Background Saururaceae are an ancient family within Piperales, comprising seven perennial herbs grouped into four relict genera: Anemopsis, Gymnotheca, Houttuynia, and Saururus; distributed primarily in East Asia (Gymnotheca, Houttuynia, and S. chinensis) and North America (Anemopsis and S. cernuus). Despite the limited number of species, phylogenetic relationships remain inconsistent across non-molecular data, nuclear genes, and chloroplast genes. Results Here, we report for the first time the plastid genomes of G. involucrata and H. emeiensis and provide an additional plastid genome of S. chinensis, enabling a comprehensive analysis of the plastid genome evolution in Saururaceae. All seven plastomes exhibit the typical Quadripartite structure, ranging from 160,226 to 161,556 bp, and contain 131 genes. (114 unique), including 85 protein-coding genes (80 unique), 37 transfer RNAs (tRNAs), eight ribosomal RNAs (rRNAs), and one pseudogene (ycf1). The plastomes are highly conserved in gene order, repeat composition, and codon usage patterns, particularly between H. cordata and H. emeiensis. Mutation hotspots were identified in both coding regions (ycf1, ndhD, ndhF, ccsA, matK; Pi > 0.03) and non-coding regions (rpl32_trnL, rps16_trnQ, ccsA_ndhD, psbM_trnD, psbZ_trnG, ndhE_ndhG, rps15_ycf1, and petA_psbJ; Pi > 0.06), and may serve as molecular markers for species delimitation and population-level studies. Phylogenetic analysis results based on whole plastomes, coding sequences (CDS), and intergenic spacers (IGS) resolve two major clades that correspond to the presence or absence of a flower bract stalk: Anemopsis – Houttuynia (lacking a bract stalk) and Gymnotheca – Saururus (with a bract stalk). Conclusion This study presents the plastid genomes of G. involucrata and H. emeiensis, revealing structural variations in the plastid genomes of Saururaceae and their implications for internal phylogeny. The findings presented herein provide a novel perspective on the adaptive evolution of Saururaceae, thus offering valuable data for a more in-depth exploration of the phylogeny of Piperales within Magnoliids.

Characteristics of plastid genomes in the Saururaceae and their phylogenomic implications

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2025年9月29日

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Wei-Hong Sun,
Yu Lv,
Lian Luo,
Ming-Xing Che,
Yan Tan,
Zhuang Zhao,
Tao Feng,
Wen-Hui Li,
Zhi-Feng Chen

摘要

Background

Saururaceae are an ancient family within Piperales, comprising seven perennial herbs grouped into four relict genera: Anemopsis, Gymnotheca, Houttuynia, and Saururus; distributed primarily in East Asia (Gymnotheca, Houttuynia, and S. chinensis) and North America (Anemopsis and S. cernuus). Despite the limited number of species, phylogenetic relationships remain inconsistent across non-molecular data, nuclear genes, and chloroplast genes.

Results

Here, we report for the first time the plastid genomes of G. involucrata and H. emeiensis and provide an additional plastid genome of S. chinensis, enabling a comprehensive analysis of the plastid genome evolution in Saururaceae. All seven plastomes exhibit the typical Quadripartite structure, ranging from 160,226 to 161,556 bp, and contain 131 genes. (114 unique), including 85 protein-coding genes (80 unique), 37 transfer RNAs (tRNAs), eight ribosomal RNAs (rRNAs), and one pseudogene (ycf1). The plastomes are highly conserved in gene order, repeat composition, and codon usage patterns, particularly between H. cordata and H. emeiensis. Mutation hotspots were identified in both coding regions (ycf1, ndhD, ndhF, ccsA, matK; Pi > 0.03) and non-coding regions (rpl32_trnL, rps16_trnQ, ccsA_ndhD, psbM_trnD, psbZ_trnG, ndhE_ndhG, rps15_ycf1, and petA_psbJ; Pi > 0.06), and may serve as molecular markers for species delimitation and population-level studies. Phylogenetic analysis results based on whole plastomes, coding sequences (CDS), and intergenic spacers (IGS) resolve two major clades that correspond to the presence or absence of a flower bract stalk: Anemopsis – Houttuynia (lacking a bract stalk) and Gymnotheca – Saururus (with a bract stalk).

Conclusion

This study presents the plastid genomes of G. involucrata and H. emeiensis, revealing structural variations in the plastid genomes of Saururaceae and their implications for internal phylogeny. The findings presented herein provide a novel perspective on the adaptive evolution of Saururaceae, thus offering valuable data for a more in-depth exploration of the phylogeny of Piperales within Magnoliids.