A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

Abstract

Isatis indigotica (2n = 14) is an important medicinal plant in China. Its dried leaves and roots (called Isatidis Folium and Isatidis Radix, respectively) are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia. Various classes of compounds isolated from this species have been identified as effective ingredients. Previous studies based on transcriptomes revealed only a few candidate genes for the biosynthesis of these active compounds in this medicinal plant. Here, we report a high-quality chromosome-scale genome assembly of I. indigotica with a total size of 293.88 Mb and scaffold N50 = 36.16 Mb using single-molecule real-time long reads and high-throughput chromosome conformation capture techniques. We annotated 30,323 highconfidence protein-coding genes. Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. In addition, we found that some key enzyme-coding gene families related to the biosynthesis of these components were expanded due to tandem duplications, which likely drove the production of these major active compounds and explained why I. indigotica has excellent antibacterial and antiviral activities. Our results highlighted the importance of genome sequencing in identifying candidate genes for metabolite synthesis in medicinal plants. Data availabilityThe PacBio long reads and Illumina short reads were uploaded to the NCBI SRA database under BioProject PRJNA549758. The final chromosome-scale genome assembly was submitted to the NCBI with accession number VHIU00000000. The genome fasta and gff3 files were uploaded to Figshare.

Genome-Wide Identification and Analysis on YUCCA Gene Family in Isatis indigotica Fort. and IiYUCCA6-1 Functional Exploration

“…Furthermore, it is extremely necessary to understand the molecular mechanism of auxin synthesis and regulation in I. indigotica. Based on the previous references of YUCCA genes in other species and the whole I. indigotica genome data (our unpublished data, another I. indigotica genome [34]), we collected the basic information of YUCCA gene family members and explored their expression patterns in different organs, different developmental periods, and different stress treatments. Moreover, the functions of YUCCA genes were discussed, taking IiYUCCA6-1 as an example.…”

The Genome Sequence of Alpine Megacarpaea delavayi Identifies Species-Specific Whole-Genome Duplication

“…De novo , homology-based, and transcript-based approaches were combined to annotate protein-coding sequences ( Chen et al, 2020 ; Kang et al, 2020 ; Zhang et al, 2020 ). In total, 41,114 genes were predicted with an average gene length and number of exons of 1853 bp and 6.57, respectively ( Table 1 ).…”

The chromosome-level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae)

“…All painting probes (Lysak et al, 2016;Schranz et al, 2006) each identifying a unique chromosome region confirmed the diploid status of the Megadenia genome. We also compared the M. pygmaeagenome with A. thaliana and C. rubella genome by MCScanX (Wang et al, 2012) using the same method as published previously(M. Kang et al, 2020). The syntenic relationships, order and orientation of the 22 GBs by CCP produced the same schematic diagram of the M. pygmaea genome (Figs.…”