Table 1.
Summary of the D. v. virgifera transcriptome assembly using the pooled dataset.
Figure 1.
Distribution of glycoside hydrolase family genes among polyphagan coleopterans.
Numbers for GH5, GH45, GH48, GH28, and GH11 genes are taken from [22] (marked with *). Exceptions are for D. v. virgifera (this study; numbers in square brackets are for partial sequences), P. cochleariae GH45, GH28 [83], and GH11 [24], G. atrocyanea GH48 [39], D. ponderosae [45], C. sordidus (preliminary results from transcriptomes are shown in parentheses; A. Valencia-Jiménez, personal communication), O. sulcatus GH48 (CAH25542.1), T. castaneum [25], [70], and P. chalceus (this study, searched from the transcriptome [69]). Numbers with † indicate that they are based on the search results from the NCBI NR database or from literatures. Since neither genomes nor transcriptomes are available for these species, the actual numbers of their GH family genes are not known. For GH5 genes, their subfamilies are indicated with ‘s’ followed by the number (e.g., s2 for subfamily 2). Accession numbers for all coleopteran GH genes included in this study are found in Table S5. The taxonomical relationship is based on [68]. ‘.’: not determined. For other insect groups, only existence (+) or absence (−) is shown.
Figure 2.
The maximum-likelihood phylogeny of GH45 proteins.
Forty seven GH45 protein sequences from eleven coleopteran species are included. Their species name abbreviations are found in Table S5. Labels for the coleopteran species belonging to the superfamily Curculionoidea are olive-colored and all other coleopteran sequences colored in black belong to the superfamily Chrysomeloidea. D. v. virgifera sequences are shown in red. Other sequences include: two mollusks (purple), Cryptopygus antarcticus (Collembola, black), Hypsibius dujardini (Tardigrada, black), 24 termite-symbiotic protists (dark green), 10 plant-parasitic nematodes (all are from Bursaphelenchus xylophilus, grey), representative fungi (chosen from 138 sequences, cyan), and representative bacteria (chosen from 18 sequences, brown). Bacterial sequences were used as outgroups. The numbers at internal branches show the bootstrap support values (%) for the maximum-likelihood and neighbor-joining phylogenies in this order. Supporting values are shown only when higher than 60%. Blue-colored branches indicate the species-specific gene duplications (based on currently available sequences) within a cluster supported by higher than 70% of bootstrap values. The scale bar represents the number of amino acid substitutions per site. See Figure S2 for more details.
Figure 3.
The maximum-likelihood phylogeny of GH48 proteins.
Twenty two GH48 protein sequences from seven coleopteran species are included. Their species name abbreviations are found in Table S5. Labels for the coleopteran species belonging to the superfamily Curculionoidea are olive-colored and all other coleopteran sequences colored in black belong to the superfamily Chrysomeloidea. D. v. virgifera sequences are shown in red. Other sequences include: representative bacteria (chosen from 653 sequences, brown) and 3 fungi (shown in cyan). Bacterial sequences were used as outgroups. The numbers at internal branches show the bootstrap support values (%) for the maximum-likelihood and neighbor-joining phylogenies in this order. Supporting values are shown only when higher than 60%. Blue-colored branches indicate the species-specific gene duplications (based on currently available sequences) within a cluster supported by higher than 70% of bootstrap values. The scale bar represents the number of amino acid substitutions per site.
Figure 4.
The maximum-likelihood phylogeny of GH28 proteins.
Eighty four GH28 protein sequences from eight coleopteran species are included. Their species abbreviations are found in Table S5. Labels for the coleopteran species belonging to the superfamily Curculionoidea are olive-colored and all other coleopteran sequences colored in black belong to the superfamily Chrysomeloidea. D. v. virgifera sequences are shown in red. Other sequences include: plant bugs (Lygus hesperus and Lygus lineolaris), representative fungi (chosen from 651 sequences, cyan), representative bacteria (chosen from 42 sequences, brown), and representative plants (chosen from 491 sequences, green). Bacterial sequences were used as outgroups. The numbers at internal branches show the bootstrap support values (%) for the maximum-likelihood and neighbor-joining phylogenies in this order. Supporting values are shown only when higher than 60%. Blue-colored branches indicate the species-specific gene duplications (based on currently available sequences) within a cluster supported by higher than 70% of bootstrap values. The scale bar represents the number of amino acid substitutions per site.
Figure 5.
The maximum-likelihood phylogeny of GH16 proteins.
Sixteen GH16 protein sequences from four coleopteran species are included. Labels for the coleopteran species belonging to the superfamily Curculionoidea, D. v. virgifera, and other beetle sequences are shown in olive, red, and orange, respectively. Their species abbreviations are found in Table S5. Arthropod, other metazoan, fungal (6 chosen from 222 sequences), and bacterial (5 chosen from 977 sequences) sequences are indicated by black, purple, cyan, and brown, respectively. Bacterial sequences were used as outgroups. The numbers at internal branches show the bootstrap support values (%) for the maximum-likelihood and neighbor-joining phylogenies in this order. Supporting values are shown only when higher than 60%. Blue-colored branches indicate the species-specific gene duplications (based on currently available sequences) within a cluster supported by higher than 70% of bootstrap values. The scale bar represents the number of amino acid substitutions per site.