RT Journal Article
SR Electronic
T1 Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 399808
DO 10.1101/399808
A1 Mathieu Seppey
A1 Panagiotis Ioannidis
A1 Brent C. Emerson
A1 Camille Pitteloud
A1 Marc Robinson-Rechavi
A1 Julien Roux
A1 Hermes E. Escalona
A1 Duane D. McKenna
A1 Bernhard Misof
A1 Seunggwan Shin
A1 Xin Zhou
A1 Robert M. Waterhouse
A1 Nadir Alvarez
YR 2018
UL http://biorxiv.org/content/early/2018/10/04/399808.abstract
AB Background The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed the largest beetle suborder, Polyphaga, mostly includes plant-eaters among its ~315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing.Results To address this, we explored the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representing the two most species-rich beetle suborders. We contrasted the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We found gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant-feeding, we identified families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There was especially strong support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes.Conclusions Our explicit modeling of the evolution of gene repertoires across 18 species identifies adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant-feeding in general, in driving beetle diversification.ABCadenosine triphosphate-binding cassette transportersAICcAkaike Information Criterion (small-sample-size corrected)BMBrownian motionBUSCOBenchmarking Universal Single-Copy Ortholog assessment toolCAFEComputational Analysis of gene Family Evolution toolCEcarboxylesteraseCYScysteine proteaseFDRfalse discovery rateGHglycoside hydrolaseGSTglutathione S-transferaseLSElineage specific expansionMAFFTMultiple Alignment using Fast Fourier Transform toolOGorthologous groupOUOrnstein-UhlenbeckP450cytochrome P450 monooxygenaseSERserine proteaseUGTuridine 5’-diphospho-glycosyltransferase