Abstract
BackgroundYellowhorn (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.FindingsIn 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.ConclusionsThe 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.
Highlights
Yellowhorn (Xanthoceras sorbifolium Bunge, National Center for Biotechnology Information (NCBI):txid99658), the single species of genus Xanthocera (Sapindaceae), is a deciduous shrub or small tree, naturally occurring on hills and slopes in Northern China [1,2,3]
For high-throughput chromosome conformation capture (Hi-C) library construction, ∼5 g freshly flushed leaves were cross-linked with 1% formaldehyde for 10 minutes at room temperature, which was quenched with a final concentration of 0.125 mol/L glycine
To predict genes based on similarity, protein sequences of Citrus sinensis, D. longan, Theobroma cacao, Olea europaea, Anacardium occidental, Vitis vinifera, Glycine max, Populus tremula, Oryza sativa, and Arabidopsis thaliana were spliced-mapped to the repeat-masked yellowhorn genome assembly using Exonerate v. 2.2.0 [49] with protein2genome model at 90% identity
Summary
Yellowhorn (Xanthoceras sorbifolium Bunge, NCBI:txid99658), the single species of genus Xanthocera (Sapindaceae), is a deciduous shrub or small tree, naturally occurring on hills and slopes in Northern China [1,2,3]. The Sapindaceae family ( known as the soapberry family) comprises 142 genera and 1,900 species including important tropical fruits and woody oil-bearing plants, such as Dimocarpus longan, Litchi chinensis, Nephelium lappaceum, Sapindus mukorossi, and yellowhorn [13, 14]. The genome of D. longan has been sequenced and assembled recently [15]. The chloroplast genome of yellowhorn has been assembled and characterized using Illumina pair-end sequencing data [16]. Genes regulating oil accumulation and fertilized ovule development have been identified in yellowhorn [17, 18]. Despite the increasing availability of genetic resources with research and economic value, a fully annotated genome is currently unavailable for yellowhorn. Our study will facilitate comparative genomics, gene functional studies, and molecular assisted breeding in the near future
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