Source: USDA/ARS/CMAVE submitted to NRP
FUNCTIONAL GENOMICS OF THE FIRE ANT SOLENOPSIS INVICTA
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
NRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0216554
Grant No.
2009-35302-05301
Cumulative Award Amt.
(N/A)
Proposal No.
2008-04019
Multistate No.
(N/A)
Project Start Date
Mar 1, 2009
Project End Date
Feb 28, 2014
Grant Year
2009
Program Code
[51.2C]- Arthropod and Nematode Biology and Management (C): Tools, Resources and Genomics
Recipient Organization
USDA/ARS/CMAVE
1600/1700 SW 23RD DRIVE
GAINESVILLE,FL 32608
Performing Department
(N/A)
Non Technical Summary
The Red Imported Fire Ant Solenopsis invicta remains a serious agricultural, ecological, and public health pest in the U.S.A. despite concerted recent efforts at non-traditional management practices, including biological control. Development of alternative management techniques are needed and likely will require intimate knowledge of factors such as the immune function, reproductive physiology, and social behavior of fire ants, and the underlying genetic determinants of these biological features, because these represent attractive targets for disruption and manipulation culminating in population suppression. The goals of the proposed research are to develop new functional genomic resources for fire ants and to employ these resources to examine the molecular and genetic bases of biological traits that can potentially be used for biological control. The proposed research will focus on studies related to immune function, reproductive physiology, and social organization. To accomplish these goals, we will develop new tools and resources for fire ants, including extensive DNA sequence data, a custom SNP (single nucleotide polymorphism) panel, an oligo microarray, a genetic linkage map, and an updated version of the fire ant database that integrates all of these so that the data are publicly accessible. The proposed research will fill an important gap in our knowledge in these areas and will lead to a better understanding of fire ant physiology, genetics, chemical ecology and the molecular basis of their susceptibility to control agents, all of which are important for biologically-based integrated pest management strategies of fire ants in the United States.
Animal Health Component
20%
Research Effort Categories
Basic
80%
Applied
20%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3043110108010%
3123110104030%
3123110108030%
3123110113030%
Knowledge Area
312 - External Parasites and Pests of Animals; 304 - Animal Genome;

Subject Of Investigation
3110 - Insects;

Field Of Science
1040 - Molecular biology; 1130 - Entomology and acarology; 1080 - Genetics;
Goals / Objectives
The specific objectives of the proposed research are 1) perform large-scale EST study to significantly increase the breadth and depth of transcriptome coverage of the fire ant Solenopsis invicta using 454 pyrosequencing technology, 2) develop an oligo microarray for fire ants for gene expression studies using all available EST sequence data (including new data from objective 1), and 3) develop a custom assay for screening SNPs for linkage and population genomic studies of fire ants.
Project Methods
DNA sequence data will be generated for the transcriptome of S. invicta by sequencing three normalized cDNA libraries using 454 pyrosequencing technology. All resulting sequences will be run through an automatic pipeline to assemble and preliminarily annotate the sequences. Microarray development will occur in two phases. First, a pilot array will be constructed to identify the best probes for the unigenes identified from the sequencing efforts (244K feature microarray). The best performing probes (and correct orientation) for each sequence then will be synthesized along with positive and negative controls on a 4 X 44K feature microarray, which will be the platform used for subsequent studies. This array will be utilized for four experiments focusing on innate immunity, reproductive physiology, and social organization (including studies of Gp-9, a single gene associated with social organization in this ant). Array probes, layout, and purchase information will be made publicly available on an updated version of a fire ant database. Intraspecific SNPs will be identified using pipeline filtering methods developed for this purpose. A SNP panel consisting of 1536 SNPs will be developed and utilized to construct a moderately dense linkage map, to identify genes linked to Gp-9, to determine whether gametic disequilibrium between Gp-9, SNPs, and co-expressed genes exists, and to determine whether these candidate genes are consistently associated with social form as has been shown for Gp-9. Finally, a web-based platform integrating these data in an easily accessible format will be developed.

Progress 03/01/09 to 02/28/14

Outputs
Target Audience: The results of this research project are of significant interest to multiple scientific communities, including researchers who study the genetic and evolutionary basis of complex behavior, chemical communication systems, and the development of genomic tools to study complex phenotypes in new model systems. Information from these studies can also be used to develop improved methods to manage this important pest species. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project provided training for two postdoctoral fellows (Fabio Manfredini and Lucinda Lawson) and eight undergraduate research assistants, seven of whom were members of an underrepresented group. The project provided interdisciplinary training in genomics, bioinformatics, physiology, behavior and evolutionary biology. How have the results been disseminated to communities of interest? This research was presented at multiple international and national conferences by the PIs and postdoctoral researchers (from 2009-2013, the PIs alone gave 14 invited presentations at conferences, 2 keynote lectures and 18 invited departmental seminars). Results of project were published in high quality peer reviewed journals and resulting data were deposited in appropriate publicly accessible databases (e.g., GenBank) as well as a fire ant database we developed as part of the project (Fourmidable). What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The full genome sequence of the fire ant was generated (>20X coverage) and published in a peer-reviewed journal. Additionally, bioinformatics tools were used to a) assemble new and existing fire ant EST sequence data, b) search for potential viral sequences, and c) begin searches for important genes/gene families (e.g. immune-related, chemoreception). Results from these latter efforts led to several additional peer-reviewed publications. In addition, a pilot oligo microarray was constructed and used to identify the most appropriate oligo sequences for development of a microarray that includes every potentially transcribed gene region in fire ants. This new whole genome microarray platform for S. invicta was then utilized for two comparative gene expression studies. The first study characterized the gene expression patterns associated with fire ant queen colony founding behavior. Colony founding in fire ants provides an excellent system in which to examine the genes underpinning cooperative behavior and how the social environment shapes the expression of these genes. We compared haplometrotic (single foundress) queens, pleometrotic (multiple foundresses) winners and pleometrotic losers. We also manipulated pairs of queens in order to switch or maintain the social ranks of the two cofoundresses. Haplometrotic and pleometrotic queens differed in the expression of genes involved in stress response, aging, immunity, reproduction and lipid biosynthesis. Smaller sets of genes were differentially expressed between winners and losers. Switching social rank had a much greater impact on gene expression patterns than the initial/final rank. Expression differences for several candidate genes involved in key biological processes were confirmed using qRT-PCR. Our findings indicate that, in S. invicta, social environment plays a major role in the determination of the patterns of gene expression, while the queen's physiological state is secondary. These results highlight the powerful influence of social environment on regulation of the genomic state, physiology and ultimately, social behavior of animals. These results were published in a peer-reviewed journal. Using this whole-genome microarray platform, we also characterized the molecular basis for worker division of labor (DOL) and we explored how a drastic change in the social environment (i.e. the sudden loss of the queen) affects global gene expression patterns of worker ants. Reproductive and worker DOL are hallmarks of social insect societies. In S. invicta, one of the most studied ant species, workers are permanently sterile and the tasks performed are modulated by the worker's internal state (age and size) and the outside environment (social environment), which potentially includes the effect of queen presence through chemical communication via pheromones. We identified numerous genes differentially expressed between foraging and nonforaging workers in queenright colonies. With a few exceptions, these genes appear to be distinct from those involved in DOL in bees and wasps. Interestingly, after queen removal, foraging workers were no longer distinct from nonforaging workers at the transcriptomic level. Furthermore, few expression differences were detected between queenright and queenless workers when we did not consider the task performed. Thus, the social condition of the colony (queenless vs. queenright) appears to impact the molecular pathways underlying worker task performance, providing strong evidence for social regulation of DOL in S.invicta. These results were published in a peer-reviewed journal. We also developed and utilized a large number of variable genetic markers to identify the native source population(s) of the S. invicta in the southern USA. Fire ants were inadvertently introduced into the USA early last century as stowaways in cargo shipped from their native South American range. They rapidly spread throughout the southern USA and, more recently, have been introduced to California and other regions of the world, including the Caribbean, Australia, New Zealand, Taiwan, Hong Kong, Macao, and China (collectively referred to as newly invaded areas [NIAs]). Previous data suggested the existence of high levels of genetic differentiation among different geographic S. invicta populations occupying the vast native range. Such strong differentiation is consistent with the hypothesis that natural enemies of S. invicta are locally adapted to their hosts. Thus, the success of natural enemies from a given locale in attacking S. invicta likely depends on the geographic origin of the host ants. If so, efforts to pinpoint the source population become highly relevant to the identification of effective biological control agents of introduced S. invicta. Results from our genetic study allowed us to pinpoint with high confidence the source population(s) of S. invicta in the USA as being near or around Formosa, Argentina. These results were published in a peer-reviewed journal. We also used these genetic markers to reconstruct the global invasion history of S. invicta. An assessment of genetic variation at a diverse set of molecular markers in 2,144 colonies from 75 geographic sites worldwide revealed that at least nine separate introductions of S. invicta have occurred and that the main southern USA population is likely the source of all but one of these introductions. The sole exception involves a putative serial invasion from the southern USA to California to Taiwan. These results illustrate in stark fashion a severe negative consequence of an increasingly massive and interconnected global trade and travel system. These results were published in a peer-reviewed journal. The genomic region responsible for two divergent forms of colony social organization in fire ants was identified using a combination of RAD tag sequencing, genome resequencing, and BAC-FISH. This genomic region was shown to be part of a pair of heteromorphic chromosomes having many of the key properties of sex chromosomes. The non-recombining region comprises most of the genes with demonstrated expression differences between individuals of the two social forms. These findings highlight how genomic rearrangements can maintain divergent adaptive social phenotypes involving many genes acting in concert by locally limiting recombination. These results were published in a peer-reviewed journal. Finally, we also are using RAD tag sequencing to develop SNP markers for additional population genomic studies of fire ants (e.g., patterns of genomic admixture between two introduced species of fire ants).

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Manfredini, F., Lucas, C., Nicolas, M., Keller, L., Shoemaker, D., and C.M. Grozinger. 2014. Molecular and social regulation of worker division of labor in fire ants. Molecular Ecology 23(3): 660-672.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Manfredini, F., Riba-Grognuz, O., Wurm, Y., Keller, L., Shoemaker, D.D., and C.M. Grozinger. 2013. Sociogenomics of cooperation and conflict during colony founding in the fire ant, Solenopsis invicta. PLoS Genetics 9(8): e1003633.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wang, J., Wurm, Y., Nipitwattanaphon, M., Riba-Grognuz , O., Huang, Y.-C., Shoemaker, D. D. , Keller, L. 2013. A Y-like social chromosome causes alternative colony organization in fire ants. Nature 493: 664-668.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Yang, C.-C., Ascunce, M. S., Luo, L.-Z., Shao, J.-G., Shih, C.-J., Shoemaker D. D. 2012. Propagule pressure and colony social organization are associated with the successful invasion and rapid range expansion of fire ants in China. Molecular Ecology 21: 817-833.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Lawson, L.P., Vander Meer, R.K., Shoemaker, D.D. 2012. Male reproductive fitness and queen polyandry are linked to variation in the supergene Gp-9 in the fire ant Solenopsis invicta. Proceedings of the Royal Society of London B 279: 3217-3222.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Wurm, Y., Wang, J., Riba-Grognuz, O., Corona, M., Nygaard, S., Hunt, B. G., Ingram, K. K., Falquet, L., Nipitwattanaphon, M., Gotzek, D., Dijkstra, M. B., Oettler, J., Shih, C.-J., Wu, W-J., Yang, C.-C., Thomas, J., Beaudoing, E., Pradervand, S., Flegel, V., Fabbretti, R., Stockinger, H., Long, L., Farmerie, W., Oakey, J., Boomsma, J. J., Pamilo, P., Yi, S. V., Heinze, J., Goodisman, M. A. D, Farinelli, L., Harshman, K., Hulo, N., Cerutti, L., Xenarios, I., Shoemaker, D. D., Keller, L. 2011. The genome of the fire ant Solenopsis invicta. Proceedings of the National Academy of Sciences USA 108: 5679-5684.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Hunt, B. G., Ometto, L., Wurm, Y., Shoemaker, D. D., Yi, S. V., Keller, L., Goodisman, M. A. D. 2011. Relaxed selection is a precursor to the evolution of phenotypic plasticity. Proceedings of the National Academy of Sciences USA 108:15936-15941.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Ascunce, M. S., Yang, C.-C., Oakey, J., Calcaterra, L., Wu, W.-J., Shih, C.-J., Goudet, J., Ross, K. G., Shoemaker, D. D. 2011. Global invasion history of the fire ant Solenopsis invicta. Science 331:1066-1068.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Choi, M.-Y., Vander Meer, R. K., Shoemaker, D. D., Valles, S. M. 2010. PBAN gene architecture and expression in the fire ant, Solenopsis invicta. Journal of Insect Physiology 57: 161-165.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Ometto, L., Shoemaker, D. D., Ross, K. G., Keller, L. 2011. Evolution of gene expression in fire ants: the effects of developmental stage, caste, and species. Molecular Biology and Evolution 28:1381-1392.
  • Type: Journal Articles Status: Submitted Year Published: 2014 Citation: Manfredini, F., Shoemaker, D., and C.M. Grozinger. Fire ant viruses: host-parasite dynamics and transcriptomic analysis of infection. In review


Progress 03/01/09 to 02/28/10

Outputs
OUTPUTS: The goal of this project is to develop new functional genomic resources for the fire ant S. invicta. The full genome sequence of the fire ant was published in a peer reviewed journal. Necessary samples for two comparative gene expression studies were collected and archived. In addition, a pilot oligo microarray was constructed and used to identify the most appropriate oligo sequences for development of a second microarray that includes every potentially transcribed gene region in fire ants. This second array that includes thousands of transcribed genes in fire ants has been developed and is currently being used for a number of gene expression studies outlined in proposal. The results of one study were presented at the Annual Entomological Society of America Meeting as well as at the International Union of for the Study of Social Insects Meeting held in Copenhagen, Denmark. PARTICIPANTS: Primary participants include DeWayne Shoemaker, Christina Grozinger, and John Wang. One component of the project resulted in training of a single postdoctoral researcher (Fabio Manfredini ) in molecular techniques and microarray analyses. A second component of project has led to training of an additional postdoctoral researcher (Lucinda Lawson) in bioinformatics and population genomics. Additional professional development: Dr. Shoemaker and Dr. Lawson spent a portion of the summer attending a genomics workshop to receive hands-on training utilizing latest software for population genomics and bioinformatics. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
A draft genome of the fire ant Solenopsis invicta was generated and published. Well developed bioinformatics tools were used to a) assemble new and existing fire ant EST sequence data, b) search for potential viral sequences, and c) begin searches for important genes/gene families, e.g. immune-related, chemoreception. These efforts resulted in discovery of several potential viral pathogens in fire ants. Additionally, a high density oligo microarray specific to fire ants was constructed. Pilot studies using RNA from samples used for 454 library construction as well as new samples were used to validate newly developed microarray. RAD tag sequencing was employed to develop SNP markers for population genomic studies of fire ants. These SNPs currently are being used to study patterns of genomic admixture between two introduced species of fire ants.

Publications

  • Gotzek, D., Clark, J., Shoemaker, D. D. 2010. Mitochondrial genome evolution in fire ants. BMC Evolutionary Biology, 10: 300.
  • Choi, M.-Y., Vander Meer, R. K., Shoemaker, D. D., Valles, S. M. 2010. PBAN gene architecture and expression in the fire ant, Solenopsis invicta. Journal of Insect Physiology, 57: 161-165.
  • Ometto, L., Shoemaker, D. D., Ross, K. G., Keller, L. 2011. Evolution of gene expression in fire ants: the effects of developmental stage, caste, and species. Molecular Biology and Evolution, 28:1381-1392.
  • Wurm, Y., Wang, J., Riba-Grognuz, O., Corona, M., Nygaard, S., Hunt, B. G., Ingram, K. K., Falquet, L., Nipitwattanaphon, M., Gotzek, D., Dijkstra, M. B., Oettler, J., Shih, C.-J., Wu, W-J., Yang, C.-C., Thomas, J., Beaudoing, E., Pradervand, S., Flegel, V., Fabbretti, R., Stockinger, H., Long, L., Farmerie, W., Oakey, J., Boomsma, J. J., Pamilo, P., Yi, S. V., Heinze, J., Goodisman, M. A. D, Farinelli, L., Harshman, K., Hulo, N., Cerutti, L., Xenarios, I., Shoemaker, D. D., Keller, L. 2011. The Genome of the Fire Ant Solenopsis invicta. Proceedings of the National Academy of Sciences USA, 108: 5679-5684.
  • Gotzek, D., Robertson, H. M., Wurm, Y., Shoemaker, D. D. 2011. Odorant binding proteins (OBPs) of the Red Imported Fire Ant, Solenopsis invicta: An example of the problems facing the analysis of widely divergent proteins. PloS One, 6(1): e1628.
  • Hunt, B. G., Ometto, L., Wurm, Y., Shoemaker, D. D., Yi, S. V., Keller, L., Goodisman, M. A. D. 2011. Relaxed selection is a precursor to the evolution of phenotypic plasticity. Proceedings of the National Academy of Sciences USA, 108:15936-15941.
  • Ascunce, M. S., Yang, C.-C., Oakey, J., Calcaterra, L., Wu, W.-J., Shih, C.-J., Goudet, J., Ross, K. G., Shoemaker, D. D. 2011. Global invasion history of the fire ant Solenopsis invicta. Science, 331:1066-1068.