Chromosome-scale assembly of the Kandelia obovata genome
| Autor: | Xia Yu, Si Ming Chen, Shuang Xiang, De Qiang Chen, Wen Chieh Tsai, Yifan Wang, Xing Kai Lai, Zhong Jian Liu, Wen Qi Hu, Wei Hong Sun, Zhuang Zhou, Shuang Quan Zou, Min Jie Hu, Yan Qiong Chen, Yi Xun Le, Di Yang Zhang, Xue Die Liu |
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| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Genome biology Evolution Rhizophoraceae Plant Science Horticulture biology.organism_classification 01 natural sciences Biochemistry Article 03 medical and health sciences 030104 developmental biology Evolutionary biology Kandelia obovata Genetics Gene family Eudicots Gene Genome size 010606 plant biology & botany Biotechnology Reference genome |
| Zdroj: | Horticulture Research |
| ISSN: | 2052-7276 2662-6810 |
| DOI: | 10.1038/s41438-020-0300-x |
| Popis: | The mangrove Kandelia obovata (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of K. obovata based on PacBio, Illumina, and Hi-C data is reported. The high-quality assembled genome size is 177.99 Mb, with a contig N50 value of 5.74 Mb. A large number of contracted gene families and a small number of expanded gene families, as well as a small number of repeated sequences, may account for the small K. obovata genome. We found that K. obovata experienced two whole-genome polyploidization events: one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots (γ event). We confidently annotated 19,138 protein-coding genes in K. obovata and identified the MADS-box gene class and the RPW8 gene class, which might be related to flowering and resistance to powdery mildew in K. obovata and Rhizophora apiculata, respectively. The reference K. obovata genome described here will be very useful for further molecular elucidation of various traits, the breeding of this coastal shelterbelt species, and evolutionary studies with related taxa. |
| Databáze: | OpenAIRE |
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