Marsdenia tenacissima genome reveals calcium adaptation and tenacissoside biosynthesis

• Published in: The Plant journal : for cell and molecular biology 2023-03, Vol.113 (6), p.1146-1159
• Main Authors: Zhou, Yanli, Fan, Wei, Zhang, Haoyue, Zhang, Jingling, Zhang, Guanghui, Wang, Ding, Xiang, Guisheng, Zhao, Changhong, Li, Lianhua, He, Simei, Lu, Yingchun, Zhao, Jiuxia, Meng, Zhengui, Zhang, Xianmin, Meng, Hengling, Yin, Xinhua, Yang, Shengchao, Long, Guangqiang
• Format: Article
• Language: English
• Subjects: Adaptation; Apocynaceae; Biosynthesis; Breeding; Ca2+ adaptation; Calcium; Calcium signalling; cell‐wall remodeling; Chromosomes; DNA sequencing; Domestication; Evolution & development; Evolutionary genetics; Gene expression; Genes; genome assembly; Genomes; Genomics; Herbal medicine; Hi‐C; Karst; Marsdenia; Marsdenia - genetics; Marsdenia tenacissima; Medicinal plants; Myc protein; Pharmacology; Phylogeny; Plant Breeding; Plants, Medicinal; Reproduction (copying); Transcription factors
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.16081

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. Significance Statement This study provide chromosome‐level genome sequence of Marsdenia tenacissima. We provide insights into calcium adaptation of plant species in Karst areas. This study put forward putative tenacissoside biosynthesis.