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. 2020 Apr 1;7(1):46.
doi: 10.1038/s41438-020-0269-5. eCollection 2020.

A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)

Ting Xue  1   2 , Xuehai Zheng  1 , Duo Chen  1 , Limin Liang  2 , Nan Chen  3 , Zhen Huang  1 , Wenfang Fan  1 , Jiannan Chen  2 , Wan Cen  2 , Shuai Chen  4 , Jinmao Zhu  1 , Binghua Chen  1 , Xingtan Zhang  4 , Youqiang Chen  1   2
Affiliations

A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)

Ting Xue et al. Hortic Res. .

Abstract

The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction. The taxonomic status of Podostemaceae has always been controversial. Here, we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae, obtained by incorporating Hi-C, Illumina and PacBio sequencing. We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes. The assembled genome size was close to the estimated size, and 659.42 Mb of the assembly was assigned to 29 superscaffolds (scaffold N50 21.22 Mb). A total of 59.20% repetitive sequences were identified, among which long terminal repeats (LTRs) were the most abundant class (28.97% of the genome). Genome evolution analysis suggested that the divergence time of Cladopus chinensis (106 Mya) was earlier than that of Malpighiales (82 Mya) and that this taxon diverged into an independent branch of Podestemales. A recent whole-genome duplication (WGD) event occurred 4.43 million years ago. Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation, photosynthesis and isoflavonoid metabolism genes in Cladopus chinensis are probably related to the genomic characteristics of this growing submerged species. Transcriptome analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses, including WUSCHEL (WUS), ASYMMETRIC LEAVES (ASL), SHOOT MERISTEMLESS (STM), NAC2, NAC8, NAC29, NAC47, NAC73, NAC83 and NAC102. These findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae.

Keywords: Bioinformatics; Genomic analysis; High-throughput screening.

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Conflict of interest statement

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

Figures

Fig. 1
Fig. 1. Cladopus chinensis.
a Flowering plants in the habitat of the species. b Roots. c Leaves on sterile stems. d Flowering plants. e Flowering shoots (an-anther; ov-ovary; st-style). Bar = 3 mm
Fig. 2
Fig. 2. Characterization of the elements in the superscaffold of the C. chinensis genome.
a The 29 assembled superscaffolds of the genome. b Distribution of GC content in the genome. c Distribution of gene density within sliding windows of 1 Mb. Higher density is shown in green. d Expression values of root- and shoot-expressed genes. e Percent coverage of TEs in nonoverlapping windows. f Schematic presentation of major interchromosomal relationships in the C. chinensis genome. Each line represents a syntenic block; block size = 3 kb
Fig. 3
Fig. 3. C. chinensis genome-wide all-by-all Hi-C interaction heat map.
The map shows high-resolution individual superscaffolds, which were scaffolded and assembled independently
Fig. 4
Fig. 4. Phylogenetic tree and evolution analysis of C. chinensis.
a Phylogenetic tree showing the number of gene families displaying expansion (green) and contraction (red) among 18 plant species. The pie charts show the proportions of expanded (green), contracted (red) and conserved (blue) gene family among all gene families. The estimated divergence time (million years ago) is displayed below the phylogenetic tree in black. *The time of the occurrence of a recent whole-genome duplication (WGD) event in C. chinensis. MRCA, most recent common ancestor. b The species tree of 18 species inferred from the complete dataset of single-copy homologous gene using concatenation (RAxML) and gene-tree-based coalescent (ASTRAL) methods
Fig. 5
Fig. 5
Ks distributions for duplicated gene pairs in C. chinensis
Fig. 6
Fig. 6. UpSet plot of the intersection of gene families in C. chinensis, A. thaliana, O. sativa, P. alba, M. esculenta, P. euphratica, J. curcas, R. communis, C. pepo and H. brasiliensis.
The numbers of gene families (clusters) are indicated for each species and species intersection
Fig. 7
Fig. 7. The evolutionary tree of WRKY and NAC gene families in C. chinensis.
a The evolutionary tree and expression values of WRKY box genes in C. chinensis, P. trichocarpa and A. thaliana. b The evolutionary tree and expression values of NAC box genes in C. chinensis, P. trichocarpa and A. thaliana. Genes in the WRKY and NAC families were clustered separately using MEGA7 software via the neighbor-joining method
Fig. 8
Fig. 8. Expression patterns of the root- and shoot-specific expression and evolutionary tree of MYB gene family in C. chinensis.
a Heatmap showing the root- and shoot-specific expression of the members of WUS, STM, ASL and NAC. Each box represents an individual gene, and the red and blue boxes represent relatively high levels and low levels of gene expression, respectively. b Evolutionary tree and expression values of MYB box genes in C. chinensis and A. thaliana. Genes in the MYB family were separately clustered using MEGA7 software via the neighbor-joining method. The genes of C. chinensis and A. thaliana are indicated by blue and purple, respectively
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