Fig. 5

Phylogenetic analysis of neoculin-related transcripts uncovers the contrasting expression levels in the orthologs. Neoculin-related and GNA family members were aligned using ClustalX. The phylogenetic tree was constructed using the neighbor-joining method (bootstrap = 1000). De novo transcriptome transcript IDs for C. latifolia and C. capitulata are shown in purple and orange, respectively. L_16562_c0_g1_i1 and L_16562_c0_g1_i2 of C. latifolia correspond to NBS and NAS, respectively (see Additional file 7). Transcript per million (TPM) values are listed to the right of the transcript IDs. Transcripts from the two species encoding highly similar protein sequences are shown in pairs. Transcripts sharing high similarity with those of NBS and NAS are referred to as the neoculin group (indicated by the red frame). Groups of other highly similar predicted proteins are shown in groups 1 and 2. The vertical lines to the right of the TMP value indicate orthologous pairs in C. latifolia and C. capitulata. The sequences and species of origin of the selected GNA family members are as follows, with the structure name from the Protein Data Bank given in parentheses: ASA, Allium sativum (1BWU); GNA, Galanthus nivalis (1MSA); and NPL, Narcissus pseudonarcissus (1NPL). Other sequences were obtained from GenBank: PRA, Polygonatum roseum (AY899824); PMA, Polygonatum multiflorum (U44775); CMA, Clivia miniata (L16512); ZCA, Zephyranthes candida (AF527385); AAA, Allium ascalonicum (L12172); ACA, Allium cepa (AY376826); AUA, Allium ursinum (U68531); THC, Tulipa hybrid cultivar (U23043); ZOA, Zingiber officinale (AY657021); ACO, Ananas comosus (AY098512); AKA, Amorphophallus konjac (AY191004); DPA, Dioscorea polystachya (AB178475); CHC, Cymbidium hybrid cultivar (U02516); and EHA, Epipactis helleborine (U02515)