Modern venomics – Current insights, novel methods and future perspectives in biological and applied animal venom research

Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit

Phylogenetic trees depicting relationships among nucleotide and protein sequences from Fad genes.

<p>(a) Maximum Likelihood tree of Fad nucleotide sequences. Bootstrap values are shown next to nodes, values under 75% not reported. Accession numbers: AtFad KR154727, <i>C</i>. <i>gigas</i> 1 CGI_10016476, <i>C</i>. <i>gigas</i> 2 CGI_10019765, <i>C</i>. <i>gigas</i> 3 XM_011415748, <i>A</i>. <i>californica</i> 1 XM_005096991, <i>A</i>. <i>californica</i> 2 XM_005093125, <i>A</i>. <i>californica</i> 3 XM_005090516, <i>A</i>. <i>californica</i> 4 XM_005090520, <i>L</i>. <i>gigantea</i> 1 XM_009052983, <i>L</i>. <i>gigantea</i> 2 XM_009051720, <i>L</i>. <i>gigantea</i> 3 XM_009046829, <i>C</i>. <i>nobilis</i> (delta-5) KJ598786, <i>H</i>. <i>discus</i> (delta-5) 1 GQ470626, <i>H</i>. <i>discus</i> (delta-5) 2 GQ466197, <i>O</i>. <i>vulgaris</i> (delta-5) JN120258, <i>S</i>. <i>officinalis</i> KP260645. Exon-intron structure for <i>L</i>. <i>gigantea</i> and <i>C</i>. <i>gigas</i> are presented as gene models with exons (red boxes) and introns (red lines) adjacent to the corresponding species. (b) Maximum Likelihood tree of Fad protein sequences. Bootstrap values are shown next to nodes, and values under 75% not reported. Accession numbers: <i>C</i>. <i>gigas</i> 1 EKC33620, <i>C</i>. <i>gigas</i> 2 EKC30965, <i>C</i>. <i>gigas</i> 3 XP_011414050, <i>A</i>. <i>californica</i> 1 XP_005097048, <i>A</i>. <i>californica</i> 2 XP_005093182, <i>A</i>. <i>californica</i> 3 XP_005090573, <i>A</i>. <i>californica</i> 4 XP_005090577, <i>L</i>. <i>gigantea</i> 1 XP_009051231, <i>L</i>. <i>gigantea</i> 2 XP_009049968, <i>L</i>. <i>gigantea</i> 3 XP_009045077, <i>C</i>. <i>nobilis</i> (delta-5) AIC34709, <i>H</i>. <i>discus</i> (delta-5) 1 ADK38580, <i>H</i>. <i>discus</i> (delta-5) 2 ADK12703, <i>O</i>. <i>vulgaris</i> (delta-5) AEK20864, <i>S</i>. <i>officinalis</i> AKE92955.</p

Assembly summary statistics, for <i>C</i>. <i>farreri</i>, <i>A</i>. <i>irradians</i> and <i>C</i>. <i>olivaceus</i> transcriptomes using Trinity <i>de novo</i> assembler.

<p>Assembly summary statistics, for <i>C</i>. <i>farreri</i>, <i>A</i>. <i>irradians</i> and <i>C</i>. <i>olivaceus</i> transcriptomes using Trinity <i>de novo</i> assembler.</p

Maximum Likelihood trees of Elovl nucleotide and protein sequences.

<p>(a) Phylogenetic tree of Elovl nucleotide sequences. Bootstrap values are shown next to nodes, and values under 75% not reported. Accession numbers: NmElovla KR154728, NmElovlb KR154729, <i>C</i>. <i>gigas</i> 1 CGI_10028198, <i>C</i>. <i>gigas</i> 2 CGI_10008431, <i>C</i>. <i>gigas</i> 3 CGI_10020977, <i>C</i>. <i>gigas</i> 4 CGI_10012627 <i>C</i>. <i>gigas</i> 5 CGI_10007566, <i>C</i>. <i>gigas</i> 6 XM_011452473, <i>C</i>. <i>gigas</i> 7 XM_011452475, <i>A</i>. <i>californica</i> 1 XM_005098245, <i>A</i>. <i>californica</i> 2 XM_005095626, <i>A</i>. <i>californica</i> 3 XM_005106603, <i>L</i>. <i>gigantea</i> 1 XM_009047472, <i>L</i>. <i>gigantea</i> 2 XM_009052848, <i>C</i>. <i>nobilis</i> (<i>Elovl2/5</i>) KF245423, <i>O</i>. <i>vulgaris</i> (<i>Elovl4</i>) KJ590963, <i>O</i>. <i>vulgaris</i> (<i>Elovl2/5</i>) JX020803, <i>S</i>. <i>officinalis KP260646</i>. Exon-intron structure for <i>L</i>. <i>gigantea</i> and <i>C</i>. <i>gigas</i> are presented as gene models with exons (red boxes) and introns (red lines) adjacent to the corresponding species. (b) Phylogenetic tree of Elovl protein sequences. Bootstrap values shown next to nodes, and values under 75% not reported. Accession numbers: <i>C</i>. <i>gigas</i> 1 CGI_10028198, <i>C</i>. <i>gigas</i> 2 EKC41251, <i>C</i>. <i>gigas</i> 3 EKC25061, <i>C</i>. <i>gigas</i> 4 EKC39214, <i>C</i>. <i>gigas</i> 5 EKC19804, <i>C</i>. <i>gigas</i> 6 XP_011450775, <i>C</i>. <i>gigas</i> 7 XP_011450777, <i>A</i>. <i>californica</i> 1 XP_005098302, <i>A</i>. <i>californica</i> 2 XP_005095683, <i>A</i>. <i>californica</i> 3 XP_005106660, <i>L</i>. <i>gigantea</i> 1 XP_009045720, <i>L</i>. <i>gigantea</i> 2 XP_009051096, <i>C</i>. <i>nobilis</i> (Elovl2/5) AGW22128, <i>O</i>. <i>vulgaris</i> (Elovl4) AIA58679, <i>O</i>. <i>vulgaris</i> (Elovl2/5) AFM93779, <i>S</i>. <i>officinalis</i> AKE92956.</p

Alignment of Elovl protein sequences showing conserved and variable regions.

<p>The histidine box (HXXHH) is indicated with a black rectangular outline. Highly conserved aa residues (K, E, DT, L, HH, N, H, MY, YY, T, LF, F) are designated with the symbol ★.</p

List of candidate genes that encode putative Fad and Elovl proteins identified from <i>L</i>. <i>pealeii</i> and <i>C</i>. <i>farreri</i> transcriptome assemblies.

<p>List of candidate genes that encode putative Fad and Elovl proteins identified from <i>L</i>. <i>pealeii</i> and <i>C</i>. <i>farreri</i> transcriptome assemblies.</p

List of mollusc Fad and Elovl genes, currently available in NCBI NR protein and UNIPROT databases.

<p>List of mollusc Fad and Elovl genes, currently available in NCBI NR protein and UNIPROT databases.</p

Alignment of Fad protein sequences showing conserved and variable regions.

<p>The haeme binding domain (HPGG) and the three histidine boxes (HXXXH, HXXHH and QXXHH) are indicated with a black rectangular outline.</p

Fad and Elovl genes extracted from the currently available complete mollusc genomes of <i>C</i>. <i>gigas</i>, <i>A</i>. <i>californica</i> and <i>L</i>. <i>gigantea</i>.

<p>Fad and Elovl genes extracted from the currently available complete mollusc genomes of <i>C</i>. <i>gigas</i>, <i>A</i>. <i>californica</i> and <i>L</i>. <i>gigantea</i>.</p

List of candidate genes that encode putative Fad and Elovl proteins identified from <i>A</i>. <i>trapezia</i>, <i>N</i>. <i>albicilla</i> and <i>N</i>. <i>melanotragus</i> transcriptome assemblies.

<p>List of candidate genes that encode putative Fad and Elovl proteins identified from <i>A</i>. <i>trapezia</i>, <i>N</i>. <i>albicilla</i> and <i>N</i>. <i>melanotragus</i> transcriptome assemblies.</p