The Litsea genome shed new lights on the evolution of the Lauraceae and the relationship among magnoliids, monocots and eudicots

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Lauraceae (or laurel family) is a family from the order Laurales in Magnoliids1. The family includes 2,500-3,000 globally distributed species, among most are economically and ecologically important tree species in southern China2. Lauraceae has small flowers, diverse morphology, and bisexual and unisexual flowers, which make it difficult to determine its morphological evolution and evolutionary position. Also, the mechanism for the particular scent of key compounds synthesis in Lauraceae is unclear. Therefore, exploring the genetic basis of particular scent, molecular mechanisms of the evolution of Lauraceae and floral morphology on the basis of genome sequencing provides insights into the biological characteristics, products application, and genetic breeding of Lauraceae. From a phylogenetic perspective, the relationships among Magnoliids, monocots, and eudicots have long been a subject of debate3-6. Chaw et al, 2018 reported the Cinnamomum kanehirae5 genome to support a sister relationship of Magnoliids and eudicots to the exclusion of monocots, while the genomes of Liriodendron chinense4 reported by Chen et al, 2019 and Persea americana genome7 suggested Magnoliids as a sister group to the clade consisting of both eudicots and monocots. Therefore, genome sequence of other Lauraceae species and the phylogenetic analysis could be of great help to address the phylogenetic position of magnoliids relative to eudicots and monocots. 

As one of the representative and key species for essential oil producing in Lauraceae, Litsea cubeba (Fig. 1) produces essential oils with approximately 95% terpenoid, which are widely used in perfumes, cosmetics, and medicine8-10. It’s also an important species to revisit the phylogenetic position of Magnoliids relative to eudicots and monocots4, 5, 11 and to study the evolutionary relationships within the Lauraceae. Our research team includes Professor Yang-Dong Wang at the Sub-tropical Forestry Research Institute of the Chinese Academy of Forestry, Professor Zhong-Jian Liu at Fujian Agriculture and Forestry University, Professor Yves Van de Peer at Ghent University and Professor Wen-Chieh Tsai at National Cheng Kung University who launched the L. cubeba genome sequencing project12 and sequenced the genome using a combination of Illumina and Pacbio sequencing systems and an optimized assembly of 1.37G with a contig N50 length of 607.34 kb was obtained. The genome was further anchored to 24 chromosomes with an anchoring rate of 94.56% via Hi-C technology. Scafflod N50 reached 1.76 Mb, and a high-quality genome map of L. cubeba was obtained.

Figure 1. The flowering plant of L. cubeba. Photo by Liang Ma

Phylogenetic trees based on the concatenated sequence alignments of both nucleotide and amino acids sequences indicated that Magnoliids as a sister group to eudicots after their common ancestor diverged from monocots, which is consistent with C. kanehirae genome paper5. To reduce long branch attraction in phylogenetic analysis, which exited in Chen et al, 2019 and Chaw et al, 2018’s papers4, 5, multi-species coalescent (MSC)-based phylogenomic analyses were conducted and same topology was obtained, which further supported a sister group relationship between Magnoliids and eudicots, to the exclusion of monocots. However, the MSC-based tree using amino acids suggests that Magnoliids form a sister group with monocots, after their divergence from eudicots. Recent study13 also suggested a sister group relationship between Magnoliids and monocots by using synteny-based phylogenies. These conflicting topologies may be the result of substantial incomplete lineage sorting (ILS) in short branches that separates magnoliids, monocots and dicots due to rapid radiation and divergence of species. Even more research is still required, the phylogenetic result provided new evidence for the relationship among Magnolidds, monocots and eudicots.

The whole genome duplication (WGD) event showed that L. cubeba has experienced two WGD events, the old one occurred before the divergence of Laurales and Magnoliales, and the last one was during the internal divergence of Lauraceae. The results also provide evidence of two WGD events not only in the Lauraceae species but also in some non-Lauraceae species in the Laurales order. 

Low-coverage genome sequencing and transcriptomic analysis were performed to reveal the molecular mechanism of the morphological evolution and aroma synthesis of Lauraceae. Phylogenetic relationship analysis of the representative genera of the Laurel family was conducted to investigate the genes that are potentially involved in the evolution of floral structures, which provided molecular evidence of the evolution of the inflorescences from racemes, panicles to pseudo-umbels, and important regulate genes involving in sex differentiation process from unisexual to bisexual flowers. In addition, the gene family mono-TPS has significantly expanded in Lauraceae, which has played an important role in the diversity formation of terpenoid compounds. Key candidate genes such as LcuTPS18, 19, 20, 25, 26, and 42 involving in the synthesis of monoterpene compounds in L. cubeba were also identified through transient over-expression and enzyme activity assay.

 In general, the L. cubeba genome provides a valuable resource for elucidating the Lauraceae evolution toolkit, supporting the sister relationship between Magnoliids and eudicots, to the exclusion of monocots, revealing key genes involving in floral structure formation and scent biosynthesis, as well as shedding important insights into the genetic diversity and evolution of Laurales.

This post is jointly written by Zhong-Jian Liu and Di-Yang Zhang at Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University.

Reference

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2.       Li, S. G. et al. Lauraceae, Flora of China, FOC 7, 102-153 (2008).

3.       Massoni, J., Couvreur, T. L. P. & Sauquet, H. Five major shifts of diversification through the long evolutionary history of magnoliidae (angiosperms). BMC Evol. Biol. 15, 49 (2015).

4.       Chen, J. et al. Liriodendron genome sheds light on angiosperm phylogeny and species-pair differentiation. Nat. Plants. 5, 18-25 (2018).

5.       Chaw, S. M. et al. Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. Nat. Plants 5, 63-73 (2019).

6.       Soltis, D. E. & Soltis, P. S. Nuclear genomes of two Magnoliids. Nat. Plants 5, 6-7(2019).

7.       Rendón-Anaya, M. et al. The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proc. Natl. Acad. Sci U. S. A. 116, 17081-17089 (2019).

8.       Huang, X. W., Feng, Y. C. & Huang, Y. Potential cosmetic application of essential oil extracted from Litsea cubeba fruits from China. J. Essent. Oil Res. 25, 112-119 (2013).

9.       Su, Y. C. & Ho, C. L. Essential oil compositions and antimicrobial activities of various parts of Litsea cubeba from Taiwan. Nat. Prod. Commun. 11, 515-8 (2016).

10.    Nguyen, H. V. et al. Litsea cubeba leaf essential oil from Vietnam: chemical diversity and its impacts on antibacterial activity. Lett. Appl. Microbiol. 66, 207-214 (2018).

11.    Soltis, D. E. & Soltis, P. S. Nuclear genomes of two Magnoliids. Nat. Plants 5, 6-7(2019).

12.    Chen, Y. C., Li, Z., Zhao, Y. X., Gao, M., Wang, J. Y., Liu, K. W., Wang, X., Wu, L. W., Jiao, Y. L., Xu, Z. L, Zhang, Q. Y., Liang, C. K., Hsiao, Y. Y., Zhang, D. Y., Lan, S. R., Huang, L. Xu, W., Tsai, W. C., Liu, Z. J., Van de Peer, Y., Wang, Y. D. The Litsea genome and the evolution of the laurel family. Nat. Commun. 11, 1675 (2020).

13.    Zhao, T. et al. Novel phylogeny of angiosperms inferred from whole-genome microsynteny analysis. bioRxiv Preprint at doi: https://doi.org/10.1101/2020.01.15.908376 (2020).

 


Go to the profile of Zhong-Jian Liu

Zhong-Jian Liu

Professor, Fujian Agricultural and Forestry University

Plant phylogenetics and evolution, Plant genomics

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