Table 1SGenBank accession numbers of the COI gene for the species used in the phylogenetic analysis

Species / GenBank accession number / Species / GenBank accession number
Conus abbreviatus / HQ852725 / Conus laterculatus / GU134372
Conus achatinus / FJ868109 / Conus lividus / JN831243
Conus ammiralis / EU812755 / Conus magus / FJ868118
Conus andremenezi / EU015727 / Conus marmoreus / EU733517
Conus arenatus / GU134370 / Conus miles / AY296840
Conus aristophanes / HQ834101 / Conus miliaris / FJ393022
Conus aurisiacus / GU134371 / Conus nux / EU423428
Conus bandanus / EU733511 / Conus omaria / EU812757
Conus bullatus / FJ937338 / Conus orbignyi / EU015721
Conus californicus / DQ885864 / Conus parius / FJ868156
Conus caracteristicu / AY588162 / Conus planorbis / FJ868158
Conus cervus / FJ868153 / Conus pulicarius / GU134375
Conus circumcisus / EU015749 / Conus quercinus / JN831246
Conus consors / EU015751 / Conus radiates / GU134376
Conus coronatus / AY588165 / Conus regius / GU134385
Conus crocatus / EU733512 / Conus sanguinolentus / HQ852559
Conus ebraeus / FJ804529 / Conus sponsalis / EU584418
Conus episcopatus / EU733514 / Conus striatus / AY588223
Conus ermineus / AY588176 / Conus teramachii / JF300171
Conus furvus / EU733515 / Conus tessulatus / GU134377
Conus generalis / EU015748 / Conus textile / EU812758
Conus geographus / AY588184 / Conus tulipa / AY588228
Conus glans / FJ868159 / Conus virgo / AY588234
Conus gloriamaris / EU733516 / Conus zonatus / GU134383
Conus imperialis / GU134382 / Conasprellaaphrodite / JF496229
Conus judaceus / FN677404 / Conasprella pagoda / EU015729

Table 2SThe number ofreads aligned to the full-length inferred putative conopeptide precursor sequences in the C.tribblei transcriptome.The name of each conopeptide is presented as Ctr_#_T/N/TN: Ctr: C. tribblei, #: arbitrary assigned number, T: only present in ‘Trinity conopeptide dataset’, N: only present in ‘Newbler conopeptide dataset’, TN: present in both Trinity and Newbler conopeptide datasets.

Read count
Conopeptide name / Trinity / Newbler
Ctr_1_T / 30 / -
Ctr_2_N / - / 5
Ctr_3_N / - / 85
Ctr_4_T / 340 / -
Ctr_6_T / 162 / -
Ctr_7_N / - / 5
Ctr_8_N / - / 196
Ctr_9_T / 37 / -
Ctr_10_TN / 7,873 / 89
Ctr_11_TN / 4,833 / 25
Ctr_13_TN / 4,249 / 45
Ctr_15_T / 270 / -
Ctr_16_T / 2,863 / -
Ctr_17_N / - / 10
Ctr_18_N / - / 10
Ctr_19_T / 48 / -
Ctr_21_N / - / 19
Ctr_22_T / 2,365 / -
Ctr_23_T / 5,310 / -
Ctr_24_T / 1,542 / -
Ctr_25_TN / 179,121 / 884
Ctr_26_TN / 616 / 9
Ctr_27_N / - / 5
Ctr_28_N / - / 403
Ctr_29_TN / 9,745 / 5
Ctr_30_TN / 12,745 / 32
Ctr_31_T / 5 / -
Ctr_32_T / 274 / -
Ctr_33_N / - / 30
Ctr_34_TN / 4,948 / 6
Ctr_35_TN / 3,907 / 14
Ctr_36_N / - / 245
Ctr_37_T / 63,201 / -
Ctr_38_TN / 6,642 / 4
Ctr_39_N / - / 72
Ctr_40_T / 29 / -
Ctr_41_N / - / 77
Ctr_42_T / 504 / -
Ctr_43_T / 831 / -
Ctr_44_TN / 1,223 / 14
Ctr_45_T / 21 / -
Ctr_46_T / 380 / -
Ctr_47_N / - / 347
Ctr_48_N / - / 660
Ctr_49_N / - / 10
Ctr_50_T / 1,877 / -
Ctr_51_T / 780 / -
Ctr_52_TN / 266 / 5
Ctr_53_N / - / 224
Ctr_54_T / 4,967 / -
Ctr_55_TN / 10,975 / 39
Ctr_58_N / - / 135
Ctr_60_TN / 424,745 / 544
Ctr_61_T / 267,324 / -
Ctr_63_T / 396 / -
Ctr_64_N / - / 5
Ctr_65_TN / 917 / 10
Ctr_66_T / 5 / -
Ctr_67_N / - / 50
Ctr_68_N / - / 45
Ctr_69_N / - / 5
Ctr_70_TN / 246,900 / 1,416
Ctr_71_N / - / 23
Ctr_72_TN / 18,284 / 63
Ctr_74_T / 10,062 / -
Ctr_75_N / - / 22
Ctr_76_N / - / 273
Ctr_77_N / - / 142
Ctr_78_T / 99 / -
Ctr_79_T / 338 / -
Ctr_80_T / 57,162 / -
Ctr_81_N / - / 66
Ctr_82_TN / 5,955 / 8
Ctr_85_TN / 1,056 / 7
Ctr_88_T / 15,221 / -
Ctr_89_N / - / 5
Ctr_90_N / - / 69
Ctr_92_T / 669 / -
Ctr_93_TN / 96,758 / 11
Ctr_95_T / 25 / -
Ctr_97_N / - / 55
Ctr_98_N / - / 7
Ctr_99_T / 155 / -
Ctr_100_T / 206 / -
Ctr_101_T / 26 / -
Ctr_102_N / - / 352
Ctr_103_T / 13 / -
Ctr_104_T / 2,396 / -
Ctr_105_N / - / 189
Ctr_106_T / 143 / -
Ctr_108_N / - / 5
Ctr_110_T / 12,806 / -
Ctr_112_T / 1,464 / -
Ctr_114_T / 5 / -
Ctr_115_T / 12 / -
Ctr_116_T / 1,845 / -
Ctr_117_T / 961 / -
Ctr_118_T / 119 / -
Ctr_119_T / 41 / -
Ctr_120_T / 13,480 / -
Ctr_121_T / 28,100 / -
Ctr_122_T / 22 / -
Ctr_123_TN / 1,325 / 30
Ctr_124_N / - / 157
Ctr_125_N / - / 25
Ctr_126_TN / 9,641 / 118
Ctr_127_TN / 1,962 / 13
Ctr_128_N / - / 9
Ctr_129_N / - / 11
Ctr_132_T / 5 / -
Ctr_133_T / 832,965 / -
Ctr_134_N / - / 5
Ctr_135_N / - / 182
Ctr_136_N / - / 115
Ctr_137_N / - / 14
Ctr_138_T / 11,868 / -
Ctr_140_T / 70 / -
Ctr_141_T / 12 / -
Ctr_142_T / 185 / -
Ctr_143_TN / 9,131 / 19
Ctr_144_N / - / 42
Ctr_145_TN / 5,146 / 47
Ctr_146_T / 205 / -
Ctr_147_T / 10 / -
Ctr_148_N / - / 22
Ctr_149_TN / 5,028 / 5
Ctr_150_TN / 16 / 5
Ctr_152_TN / 384 / 5
Ctr_153_T / 12 / -
Ctr_154_T / 443 / -
Ctr_155_T / 137 / -
Ctr_156_T / 41 / -
Ctr_157_T / 2,021 / -
Ctr_159_N / - / 12
Ctr_160_N / - / 8
Ctr_161_T / 483 / -
Ctr_196_T / 1,458 / -

The Illumina reads were aligned to the Trinity-assembled transcripts, and the number of reads generated from each transcripts and the expression level of each transcript represented as fragments per kilobase per million mapped reads (FPKM) were computed by RSEM (Li and Dewey, 2011)using the default settings. Similarly, the Roche 454 reads were aligned to the Newbler assemblyby Bowtie2; the reads were aligned under sensitive mode which allows no mismatches(N=0) per seed (L=20) while 15 consecutive seed extension attempts (D=15) and 2 attempts to “re-seed” the reads (R=2) were allowed.The number of distinct and valid aligned reads is reported.

References:

Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Bioinformatics 12: 323

Table 3S The most highly expressed transcripts(excluding the putative conopeptides presented in Table 2S) in the C. tribblei transcriptome. The gene expression values represented as fragments per kilobase per million mapped reads (FPKM), and the read count were computed using RSEM for Trinity-assembled transcripts as explained inTable 2S.The gene expression values represent the expression level of transcripts in the pooled sample of 20 venom ducts.

Transcript name / Read count / FPKM / Blast annotation
comp53932_c1_seq1 / 3,517,460 / 85,918.49 / RRNA intron-encoded homing endonuclease
comp31647_c0_seq1 / 5,658,039 / 77,697.11 / Transcript antisense to ribosomal RNA protein 1
comp43646_c0_seq2 / 166,158 / 1,7497.7 / Uracil-DNA glycosylase cell wall-associated hydrolase
comp48963_c0_seq2 / 93,832 / 6,025.19 / retrotransposable element ORF2 protein
comp43675_c0_seq1 / 87,795 / 4,232.85 / Soma ferritin
comp52856_c0_seq2 / 6,922 / 3,996.02 / Polyubiquitin
comp50358_c1_seq1 / 8,021 / 2,859.95 / Uncharacterized protein
comp45840_c0_seq1 / 21,321 / 2,568.92 / Uncharacterized protein
comp53329_c0_seq1 / 84,885 / 2,157.34 / Protein disulfide isomerase
comp23567_c1_seq1 / 53,450 / 1,499.9 / Elongation factor 1-alpha
comp52968_c0_seq1 / 75,788 / 1,201.62 / Cytochrome c oxidase subunit 1
comp53979_c0_seq1 / 39,149 / 1,133.46 / Actin, cytoplasmic
comp51524_c0_seq2 / 18,519 / 888.37 / Matrilin
comp47468_c0_seq1 / 44,258 / 875.88 / Elongation factor 2
comp23574_c0_seq1 / 38,443 / 820.36 / Protein disulfide isomerase
comp45617_c0_seq1 / 19,126 / 798.53 / Translationally-controlled tumor protein
comp51834_c0_seq2 / 22,168 / 602.53 / Tubulin beta chain
comp51524_c0_seq3 / 25,176 / 598.63 / Collagen alpha-5(VI) chain
comp53295_c0_seq1 / 32,627 / 577.56 / Cytochrome b
comp52762_c7_seq3 / 2,991 / 411.86 / Histone H4
comp53022_c0_seq1 / 20,926 / 370.82 / Cytochrome c oxidase subunit 3
comp52091_c0_seq1 / 13,088 / 357.86 / ELAV-like protein 1 RNA-binding protein
comp43485_c0_seq1 / 10,366 / 335.37 / Eukaryotic initiation factor 4A-I
comp25356_c0_seq1 / 5,327 / 317.94 / Uncharacterized protein
comp43628_c0_seq1 / 4,962 / 278.9 / Uncharacterized protein
comp49005_c0_seq1 / 13,874 / 263.95 / Protein disulfide-isomerase A3
comp23580_c0_seq1 / 4,710 / 258.11 / Nucleoside diphosphatekinase B
comp47717_c0_seq1 / 10,022 / 247.08 / ADP,ATP carrier protein
comp47499_c0_seq1 / 2,581 / 231.42 / Eukaryotic translation initiation factor 5A
comp54188_c0_seq1 / 6,798 / 230.65 / Elongation factor 1-gamma
comp24216_c0_seq1 / 2,380 / 208.98 / Transcription factor BTF3 homolog 4
comp53286_c0_seq2 / 4,078 / 208.63 / Prohormone-4
comp31001_c0_seq1 / 12,457 / 206.72 / Calmodulin
comp51796_c3_seq1 / 23,550 / 202.93 / Polyadenylate-binding protein 4
comp45213_c0_seq1 / 5,731 / 199.02 / Peroxiredoxin-2
comp53789_c0_seq1 / 13,304 / 193.66 / NADH-ubiquinoneoxidoreductase chain 5
comp50934_c1_seq1 / 10,548 / 187.38 / RNA-directed DNA polymerase from mobile element jockey
comp31129_c0_seq1 / 4,252 / 181.12 / Elongation factor 1-beta
comp47554_c0_seq2 / 4,537 / 179.28 / Ferritin (Fragment)
comp43406_c0_seq1 / 8,606 / 179.22 / Carbonic anhydrase 2