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.
Highlights
Mangrove forests are coastal ecosystems with unique biodiversity that provides many ecosystem services and functions[1]
The survey analysis indicated that the K. obovata genome size is 211.86 Mb and has a low level of heterozygosity of approximately 0.38% (Supplementary Fig. 1)
K. obovata is well known as a coastal shelterbelt and landscape tree in tropical and subtropical areas, research on this species has been hampered by a lack of genetic data
Summary
Mangrove forests are coastal ecosystems with unique biodiversity that provides many ecosystem services and functions[1]. Mangrove loss will increase the threat of coastal hazards (i.e., erosion, storm surges, and tsunamis) to human safety and shoreline development[2]. This will reduce coastal water quality and biodiversity and threaten adjacent coastal habitats, thereby weakening the main resources on which the human community relies, including a large number of products and services provided by mangroves[3,4]. The mangrove species Kandelia obovata belongs to Rhizophoraceae, which is called “Qiuqie” in Chinese, with the Latin name of K. candel in “Flora Reipublicae Popularis Sinicae”[5]. In 2008, its Latin name was changed to K. obovata in the “Flora of China”[6]. K. obovata adapts to transitional ecosystems where the land and ocean meet by overcoming periodic and aperiodic tidal effects, which induce high salinity, severe erosion, and anaerobic conditions[8]
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