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

Ting Xue; Xuehai Zheng; Duo Chen; Limin Liang; Nan Chen; Zhen Huang; Wenfang Fan; Jiannan Chen; Wan Cen; Shuai Chen; Jinmao Zhu; Binghua Chen; Xingtan Zhang; Youqiang Chen

doi:10.1038/s41438-020-0269-5

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

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

Authors

Ting Xue^{1

2}, Xuehai Zheng¹, Duo Chen¹, Limin Liang², Nan Chen³, Zhen Huang¹, Wenfang Fan¹, Jiannan Chen², Wan Cen², Shuai Chen⁴, Jinmao Zhu¹, Binghua Chen¹, Xingtan Zhang⁴, Youqiang Chen^{1

2}

Affiliations

¹ 1Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, China.
² 2Center of Engineering Technology Research for Microalga Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China.
³ 3College of Fine Arts, Fujian Normal University, Fuzhou, China.
⁴ 4FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.

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.