title: Candidate egg case silk genes for the spider Argiope argentata from differential gene expression analyses.
abstract: Orb-web weaving spiders produce a variety of task-specific silks from specialized silk glands. The genetics underlying the synthesis of specific silk types are largely unknown, and transcriptome analysis could be a powerful approach for identifying candidate genes. However, de novo assembly and expression profiling of silk glands with RNA-sequencing (RNAseq) are problematic because the few known gene transcripts for silk proteins are extremely long and highly repetitive. To identify candidate genes for tubuliform (egg case) silk synthesis by the orb-weaver Argiope argentata (Araneidae), we estimated transcript abundance using two sequencing methods: RNAseq reads from throughout the length of mRNA molecules, and 3' digital gene expression reads from the 3' region of mRNA molecules. Both analyses identified similar sets of genes as differentially expressed when comparing tubuliform and nonsilk gland tissue. However, incompletely assembled silk gene transcripts were identified as differentially expressed because of RNAseq read alignments to highly repetitive regions, confounding interpretation of RNAseq results. Homologues of egg case silk protein (ECP) genes were upregulated in tubuliform glands. This discovery is the first description of ECP homologues in an araneid. We also propose additional candidate genes involved in synthesis of tubuliform or other silk types.
authors: Department of Biology, University of California, Riverside, CA, USA.
authors: R C
authors: RC
authors: Chaw
authors: Department of Biological Sciences, California State Polytechnic University, Pomona, CA, USA.
authors: P
authors: P
authors: Arensburger
authors: Department of Biology, University of California, Riverside, CA, USA.|Department of Biology, Washington and Lee University, Lexington, VA, USA.
authors: T H
authors: TH
authors: Clarke
authors: Department of Biology, Washington and Lee University, Lexington, VA, USA.
authors: N A
authors: NA
authors: Ayoub
authors: Department of Biology, University of California, Riverside, CA, USA.
authors: C Y
authors: CY
authors: Hayashi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D005260:Female; D015870:Gene Expression; D010802:Phylogeny; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D047011:Silk / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D013112:Spiders / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D047011:Silk
keywords: 3′ digital gene expression; RNAseq; spider egg case; tubuliform silk glands