Chromosome-scale assembly of the Kandelia obovata genome

Min-Jie Hu; Wei-Hong Sun; Wen-Chieh Tsai; Shuang Xiang; Xing-Kai Lai; De-Qiang Chen; Xue-Die Liu; Yi-Fan Wang; Yi-Xun Le; Si-Ming Chen; Di-Yang Zhang; Xia Yu; Wen-Qi Hu; Zhuang Zhou; Yan-Qiong Chen; Shuang-Quan Zou; Zhong-Jian Liu

doi:10.1038/s41438-020-0300-x

Chromosome-scale assembly of the Kandelia obovata genome

Hortic Res. 2020 May 2;7(1):75. doi: 10.1038/s41438-020-0300-x. eCollection 2020.

Authors

Min-Jie Hu^#¹, Wei-Hong Sun^#^{2

3}, Wen-Chieh Tsai⁴, Shuang Xiang^{2

3}, Xing-Kai Lai⁵, De-Qiang Chen^{2

3}, Xue-Die Liu², Yi-Fan Wang², Yi-Xun Le², Si-Ming Chen^{2

6}, Di-Yang Zhang³, Xia Yu³, Wen-Qi Hu³, Zhuang Zhou³, Yan-Qiong Chen³, Shuang-Quan Zou^{2

3}, Zhong-Jian Liu^{3

7}

Affiliations

¹ 1Key Laboratory of Humid Sub-tropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007 China.
² 2Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
³ 3Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
⁴ 4Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 China.
⁵ Administration of the Quanzhou Bay Estuary Wetland Nature Reserve, Quanzhou, 362000 China.
⁶ 6Ocean College, Minjiang University, Fuzhou, 350002 China.
⁷ 7Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005 China.

^# Contributed equally.

Abstract

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.

Keywords: Evolution; Genome.