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

First author: Ting Xue; Affiliations: Fujian Normal University (福建师范大学): Fuzhou, China

Corresponding author: Youqiang Chen 

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.

川苔草科（Podostemonaceae）是一类在生态和形态上比较特殊的水生被子植物，仅在原始水文且水质较高的河流中生存，并且灭绝的风险相对较高。川苔草科下的分类状态一直存在争议。本文中，作者通过整合Hi-C、Illumina以及PacBio测序，报道了川苔草科第一个基因组序列，即川苔草（学名：Cladopus chinensis）的高质量参考基因组。川苔草的基因组组装大小约为827.92  Mb，contig N50长为1.42  Mb，共注释了27370个蛋白编码基因。组装的川苔草基因组大小接近预估的基因组大小，其中659.42  Mb的基因组可以锚定到29个superscaffolds，scaffold N50长为21.22  Mb。川苔草基因组中的重复序列占了59.20%，其中长末端重复序列LTR是占比最大的一类，占了基因组的28.97%。基因组演化分析显示川苔草的分化时间约在106个百万年前，要比杨柳目（Malpighiales）82个百万年的分化时间要早，并且该支系分化形成了川苔草目中的一个独立分支。川苔草基因组上在443万年前发生过一次全基因组复制事件。比较基因组分析显示，川苔草基因组中与氧化磷酸化、光合作用以及异黄酮代谢基因家族存在扩增和收缩，可能与该植物生长在水下的基因组特征相关。转录组分析揭示了相比于根组织，茎组织中上调表达的基因显著富集了NAC基因家族以及茎发育和防御响应相关的基因，包括WUS、ASL、STM、NAC2/8/29/47/73/83/102。本文的发现揭示了稀有水生被子植物的基因组多样性，并且为川苔草科的物种分类和特殊茎尖分生组织研究提供了宝贵的参考。

通讯：陈由强 (http://life.fjnu.edu.cn/27/2c/c4524a75564/page.htm)

个人简介：1977-1981年，福建林学院，学士；1984年，福建林学院，硕士；2002年，福建农林学大学，博士。

研究方向：主要从事植物生理与分子生物学、甘蔗汁和渣生产乙醇以及食品加工技术等方面研究。。

doi: https://doi.org/10.1038/s41438-020-0269-5

Journal: Horticulture Research

Published date: April 01, 2020