The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids

Abstract

Saururus chinensis, an herbaceous magnoliid without perianth, represents a clade of early-diverging angiosperms that have gone through woodiness-herbaceousness transition and pollination obstacles: the characteristic white leaves underneath inflorescence during flowering time are considered to be a substitute for perianth to attract insect pollinators. Here, using the newly sequenced S. chinensis genome, we revisited the phylogenetic position of magnoliids within mesangiosperms, and recovered a sister relationship for magnoliids and Chloranthales. By considering differentially expressed genes, we identified candidate genes that are involved in the morphogenesis of the white leaves in S. chinensis. Among those genes, we verified -in a transgenic experiment with Arabidopsis -that increasing the expression of the 'pseudo-etiolation in light' gene (ScPEL) can inhibit the biosynthesis of chlorophyll.ScPEL is thus likely being responsible for the switches between green and white leaves, suggesting that changes in gene expression may underlie the evolution of pollination strategies. Despite being an herbaceous plant, S. chinensis still has vascular cambium and maintains the potential for secondary growth as a woody plant, because the necessary machinery, i.e., the entire gene set involved in lignin biosynthesis, is well preserved. However, similar expression levels of two key genes (CCR and CAD) between the stem and other tissues in the lignin biosynthesis pathway are possibly associated with the herbaceous nature of S. chinensis. In conclusion, the S. chinensis genome provides valuable insights into the adaptive evolution of pollination in Saururaceae and reveals a possible mechanism for the evolution of herbaceousness in magnoliids.

A reference genome for the Chinese Lizardtail Herb (Saururus chinensis)

“…A comprehensive dataset for the S. chinensis genome was acquired, comprising ∼22.95 Gb of Illumina reads, ∼66.56 Gb of ONT reads, and ∼40.50 Gb of Hi-C reads (Supplementary Table S2). The estimated genome size of S. chinensis stood at ∼528.084 Mb (Supplementary Table S3), a concordance with the result reported by Xue et al (2023). The final assembled genome spanned 522.247 Mb, exhibited a Scaffold N50 length of 46.948 Mb and a Contig N50 length of 4.180 Mb (Supplementary Table S1), and revealed the presence of eleven chromosomes (Fig.…”

“…BUSCO evaluation (Manni et al 2021) demonstrated that ∼95.91% of the complete BUSCOs were aligned with total gene models (Supplementary Table S1), indicating an acceptable level of gene-set completeness. In summary, we had obtained an enhanced chromosome-level genome for S. chinensis , which was characterized by heightened genome continuity and a more complete gene set (Supplementary Table S1), surpassing the previous version (Xue et al, 2023).…”

“…An amplification-free whole genome sequencing library was constructed using the Ligation Sequencing Kit (No: SQK-LSK110; ONT, UK) and then sequenced by a PromethION sequenator (ONT, UK). A Hi-C library was constructed following a recognized Hi-C protocol (restriction enzyme: HindIII) described in earlier studies (Grob et al, 2014; Rao et al, 2014; Hu et al, 2019; Tang et al, 2020; Qin et al, 2021; Cui et al, 2022; Xue et al, 2023) and then sequenced by an Illumina NovaSeq6000 sequenator (Illumina, USA). Total RNAs were extracted using an RNAprep Pure Plant Kit (Cat.…”

“…To date, four genomes have been systematically reported within the aforementioned three families in the Piperales, namely Aristolochia fimbriata (Qin et al, 2021) and A. contorta (Cui et al, 2022) in Aristolochiaceae, Piper nigrum (Hu et al, 2019) in Piperaceae, and S. chinensis (Xue et al, 2023) in Saururaceae. It is important to note that P. nigrum and S. chinensis exhibit discernible low levels of gene-set completeness with respect to A. fimbriata and A. contorta.…”

The high‐quality genome of Cryptotaenia japonica and comparative genomics analysis reveals anthocyanin biosynthesis in Apiaceae

“…Finally, a non‐redundant, consensus protein‐coding gene set was constructed. Additional gene functional annotation of C. japonica was performed by searching the NR (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plant/), Swiss‐Port (ftp://ftp.uniprot.org/), InterPro, Pfam, GO and KEGG databases (Xue et al., 2023).…”