rapidly in recent years (Cheng et al, 2018b, 2019; Liu et al, 2020). Northeast China is the main distribution and cultivation area of hazelnut. Most hazelnut products in the international market are derived from the European hazelnut (C. avellana), the extreme low winter temperatures in Northeast China are not suitable for the cultivation of this species. Genome analysis of C. heterophylla would be important to provide new insights into the key adaptations that contribute to the breeding and culture of C. heterophylla
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