Marsdenia tenacissima genome reveals calcium adaptation and tenacissoside biosynthesis

Abstract

SUMMARY Marsdenia tenacissima is a medicinal plant widely distributed in the calcium‐rich karst regions of southwest China. However, the lack of a reference genome has hampered the implementation of molecular techniques in its breeding, pharmacology and domestication. We generated the chromosome‐level genome assembly in Apocynaceae using combined SMRT sequencing and Hi‐C. The genome length was 381.76 Mb, with 98.9% of it found on 11 chromosomes. The genome contained 222.63 Mb of repetitive sequences and 21 899 predicted gene models, with a contig N50 of 6.57 Mb. Phylogenetic analysis revealed that M. tenacissima diverged from Calotropis gigantea at least 13.43 million years ago. Comparative genomics showed that M. tenacissima underwent ancient shared whole‐genome duplication. This event, together with tandem duplication, contributed to 70.71% of gene‐family expansion. Both pseudogene analysis and selective pressure calculations suggested calcium‐related adaptive evolution in the M. tenacissima genome. Calcium‐induced differentially expressed genes (DEGs) were mainly enriched in cell‐wall‐related processes. Domains (e.g. Fasciclin and Amb_all) and cis‐elements (e.g. MYB and MYC) frequently occurred in the coding and promoter regions of cell‐wall DEGs, respectively, and the expression levels of these genes correlated significantly with those of calcium‐signal‐related transcription factors. Moreover, calcium addition increased tenacissoside I, G and H contents. The availability of this high‐quality genome provides valuable genomic information for genetic breeding and molecular design, and lends insights into the calcium adaptation of M. tenacissima in karst areas.

Chromosome-scale genome assembly ofApocynum pictum, a drought-tolerant medicinal plant from the Tarim Basin

“…We performed maximum likelihood phylogenetic analyses using protein sequences from 10 species: two from Apocynoideae ( Apocynum pictum and Apocynum venetum ), two from Rauvolfioideae ( Catharanthus roseus 13 and Voacanga thouarsii 14 ), three from Asclepiadoideae ( Marsdenia tenacissima 15 , Asclepias syriaca 16 , and Calotropis gigantea 17 ), two from the Rosids ( Arabidopsis thaliana and Vitis vinifera ), and one from the monocots ( Oryza sativa ) as an outgroup species (Supplementary Table S9). Apocynoideae, Rauvolfioideae, and Asclepiadoideae are subfamilies of the flowering plant family Apocynaceae, and the rosids A. thaliana and V. vinifera were used to calibrate the divergence times of the species tree.…”

“…We used synonymous substitution rates (Ks) to investigate the polyploidization histories of A. pictum and two other Apocynaceae species with high-quality chromosome-scale genome assemblies, M. tenacissima 15 from the Asclepiadoideae and C. roseus 13 from the Rauvolfioideae (Figure 3A). We estimated the Ks distribution of orthologous gene pairs in intergenomic syntenic blocks and observed distinct narrow peaks at 0.36 and 0.46, suggesting that M. tenacissima diverged from the common ancestor after the divergence of A. pictum and C. roseus .…”

Haplotype‐resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution

“…These areas are mainly composed of rocks with large amounts of soluble minerals, making them vulnerable to chemical erosion and dissolution, and resulting in a groundwater system with scarce surface water (Gutiérrez et al., 2014). Karst soils are poor and have 10 times higher calcium concentrations (up to 37.68 g kg −1 ) compared to iron and zinc (Hui et al., 2015; Zhou et al., 2023). The sustainability of karst ecosystems is threatened by human disturbance and global weather change, leading to an increase in rock desertification (Jiang et al., 2014; Lian et al., 2015).…”

“…For example, the expansion of the WRKY gene family promoted the adaptive evolution of the karst cave plant Primulina huaijiensis (Feng et al., 2020). In Marsdenia tenacissima , cations such as zinc and iron were constrained by gene pseudogenization, and the expansion of differentially expressed genes associated with calcium and the accumulation of tenacissosides contributed to its adaptive evolution (Zhou et al., 2023). These studies provide a preliminary scientific basis for better protection and application of the area's biodiversity and ecosystems, such as selecting candidates for rock desertification management.…”