Jessica Aguilar

All Publications

• Insights into the evolution of herbivory from a leaf-mining fly ECOSPHERE Aguilar, J. M., Gloss, A. D., Suzuki, H. C., Verster, K. I., Singhal, M., Hoff, J., Grebenok, R., Nabity, P. D., Behmer, S. T., Whiteman, N. K. 2024; 15 (4)

  View details for DOI 10.1002/ecs2.4764

  View details for Web of Science ID 001206586400001

• Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. G3 (Bethesda, Md.) Peláez, J. N., Gloss, A. D., Goldman-Huertas, B., Kim, B., Lapoint, R. T., Pimentel-Solorio, G., Verster, K. I., Aguilar, J. M., Nelson Dittrich, A. C., Singhal, M., Suzuki, H. C., Matsunaga, T., Armstrong, E. E., Charboneau, J. L., Groen, S. C., Hembry, D. H., Ochoa, C. J., O'Connor, T. K., Prost, S., Zaaijer, S., Nabity, P. D., Wang, J., Rodas, E., Liang, I., Whiteman, N. K. 2023

  Abstract

  Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families - genes directly mediating interactions with plant chemical defenses - underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago [mya]), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several non-herbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza have among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila.

  View details for DOI 10.1093/g3journal/jkad133

  View details for PubMedID 37317982

• Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. bioRxiv : the preprint server for biology Pelaez, J. N., Gloss, A. D., Goldman-Huertas, B., Kim, B., Lapoint, R. T., Pimentel-Solorio, G., Verster, K. I., Aguilar, J. M., Dittrich, A. C., Singhal, M., Suzuki, H. C., Matsunaga, T., Armstrong, E. E., Charboneau, J. L., Groen, S. C., Hembry, D. H., Ochoa, C. J., O'Connor, T. K., Prost, S., Zaaijer, S., Nabity, P. D., Wang, J., Rodas, E., Liang, I., Whiteman, N. K. 2023

  Abstract

  Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genetic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families - genes directly mediating interactions with plant chemical defenses - underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many lineages are ancient (>150 million years ago [mya]), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several non-herbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza have among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on plants (bitter or electrophilic phytotoxins) or their ancestral diet (yeast and fruit volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight strong gene candidates that have also been linked to other dietary transitions in Drosophila .

  View details for DOI 10.1101/2023.03.16.532987

  View details for PubMedID 36993186

  View details for PubMedCentralID PMC10055167

• Highly contiguous assemblies of 101 drosophilid genomes. eLife Kim, B. Y., Wang, J., Miller, D. E., Barmina, O., Delaney, E. K., Thompson, A., Comeault, A. A., Peede, D., D'Agostino, E. R., Pelaez, J., Aguilar, J. M., Haji, D., Matsunaga, T., Armstrong, E., Zych, M., Ogawa, Y., Stamenkovic-Radak, M., Jelic, M., Veselinovic, M. S., Tanaskovic, M., Eric, P., Gao, J., Katoh, T. K., Toda, M. J., Watabe, H., Watada, M., Davis, J. S., Moyle, L., Manoli, G., Bertolini, E., Kostal, V., Hawley, R. S., Takahashi, A., Jones, C. D., Price, D. K., Whiteman, N. K., Kopp, A., Matute, D. R., Petrov, D. A. 2021; 10

  Abstract

  Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

  View details for DOI 10.7554/eLife.66405

  View details for PubMedID 34279216