College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China.
College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China.
Gigascience. 2019 Jun 1;8(6). doi: 10.1093/gigascience/giz071.
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.
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.
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.
黄杞（Xanthoceras sorbifolium Bunge），原产于中国北方的落叶灌木或小乔木，具有巨大的经济价值。黄杞种子富含油脂，含有不饱和长链脂肪酸，可用于生产食用油和神经酸胶囊。然而，由于缺乏高质量的基因组序列，阻碍了对其进化和基因功能的理解。
本研究通过整合 Illumina 测序、Pacific Biosciences 单分子实时测序、10X Genomics 连接读取、Bionano 光学图谱和 Hi-C，对黄杞的全基因组进行了测序和组装。黄杞基因组组装大小为 439.97 Mb，由 15 条假染色体组成，覆盖组装基因组的 95.42%（419.84 Mb）。重复序列占黄杞基因组的 56.39%。基因组包含 21,059 个编码蛋白的基因。其中，通过与其他数据库进行搜索，有 18,503（87.86%）个基因具有≥1 个“注释”术语的功能注释。转录组分析表明，在雌雄同体花、雄花、幼果、叶和芽中，分别有 341、135、125、113 和 100 个基因特异性表达。系统发育分析表明，黄杞和龙眼（Dimocarpus longan）自最近的共同祖先分化出来约 4600 万年前。
黄杞基因组的可用性及其随后的注释，以及组织特异性功能基因的鉴定，为植物比较基因组学、进化研究和分子设计育种提供了有价值的参考。
