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The Chinese chestnut (Castanea mollissima Bl.) is a woody nut crop with a high ecological value. Although many cultivars have been selected from natural seedlings, elite lines with comprehensive agronomic traits and characters remain rare. To explore genetic resources with aid of whole genome sequence will play important roles in modern breeding programs for chestnut. In this study, we generated a high-quality C. mollissima genome assembly by combining 90× Pacific Biosciences long read and 170× high-throughput chromosome conformation capture data. The assembly was 688.93 Mb in total, with a contig N50 of 2.83 Mb. Most of the assembled sequences (99.75%) were anchored onto 12 chromosomes, and 97.07% of the assemblies were accurately anchored and oriented. A total of 33,638 protein-coding genes were predicted in the C. mollissima genome. Comparative genomic and transcriptomic analyses provided insights into the genes expressed in specific tissues, as well as those associated with burr development in the Chinese chestnut. This highly contiguous assembly of the C. mollissima genome provides a valuable resource for studies aiming at identifying and characterizing agronomical-important traits, and will aid the design of breeding strategies to develop more focused, faster, and predictable improvement programs.

The positions of enhancers and promoters on genomic DNA remain poorly understood. Chromosomes cannot be observed during the cell division cycle because the genome forms a chromatin structure and spreads within the nucleus. However, high-throughput chromosome conformation capture (Hi-C) measures the physical interactions of genomes. In previous studies, DNA extrusion loops were directly derived from Hi-C heat maps. Multidimensional Scaling (MDS) is used in this assessment to more precisely locate enhancers and promoters. MDS is a multivariate analysis method that reproduces the original coordinates from the distance matrix between elements. We used Hi-C data of cultured osteosarcoma cells and applied MDS as the distance matrix of the genome. In addition, we selected columns 2 and 3 of the orthogonal matrix U as the desired structure. Overall, the DNA loops from the reconstructed genome structure contained bioprocesses involved in transcription, such as the pre-transcriptional initiation complex and RNA polymerase II initiation complex, and transcription factors involved in cancer, such as Foxm1 and CREB3. Therefore, our results are consistent with the biological findings. Our method is suitable for identifying enhancers and promoters in the genome.

The Chinese chestnut (Castanea mollissima Bl.) is a woody nut crop with a high ecological value. Although many cultivars have been selected from natural seedlings, elite lines with comprehensive agronomic traits and characters remain rare. To explore genetic resources with aid of whole genome sequence will play important roles in modern breeding programs for chestnut. In this study, we generated a high-quality C. mollissima genome assembly by combining 90× Pacific Biosciences long read and 170× high-throughput chromosome conformation capture data. The assembly was 688.93 Mb in total, with a contig N50 of 2.83 Mb. Most of the assembled sequences (99.75%) were anchored onto 12 chromosomes, and 97.07% of the assemblies were accurately anchored and oriented. A total of 33,638 protein-coding genes were predicted in the C. mollissima genome. Comparative genomic and transcriptomic analyses provided insights into the genes expressed in specific tissues, as well as those associated with burr development in the Chinese chestnut. This highly contiguous assembly of the C. mollissima genome provides a valuable resource for studies aiming at identifying and characterizing agronomical-important traits, and will aid the design of breeding strategies to develop more focused, faster, and predictable improvement programs.

Background Yellowhorn (Xanthoceras sorbifolium Bunge), a deciduous shrub or small tree native to north China, is of great economic value. Seeds of yellowhorn are rich in oil containing unsaturated long-chain fatty acids that have been used for producing edible oil and nervonic acid capsules. However, the lack of a high-quality genome sequence hampers the understanding of its evolution and gene functions. Findings In this study, a whole genome of yellowhorn was sequenced and assembled by integration of Illumina sequencing, Pacific Biosciences single-molecule real-time sequencing, 10X Genomics linked reads, Bionano optical maps, and Hi-C. The yellowhorn genome assembly was 439.97 Mb, which comprised 15 pseudo-chromosomes covering 95.42% (419.84 Mb) of the assembled genome. The repetitive fractions accounted for 56.39% of the yellowhorn genome. The genome contained 21,059 protein-coding genes. Of them, 18,503 (87.86%) genes were found to be functionally annotated with ≥1 "annotation" term by searching against other databases. Transcriptomic analysis showed that 341, 135, 125, 113, and 100 genes were specifically expressed in hermaphrodite flower, staminate flower, young fruit, leaf, and shoot, respectively. Phylogenetic analysis suggested that yellowhorn and Dimocarpus longan diverged from their most recent common ancestor ∼46 million years ago. Conclusions The availability and subsequent annotation of the yellowhorn genome, as well as the identification of tissue-specific functional genes, provides a valuable reference for plant comparative genomics, evolutionary studies, and molecular design breeding.

Background Kiwifruit (Actinidia spp.) is a dioecious plant with fruits containing abundant vitamin C and minerals. A handful of kiwifruit species have been domesticated, among which Actinidiaeriantha is increasingly favored in breeding owing to its superior commercial traits. Recently, elite cultivars from A. eriantha have been successfully selected and further studies on their biology and breeding potential require genomic information, which is currently unavailable. Findings We assembled a chromosome-scale genome sequence of A. eriantha cultivar White using single-molecular sequencing and chromatin interaction map–based scaffolding. The assembly has a total size of 690.6 megabases and an N50 of 21.7 megabases. Approximately 99% of the assembly were in 29 pseudomolecules corresponding to the 29 kiwifruit chromosomes. Forty-three percent of the A. eriantha genome are repetitive sequences, and the non-repetitive part encodes 42,988 protein-coding genes, of which 39,075 have homologues from other plant species or protein domains. The divergence time between A. eriantha and its close relative Actinidia chinensis is estimated to be 3.3 million years, and after diversification, 1,727 and 1,506 gene families are expanded and contracted in A. eriantha, respectively. Conclusions We provide a high-quality reference genome for kiwifruit A. eriantha. This chromosome-scale genome assembly is substantially better than 2 published kiwifruit assemblies from A. chinensis in terms of genome contiguity and completeness. The availability of the A. eriantha genome provides a valuable resource for facilitating kiwifruit breeding and studies of kiwifruit biology.