Terpene synthase genes in Melaleuca alternifolia: comparative analysis of lineage-specific subfamily variation within Myrtaceae

Abstract

Terpenes are a multifarious group of secondary compounds present throughout the living world that function primarily in defence, or otherwise in regulating interactions between an organism and its environment. Terpene synthases (TPS) are a mid-sized gene family whose diversity and make-up reflects a plant’s ecological requirements and unique adaptive history. Here we catalogue TPS in Melaleuca alternifolia and examine lineage-specific expansion in TPS relative to other sequenced Myrtaceae. Overall, far fewer (37) putative TPS genes were identified in M. alternifolia compared with Eucalyptus grandis (113) and E. globulus (106). The number of genes in clade TPS-b1 (12), which encode enzymes that produce cyclic monoterpenes, was proportionally larger in M. alternifolia than in any other well-characterised plant. Relative to E. grandis, the isoprene-/ocimene-producing TPS-b2 clade in M. alternifolia tended to be proportionally smaller. This suggested there may be lineage-specific subfamily change in Melaleuca relative to other sequenced Myrtaceae, perhaps as a consequence of its semi-aquatic evolutionary history.

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Acknowledgements

The authors wish to acknowledge the assistance of R. Wood, A. Kawamata and J. Bloomfield and T. Rhodes for his help in the laboratory. Jed Calvert would also like to thank Shirali, for her constant support and supply of fresh perspectives. This work was supported by the Australian Research Council (Grant No. DP140102552).

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Correspondence to Mervyn Shepherd.

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Handling editor: Yunpeng Zhao.

Electronic supplementary material

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Information on Electronic Supplementary Material

Online Resource 1: Methods and results for generating a draft genome sequence for Melaleuca alternifolia.

Online Resource 2: Flow cytometry methods for genome size estimation in Melaleuca alternifolia.

Online Resource 3: TPS subfamily conserved amino acid sequences used as queries for BLASTing the Melaleuca alternifolia assembly. Originally published in a supplementary file with Külheim et al. 2015.

Online Resource 4: tBLASTn searches of Melaleuca alternifolia (Southern Cross Plant Science unmasked vv1.1) genome using queries listed in Kulheim et al. (2015) (Calvert et al._ESM_3.pdf) to find TPS genes not predicted by MAKER v2.31.8.

Online Resource 5: Top e-values for conserved TPS subfamily domain queries in Melaleuca alternifolia and Eucalyptus grandis.

Online Resource 6: Maximum-likelihood tree produced using the 113 amino acid sequences of Eucalyptus grandis TPS genes (from subfamilies a, b, c, e, f and g) identified by Külheim et al. (2015). Tree is rooted at the branching of type I and III genes. Phylogeny shows high structural similarity to Külheim et al. down to branch length, which denotes relationship distance. Scale = average number of amino acid substitutions per branch (JPEG produced using Figtree v1.4.2. And GIMP).

Online Resource 7: FASTA Alignment of 113 E. grandis TPS genes plus the 37 Melaleuca alternifolia candidate gene models identified using BLAST, as well as the coding sequence for a putative monoterpene synthase transcript obtained by Shelton et al. (2004a, b; GenBank accession AY279379.1). Using PhyML 3.0 (http://phylogeny.lirmm.fr; Dereeper et al. 2008) with default settings, a ClustalW alignment was constructed from the 113 sequences. Gblocks curation was skipped.

Online Resource 8: 37 Melaleuca alternifolia TPS gene models listed by subfamily. Quality class ranking as per Külheim et al. (2015) is as follows: 1 = Full length, no prem stop codons; 2 = Full length, up to 2 stop codons; 3 = Full length, no stop codon; 4 = Pseudogenes, more than 2 stop codons; 5 = Partial gene.

Online Resource 9: Amino acid sequences of thirty-seven candidate TPS genes with high similarity to conserved TPS regions identified in the Melaleuca alternifolia genome.

Online Resource 10: Melaleuca alternifolia and Eucalyptus grandis gene models predicted by ChloroP 1.1 to contain chloroplast transit peptides.

Online Resource 11: Melaleuca alternifolia TPS gene models (37) analysed using PCLR (Schein et al. 2001) for the presence of chloroplast transit peptides (cTP).

Online Resource 12: Phylogenetic tree file. Replication of the Külheim et al. 2015 phylogenetic tree for TPS genes in Eucalyptus grandis, used as a foundation for comparative analysis.

Online Resource 13: Phylogenetic tree file. Replication of the Külheim et al. 2015 phylogenetic tree for TPS genes in Eucalyptus grandis, with inclusion of 37 Melaleuca alternifolia putative TPS genes and one putative monoterpene synthase gene (Shelton et al. 2004a, b).

Online Resource 14: Methods for collection of C. citriodora subsp. variegata data provided in Table 1.

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Calvert, J., Baten, A., Butler, J. et al. Terpene synthase genes in Melaleuca alternifolia: comparative analysis of lineage-specific subfamily variation within Myrtaceae. Plant Syst Evol 304, 111–121 (2018). https://doi.org/10.1007/s00606-017-1454-3

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Keywords

  • Corymbia
  • Eucalyptus
  • Monoterpene
  • Tea tree