Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli

Abstract

Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family, is an important aromatic plant that has been widely used in medicine and perfumery. Here, we report a 1.94 Gb chromosome-scale assembly of the patchouli genome (contig N50 = 7.97 Mb). The gene annotation reveals that tandem duplication of sesquiterpene biosynthetic genes may be a major contributor to the biosynthesis of patchouli bioactivity components. We further phase the genome into two distinct subgenomes (A and B), and identify a chromosome substitution event that have occurred between them. Further investigations show that a burst of universal LTR-RTs in the A subgenome lead to the divergence between two subgenomes. However, no significant subgenome dominance is detected. Finally, we track the evolutionary scenario of patchouli including whole genome tetraploidization, subgenome divergency, hybridization, and chromosome substitution, which are the key forces to determine the complexity of patchouli genome. Our work sheds light on the evolutionary history of patchouli and offers unprecedented genomic resources for fundamental patchouli research and elite germplasm development.

Functional analysis of Pogostemon cablin farnesyl pyrophosphate synthase gene and its binding transcription factor PcWRKY44 in regulating biosynthesis of patchouli alcohol

“…This finding provides a new perspective for characterizing the biosynthesis of terpenes and/or patchoulol. The genome of P. cablin has been reported so far, and there are at least four FPPS genes in the patchouli genome (Shen et al, 2022), which are consistent with our previous transcriptome analysis results (Tang et al, 2019). In this study, FPPS3 in Tang's paper was selected, and named PcFPPS for study, because it was expressed at a higher level in flowers and leaves than the other three genes.…”

Haplotype-phased genome unveils the butylphthalide biosynthesis and homoploid hybrid origin of Ligusticum chuanxiong

“…S3B), echoing the high genome heterozygosity (4.22%). Given that the phenomenon was previously reported in other highly heterozygous genomes, e.g., Pogostemon cablin (3.69%) (34), we inferred that the assembled genome of L. chuanxiong contained two divergent haplotypes, which was further validated by Hi-C data. By Hi-C technology, most contigs (96.11% of the genome length) were anchored onto 22 chromosomes, and the predominant "1:1" Hi-C cross-link signals indicated 11 homoeologous chromosome pairs in L. chuanxiong (fig.…”

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

“…The majority of published assemblies of allopolyploids come from plants, where polyploidy might have shaped the genomes of around 70% of species [57]. Many allopolyploid plant genomes, however, show a higher level of synteny and structural conservation than we observe for M. javanica [13,45,58]. Similarly the few available chromosomal allopolyploid animal genome sequences available [14,15] do not show extensive deletions and chromosomal fissions as does our genome.…”