De novo characterization of two transcriptomes from North American Papaipema stem-borers (Lepidoptera: Noctuidae)

Authors: OPPENHEIM, SARA - American Museum Of Natural History; DESALLE, ROB - American Museum Of Natural History; Goldstein, Paul; FEINDT, WIEBKE - Non ARS Employee

Submitted to: Insect Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/27/2017
Publication Date: 1/24/2018
Citation: Oppenheim, S., Desalle, R., Goldstein, P.Z., Feindt, W. 2018. De novo characterization of two transcriptomes from North American Papaipema stem-borers (Lepidoptera: Noctuidae). Insect Molecular Biology. p. 17.

Interpretive Summary: Papaipema is a group of species range that are highly polyphagous agricultural pests such as the common stalk borer in corn, but many are also specialist borers on over 20 families of flowering plants. We performed the first molecular transcriptome assemblies and rigorous annotations for two specialist species with unusual larval host plants, one associated with royal fern and another associated with giant cane. We and identified 15,547 genes for the former and 15,582 genes for the latter. This transcriptomic data may show how herbivorous insects expand their diets and anticipates threats to American agriculture. This research is relevant to geneticists, chemical ecologists, and pest management researchers.

Technical Abstract: Papaipema species (Lepidoptera: Noctuidae) range from highly polyphagous agricultural pests to speStem-borers in the genus Papaipema species (Lepidoptera: Noctuidae) range from highly polyphagous agricultural pests to specialists on genera in more than 20 families of flowering plants, many of them highly toxic. Papaipema is the largest genus of noctuids endemic to North America and is provides an excellent study system for investigating the evolution of noctuid host plant usepotentially useful for genomic studies of diet breadth, endophagy, and diapause. Although it is the largest genus of noctuids endemic to North America To improve the availability of genomic resources for such investigations,, and little is known genomically. wWe performed de novo transcriptome sequencing and assemblyies for two specialist Papaipema with unusual larval host plantss: P. speciosissima, which is associated with royal fern Osmunda regalis and the undescribed P. "sp. 4", associated with giant cane Arundinaria gigantea. Overall, the resulting transcriptomes were quite similar in terms of completeness, gene count, and gene identity, but we identified some 8,000 genes (~17% of each transcriptome) that were not shared between the two species. While some of these had orthologs in other lepidopteran species, ~5% of each transcriptome consisted of genes that were entirely species-specific. We examined the function of these species-specific genes and found that almost half of them were related to retrotransposons. The role of species-specific genes in the evolution of divergent host use phenotypes is discussed, and we examine the expansion of certain retrot ansposon families in Papaipema.cialists on more than 20 families of flowering plants and is potentially useful for genomic studies of diet breadth, endophagy, and diapause. Although it is the largest genus of noctuids endemic to North America, and little is known genomically. We performed de novo transcriptome assemblies for two specialist Papaipema with unusual larval host plants: P. speciosissima is associated with royal fern Osmunda regalis and the undescribed P. "sp. 4" associated with giant cane Arundinaria gigantea. We identified 15,547 genes and 28,189 isoforms for P. sp.4, and 15,582 genes and 31,877 isoforms for P. speciosissima. Enriched InterPro signatures revealed TE-related domains and families more commonly among species-specific genes than among clustered genes, including 175 genes sufficiently complete to be grouped into three TE families: BEL/Pao, Ty1/Copia, and Ty3/Gypsy, all of which are LTR (long terminal repeat) retrotransposons.