Chromosome-level genome assembly of Aristolochia contorta provides insights into the biosynthesis of benzylisoquinoline alkaloids and aristolochic acids

Abstract

Aristolochic acids (AAs) and their derivatives exist in multiple Aristolochiaceae species which had been or are being used as medicinal materials. During the past decades, AAs have received increasing attention due to their nephrotoxicity and carcinogenecity. Elimination of AAs in medicinal materials using biotechnological approaches is important to improve medication safety. However, it has not been achieved because of the limited information of AA biosynthesis available. Here, we report a high-quality reference-grade genome assembly of the AA-containing vine, Aristolochia contorta. Total size of the assembly is 209.27 Mb, which is assembled into 7 pseudochromosomes. Synteny analysis, Ks distribution and 4DTv suggest absences of whole-genome duplication events in A. contorta after the angiosperm-wide WGD. Based on genomic, transcriptomic and metabolic data, pathways and candidate genes of benzylisoquinoline alkaloid (BIA) and AA biosynthesis in A. contorta were proposed. Five O-methyltransferase genes, including AcOMT1–3, AcOMT5 and AcOMT7, were cloned and functionally characterized. The results provide a high-quality reference genome for AA-containing species of Aristolochiaceae. It lays a solid foundation for further elucidation of AA biosynthesis and regulation and molecular breeding of Aristolochiaceae medicinal materials.

Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya (Annona cherimola)

“…Because previous studies have described WGD events in L. chinense (Ks ~ 0.7) and C. kanehirae (Ks ~ 0.5 and Ks ~ 0.8), both species were used as control of the results obtained. Ks distribution analysis suggested the absence of a WGD event in A. cherimola , confirming the results in other species belonging to the Magnoliid clade, such as A. fimbriata (Qin et al, 2021) and A. contorta (Cui et al, 2022). However, work on the M. biondii genome (Dong et al, 2021) suggested that a WGD event took place just before the separation between Magnoliales and Laurales, in agreement with the genome evolution of Litsea (Chen, Li, et al, 2020).…”

“…Indeed, although early divergent angiosperm phylogeny studies have been published, the relations among eudicots, monocots, and magnoliids are still incongruent, probably because of the limited informative sequence generated among these groups. To date, draft reference genomes have been published for 15 species of the Magnoliid clade: two in the Calycanthaceae (Laurales) ( Chimonanthus salicifolius [Lv et al, 2020] and Chimonanthus praecox [Shang et al, 2020; Shen et al, 2021]); seven in the Lauraceae (Laurales) ( Cinnamomum camphora [Shen et al, 2022; Jiang et al, 2022], Cinnamomum kanehirae [Chaw et al, 2019], Lindera glauca [Xiong et al, 2022], Litsea coreana [Zhang et al, 2022], Litsea cubeba [Chen, Hu, et al, 2020], Phoebe bournei [Han et al, 2022], and Persea americana [Nath et al, 2022; Rendón‐Anaya et al, 2019; Sharma et al, 2021; Talavera et al, 2019]); one in the Annonaceae (Magnoliales) ( A. muricata [Strijk et al, 2021]); three in the Magnoliaceae (Magnoliales) ( Liriodendron chinense [Chen, Hao, et al, 2019], Magnolia biondii [Dong et al, 2021], and Magnolia officinalis [Yin et al, 2021]); two in the Aristolochiaceae (Piperales) ( Aristolochia fimbriata [Qin et al, 2021] and Aristolochia contorta [Cui et al, 2022]); and one in the Piperaceae (Piperales) ( Piper nigrum [Hu et al, 2019]). Thus, Annonaceae, the largest family on this clade and one of the most species‐rich pantropical plant families (Couvreur et al, 2019), is only represented by one genome until now.…”

Phylogenetic studies of magnoliids: Advances and perspectives

“…Consistently, the results of nuclear genome sequencing analysis of C. camphora , A. glabra, P. bournei, A. contorta , C. burmannii , etc. support that magnoliids are sister plants to eudicots ( Cui et al., 2022 ; Han et al., 2022 ; He et al., 2022 ; Li et al., 2022 ; Shen et al., 2022 ; Sun et al., 2022 ; Wang et al., 2022 ).…”

“…The reported species of magnoliids with sequenced nuclear genomes include Magnoliales, Laurales, and Piperales (17 species, 23 references in total). Examples include Laurales: Cinnamomum kanehirae ( Chaw et al., 2019 ), avocado ( Persea americana ) ( Rendón-Anaya et al., 2019 ; Nath et al., 2022 ), Litsea cubeba ( Chen Y. C. et al., 2020 ), Phoebe bournei ( Chen S. P. et al., 2020 ; Han et al., 2022 ), Cinnamomum camphora ( Jiang et al., 2022 ; Shen et al., 2022 ; Sun et al., 2022 ; Wang et al., 2022 ), C. burmannii ( Li et al., 2022 ), Litsea coreana ( Zhang et al., 2022 ) of Lauraceae, Chimonanthus praecox ( Shang et al., 2020 ; Shen et al., 2021 ) and C. salicifolius ( Lv et al., 2020 ) of Calycanthaceae; Magnoliales: L. chinense ( Chen et al., 2019 ), Magnolia biondii ( Dong et al., 2021 ), M. officinalis ( Yin et al., 2021 ); Annona muricata ( Strijk et al., 2021 ), A. glabra ( He et al., 2022 ); Pepperales: Piper nigrum ( Hu et al., 2019 ), Aristolochia fimbriata ( Qin et al., 2021 ) and A. contorta ( Cui et al., 2022 ). Twenty of the 23 references in the genome analysis magnoliids discussed the evolutionary status of magnoliids, providing new insights into the early evolution of angiosperms, but the results of the analysis are inconsistent.…”

A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots

“…The protein sequences of the reference gene families involved in flavonoid and triterpenoid biosynthesis in A. thaliana or P. ginseng were downloaded from UniProt. These sequences were used as a query for a BLAST search against the protein sequences of AMM with an e value cutoff of 1e −40 ( Cui et al., 2022 ). Next, all the homologous sequences were submitted to the Pfam database for domain analysis ( Mistry et al., 2021 ).…”