Abstract
Pyrethrum (Tanacetum cinerariifolium), which is a perennial Asteraceae plant with white daisy-like flowers, is the original source of mosquito coils and is known for the biosynthesis of the pyrethrin class of natural insecticides. However, the molecular basis of the production of pyrethrins by T. cinerariifolium has yet to be fully elucidated. Here, we present the 7.1-Gb draft genome of T. cinerariifolium, consisting of 2,016,451 scaffolds and 60,080 genes predicted with high confidence. Notably, analyses of transposable elements (TEs) indicated that TEs occupy 33.84% of the genome sequence. Furthermore, TEs of the sire and oryco clades were found to be enriched in the T. cinerariifolium-specific evolutionary lineage, occupying a total of 13% of the genome sequence, a proportion approximately 8-fold higher than that in other plants. InterProScan analysis demonstrated that biodefense-related toxic proteins (e.g., ribosome inactivating proteins), signal transduction-related proteins (e.g., histidine kinases), and metabolic enzymes (e.g., lipoxygenases, acyl-CoA dehydrogenases/oxygenases, and P450s) are also highly enriched in the T. cinerariifolium genome. Molecular phylogenetic analysis detected a variety of enzymes with genus-specific multiplication, including both common enzymes and others that appear to be specific to pyrethrin biosynthesis. Together, these data identify possible novel components of the pyrethrin biosynthesis pathway and provide new insights into the unique genomic features of T. cinerariifolium.
Highlights
Pyrethrum (Tanacetum cinerariifolium), which is a perennial Asteraceae plant with white daisy-like flowers, is the original source of mosquito coils and is known for the biosynthesis of the pyrethrin class of natural insecticides
Molecular phylogenetic analysis of these proteins revealed that T. cinerariifolium jasmone hydroxylase (TcJMH) formed a subclade with one other T. cinerariifolium protein, two A. annua proteins, and one C. seticuspe protein (Fig. 5B and Supplemental Fig. 5, Clade I) within a large clade consisting of two T. cinerariifolium proteins and 18 Asteraceae proteins (Fig. 5B and Supplemental Fig. 5, Clade II). This inclusion within a large clade is in contrast with the fact that the conversion of jasmone to jasmolone has been reported only in the Tanacetum genus8. These results suggested that such non-Tanacetum TcJMH-like protein genes are non-functional or are involved in a pathway for biosynthesis of phytochemicals other than those observed in T. cinerariifolium
Our results collectively indicated that a gene encoding the squamosa promoter-binding (SPB) transcription factor was proximal to the locus encoding TcLOX, and that genes encoding two GDSL lipases lie proximal to the locus encoding TcGLIP, suggesting that these novel genes may be co-regulated with those encoding pyrethrin-related enzymes known to be involved in pyrethrin biosynthesis
Summary
Sequence assembly and annotation of T. cinerariifolium genome. Paired-end (PE) libraries and mate-pair (MP) libraries (with 3-, 5- and 8-kb insert sizes; MP-3 kb, MP-5 kb, and MP-8 kb, respectively) of the T. cinerariifolium genome were generated and sequenced using Hiseq X and Hiseq4000 instruments. This sequence analysis suggested that the T. cinerariifolium-enriched RIPs include insecticides similar to SNA-I These findings indicated that T. cinerariifolium possesses low-molecular-weight insecticides such as sesquiterpene lactones and pyrethrins and a greater number of genes (compared with other plants) encoding native proteins with toxicity against insects. A BLASTP search using A. thaliana ethylene-response 1 (ETR1), an ethylene-activated kinase, as a query detected Tci_144982, a predicted protein that includes a G-X-G motif-containing HATPase_c domain, with an E-value score of 0 and 69.18% identity (Supplemental Fig. 3B) This sequence analysis suggested that T. cinerariifolium-enriched histidine kinases include ethylene-receptor-type histidine kinases similar to ETR1. Gene was positioned on scaffold sc00057709 and exhibited co-localization with the gene encoding Tci_214196 (a protein that lacks apparent homologs by BLASTP) and one TE gene (Fig. 6C) These results indicated that genes encoding other pyrethrin-associated enzymes were not distributed proximal to the loci encoding either TcJMH or TcCDS. Our results collectively indicated that a gene encoding the SPB transcription factor was proximal to the locus encoding TcLOX, and that genes encoding two GDSL lipases lie proximal to the locus encoding TcGLIP, suggesting that these novel genes may be co-regulated with those encoding pyrethrin-related enzymes known to be involved in pyrethrin biosynthesis
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