Cactusflybase is live

The cactusflybase site currently houses the sequences and annotation of our seven new de novo chromosome-level assemblies of D. mojavensis (from Catalina Island, Mojave Desert, Sonora Desert and Baja California populations), D. arizonae (from the Sonora Desert and Chiapas populations) and D. navojoa. You can read our Biorxiv preprint of our in review manuscript on the generation and analysis of our new cactophilic Drosophila genomes. Coming very soon we will add new genomes of South American cactophilic Drosophila from the buzzatii group, which we collaborated with Dr. Esteban Hasson’s group at the Universidad de Buenos Aires (see the Biorxiv version of the buzzatti group manuscript).

The cactusflybase site will also be a repository of information of our new cactophilic Drosophila transgenic toolbox. As part of a recently funded NSF EDGE award we will generate transgenic lines of D. mojavensis, D. arizonae and D. buzzatii for the community. Stay tuned more information coming soon.

Communications Biology paper is out

Our study examined how divergent evolutionary trajectories, likely a result of strong sexual selection, shape the transcriptional response of female lower reproductive tracts in cactophilic Drosophila. Since we had to do many heterospecific crosses (between D. arizonae and D. mojavensis), we watched many many fly pairs not mate :). Really proud of our work and my fellow authors.

Our new GENETICS paper on the genetic basis of Bt toxin resistance in Helicoverpa zea is out

Very happy to see our paper on uncovering a novel candidate gene (Kinesin-12) associated with the resistance to the Bt toxin Cry1Ac in the agricultural pest Helicoverpa zea is out in GENETICS ( This paper had it all, a de novo chromosome level assembly of H. zea, bulk segregant analysis of Cry1Ac resistance followed by fine-scale mapping, RNAseq analysis of H. zea guts to support identification of candidate, and population analysis. This lead to the identification of Kinesin-12, a gene not previously linked to Bt toxin resistance, as a significant contributor to Cry1Ac resistance in this important agricultural pest. This was a wonderful collaborative project lead by lab postdoc, Dr. Kyle Benowitz (currently an Assistant Professor at Austin Peay State University). Lab manager Carson Allan was also instrumental in the success of the project. This project would not have been possible without the other members of the Helicoverpa team, Dr. Bruce Tabashnik (UA Entomology), Dr. Yves Carriere (UA Entomology), Dr. Jeff Fabrick (USDA ARS), Dr. Xianchun Li (UA Entomology), Ben Degain (Carriere lab).

Bittersweet moment: Kyle and Fernando depart the lab for new positions

It was a wonderful and productive fours years and although I new this moment will eventually happen, it is sad to see postdocs Kyle Benowitz and Fernando Diaz leave the lab. I am very proud of them for all the success and work they have achieved while in the lab at the University of Arizona. This is especially the case given all that they had to deal with over the last year and a half with the COVID-19 pandemic. It was a tough year to be looking for academic jobs, but they persevered. And although we will still be collaborating on projects and manuscripts for sometime, I will miss their presence and impact on my lab. Kyle is heading to Austin Peay State University as an Assistant Professor in the Department of Biology, and Fernando will be a Visiting Assistant Professor of Biology at Colgate University. Wishing them the very best, much success and happiness.

NPR story about our lab doing science in the time of COVID

Our lab was featured in a story about getting science done during a pandemic. On the written story you can see a picture of Fernando Diaz (postdoc) in the field in Organ Pipe National Monument, a picture of some of our fly cages taken by Carson Allan (lab manager), and the reference to being in the lab around the clock was to the experiments that Kyle Benowitz (postdoc) did.

New USDA-NIFA funded project on the genomics of Bt resistance starts!!

On June 15, 2020 we officially started our work on uncovering the genetics of Bt resistance in the agricultural pest Helicoverpa zea (Corn earworm, CEW). This work is in collaboration with friends and great colleagues from the Department of Entomology at the University of Arizona, Bruce Tabashnik and Yves Carriere, and from the USDA ALARC, Jeff Fabrick.

Chromosome-level genome assembly pipeline paper published in Molecular Ecology Resources

Working on ecologically interesting species is a powerful way to link patterns of variation from genes/genomes to organism level traits to the selective forces shaping it. To facilitate this, having a chromosome-level genome assembly is very helpful.  In this paper we outline how this is an attainable goal.  We provide a step-by-step guide for investigators that work on ecologically exciting species, but do not have a vast computational background.


Comparative genomic analysis of D. mojavensis paper published

Happy to see our BMC Genomics paper out.  This is the first ever paper that examines the pattern of genomic evolution across the four cactus host populations of Drosophila mojavensis.  So glad to see all of Carson’s hard work finally in print.

Allan, C. W. and Matzkin, L. M.  (2019).  Genomic analysis of the four ecologically distinct cactus host populations of Drosophila mojavensis. BMC Genomics. 20(1):732. doi:10.1186/s12864-019-6097-z