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. 2020 May 2;7:75.
doi: 10.1038/s41438-020-0300-x. eCollection 2020.

Chromosome-scale Assembly of the Kandelia obovata Genome

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Free PMC article

Chromosome-scale Assembly of the Kandelia obovata Genome

Min-Jie Hu et al. Hortic Res. .
Free PMC article

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.

Conflict of interest statement

Conflict of interestThe authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1. Morphological features of the flower and fruit of K. obovata.
a K. obovata trees in a coastal wetland. b Flowers. c Young fruits. d Cone-like fruits
Fig. 2
Fig. 2
Intensity signal heat map of the Hi-C chromosome
Fig. 3
Fig. 3. The expansion and contraction of gene families.
The green number indicates the number of expanded gene families, and the red number indicates the number of contracted gene families. The blue color in the circle shows the gene families whose copy numbers are constant, while the orange color represents the proportion of 11,968 gene families in the most recent common ancestor that have expanded or contracted during late differentiation
Fig. 4
Fig. 4. Ks distributions between K. obovata and R. apiculata and K. obovata and V. vinifera and within K. obovata and R. apiculata.
Peaks of intraspecies Ks distributions indicate ancient whole-genome polyploidization events, and peaks of interspecies Ks distributions indicate speciation events
Fig. 5
Fig. 5. Collinear point diagram and Ks values corresponding to the collinear blocks.
a The collinear point diagram of K. obovata. b Distribution of log10 (Ks) values of the collinear blocks in K. obovata. c The collinear point diagram of R. apiculata. d Distribution of log10 (Ks) values of the collinear blocks in R. apiculata. The ordinate of b, d is the number of gene pairs corresponding to the Ks value, and the abscissa is the log10 (Ks) value
Fig. 6
Fig. 6. Phylogenetic analysis of MADS-box genes from A. thaliana, O. sativa, P. equestris, K. obovata, and R. apiculata.
a Phylogenetic tree of type I MADS-box genes. b Phylogenetic tree of type II MADS-box genes. The number on the left in parentheses represents the homologous MADS genes of K. obovata, and the number on the right represents the homologous MADS genes of R. apiculata. The bolded gene ID numbers beginning with “Ko” represent the gene IDs of K. obovata; those beginning with “Ra” represent the gene IDs of R. apiculata
Fig. 7
Fig. 7. Phylogenetic reconstruction of the NLR proteins in K. obovata and R. apiculata.
The NBS domain of human apoptotic protease-activating factor-1 (APAF-1) is located at the root of the tree. The bolded gene ID numbers beginning with “Ko” represent the gene IDs of K. obovata; those beginning with “Ra” represent the gene IDs of R. apiculata

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