The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)
| Autor: | Nian Wang, Jian Ning Liu, Rui Zhang, Jingfeng Sun, Fuling Yuan, Ya Lin Sang, Long Yang, Huayang Li, Qingyun Li, Qicheng Duan, Xiangwen Hou, Keqiang Yang, Qiang Liang, Shou-Ke Li |
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| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
Sequence assembly Health Informatics Genomics Computational biology Biology Data Note Illumina paired-end sequencing 01 natural sciences Genome 03 medical and health sciences Sapindaceae 10X Genomics Chromium high-throughput chromosome conformation capture Gene Illumina dye sequencing 030304 developmental biology Whole genome sequencing Comparative genomics PacBio sequencing 0303 health sciences Base Sequence Whole Genome Sequencing Phylogenetic tree Gene Expression Profiling yellowhorn (Xanthoceras sorbifolium Bunge) High-Throughput Nucleotide Sequencing Computer Science Applications BioNano Genomics Genome Plant 010606 plant biology & botany |
| Zdroj: | GigaScience |
| ISSN: | 2047-217X |
| DOI: | 10.1093/gigascience/giz071 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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