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Pair of Spider Genomes Offer Look into Venom and Silk Production

NEW YORK (GenomeWeb) – An assembly of the social velvet spider genome and a draft assembly of the tarantula genome, reported in Nature Communications today, have provided a peek into the evolution of spider venom and silk production.

To subdue and ensnare their prey — typically insects and other pests — spiders use a combination of venom and silk webs, and can catch prey seven times their own body weight, the researchers noted. Both venom, because of its toxicity, and silk, because of its strength and elasticity, have sparked industrial interest, they added.

Through a combination of genomic, transcriptomic, and proteomic analyses of the two spider species, researchers led by BGI-Shenzen's Jun Wang found that spider venom genes seem to have evolved through sequential duplication and that proteases are needed to give venom its toxic effect, while spider silk genes have undergone dynamic evolution and the silk itself is comprised of both ampullate and acinoform proteins.

"These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk," the researchers said.

The researchers sequenced both the araneomorph African social velvet spider Stegodyphus mimosarum and the mygalomorph Brazilian white-kneed tarantula Acanthoscurria geniculata on the Illumina HiSeq 2000 to 91x and 40x coverage, respectively.

For the velvet spider, the researchers generated a de novo assembly of its 2.55-gigabase genome. They estimated that the velvet spider genome contains some 27,235 protein-coding genes, about 70 percent of which could be functionally annotated through comparative analyses.

They noted that the long introns and short exons in this spider genome recalled patterns seen in the human genome, suggesting to Wang and his colleagues that spiders and mammals are under similar selective forces.

By folding in mass spectrometry data, they also found some 1,370 velvet spider proteins, 157 of which were found in venom, 132 in silk, and 1,265 in body tissues.

Meanwhile, the 6.5-gigabase tarantula genome had higher heterozygosity, leading to a more fragmented assembly.

Still, using LC-MS/MS, the researchers sequenced proteins from tarantula venom, thorax, abdomen, hemolymph, and silk, and they identified 120 venom proteins, 15 silk proteins, and 2,122 body proteins.

The researchers also clarified the relationship between spiders and other Acari arachnids. Drawing on the amino acid sequences of some 450 genes with orthologs in the two spiders as well as in other species, the researchers found support for the notion that ticks and mites don't form a monophyletic group.

Further, phylogenetic dating using a relaxed molecular clock indicated that velvet spiders and tarantulas split some 270 million years ago, while ticks and spiders split 390 million years ago and mites and spiders split 355 million years ago.

The spiders also had a number of gene expansions unique to them. A number of those genes, Wang and his colleagues wrote, are linked to metalloproteases thought to be involved in extra-oral digestion.

The protein composition of venom from the two spiders was distinct, the researchers added, though both contained high levels of cysteine-rich peptides, which may mediate the toxic effects of the venom.

In particular, the tarantula venom proteome included a 45-kilodalton gel electrophoresis band that the researchers resolved through MS-based label-free quantitation based on extracted-ion chromatography to be homologous to the cysteine-rich secretory protein 3 (CRISP3), a venom allergen found in cone snail, wasp, snake, and lizard venom.

It also included a hyaluronidase as well as other putative proteases, one of which had previously been dubbed 'venom proprotein convertase' and is homologous to other proprotein convertases.

In the velvet spider venom, the researchers determined that nearly a dozen of the 33 quantified proteins are likely proteases, and three of those are apparent isoforms of the putative cysteine-rich venom protease thought to be involved in toxin activation.

"Venom proteases have previously been suggested to cause tissue destruction and thus facilitate toxin penetration or to be involved in the initial extra-oral digestion of the prey," Wang and his colleagues said. "While this function could not be excluded, the findings in this study indicate that these venom proteases primarily play a role in the activation of protoxins."

Other proteins isolated in the spider venom included lipases, though mainly in the velvet spider venom, spidroin proteins that are typically involved in spider silk, and knottins, which are small cysteine-rich proteins that have a neurotoxic effect.

The velvet spider genome, the researchers noted, included more than 50 knottin-like protoxin-encoding genes, 20 of which were supported by both transcriptomic and proteomic data. All of those, they added, aligned and clustered in nine related Stegotoxin families, based on sequence similarities. Based on that along with their exon-intron structure, the researchers suggested that these protein families evolved through segmental duplication.

Meanwhile, Wang and his colleagues found that the composition of spider silk is complex and diverse.

Through a phylogenetic analysis of the N- and C-termini of its putative spidroin sequences from the velvet spider along with previously sequenced spidroins, the researchers confirmed the classification of those sequences with high support, though the major and minor ampullate spidroin sequences exhibited a more scattered signal.

Those putative major ampullate spidroin sequences, the researchers added, had higher glycine and alanine content as compared to the putative minor ampullate spidroin sequences, and exhibit some of the characteristic motifs of previously published major ampullate sequences.

The velvet spider also contained copies of aciniform, tubiliform, piriform, and minor spidroin ampullate sequences along with some 10 copes of the major ampullate sequences and four novel spidroin sequences, one of which groups with flagelliform spidroin.

Through a phylogenetic analysis, those major ampullate spidroin sequences appeared to form a monophyletic group to published spidroin sequences and indicate highly dynamic gene evolution. For instance, the comparison highlights a whole-gene duplication event, a gene conversion of a C-terminal domain, and a loss-of-function event.

"Our data reveal very dynamic evolution of major ampullate genes, including recent duplication, deletion, and gene conversion," Wang and his colleagues noted.

Additionally, proteomic analysis of dragline and egg case silk found that aciniform silk has multiple functions in the velvet spider. Both tubiliform and aciniform are used to weave the egg case while major ampullate and aciniform spidroins comprise dragline silk.

Aside from spidroins, Wang and his colleagues also reported more than a hundred other proteins in the silk, including a number of hydroxyacid oxidase-like proteins and a large spidroin-like protein with long internal GA-repeats that, based on a Blast analysis, appeared to show some convergent evolution with a silkworm silk gene.

Only a dozen tarantula transcriptome sequences, though, had any similarity to published spidroins.

"The silk gene composition of the tarantula described here is not as complete as for the velvet spider, but our results suggest that the silk gene composition in mygalomorph spiders is far less complex than in araneomorph spider," Wang and his colleagues said. "This is consistent with the evolution of functionally more diverse silk and silk use by araneomorph spiders, for example, in elaborate prey capture webs, and less diverse silk use in tarantula spiders."