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Monarch Genome

We received ARRA funds from the NIH to generate a high depth sequence of the monarch butterfly genome using a combination of state-of-the-art "next generation" sequencing technologies, and then to appropriately assemble, annotate and interpret the genome. A sequenced and fully annotated genome is critical in the effort to develop the monarch butterfly as a model organism to study the molecular mechanisms of the circadian clock and sun compass orientation used during migration. The draft genome can be found here.


Of butterflies and moths. There are more than 150,000 species of butterflies and moths, collectively known as the Lepidoptera. Many of these species are economically important (e.g., as pollinators, for silk production, and as agricultural pests) and many serve as unique models for specific biological processes (e.g., sun compass navigation, circadian clock mechanisms, mimicry, derived wing color patterns, and color vision). Yet, genomic resources for the Lepidoptera have been limited.

Why monarch butterflies? The monarch butterfly (Danaus plexippus) is the world’s most captivating and well-known butterfly species. Monarchs are famous for their orange and black-edged wings, their milkweed-derived chemical defenses, and their involvement in mimicry with viceroy butterflies.  But the monarch’s greatest claim to fame is its spectacular fall migration.

Monarch migration is a model for sun compass navigation. Migrating monarch butterflies navigate using a time-compensated sun compass. Because this navigational capability is genetically determined, we have developed the monarch butterfly as a model to study the genetic, molecular and cellular basis of time-compensated sun compass orientation (see Publications). Our ultimate goal is to understand the fundamental mechanisms of this process: How does the sun compass receive and process light input? How does the circadian clock interact with the sun compass to enable migrants to maintain a fixed south-southwesterly flight bearing as the sun moves across the sky each day? More broadly, this knowledge will help elucidate how information about time and space is integrated in the brain.

Understanding monarch navigation may help the beesKnowledge of the monarch butterfly’s remarkable navigational capabilities may have broad implications for understanding navigation in other species. For example, studies of monarch navigation may apply directly to navigation in foraging bees, which also use a sun compass. Bees are the major pollinators of plants, and the recent rapid decline in bee numbers may be due to disrupted navigation behavior—the bees could simply be lost, unable to find their way back to the hive (op-ed piece by May Berenbaum in the New York Times). Thus, a better understanding of insect navigation would have profound economic and agricultural consequences.

Monarch butterflies have a novel circadian clock mechanism that will inform our understanding of the human clock. This mechanism has aspects of BOTH the fruit fly (Drosophila) and the mammalian clockwork—two of the most important models for understanding circadian clocks—making the monarch an ideal system in which to study unique aspects of both clocks. A fundamental understanding of the core circadian clock mechanism, which the monarch butterfly can help inform, would hold promise for developing innovative treatment strategies for disorders of the human circadian clock.

Broad international impact. As the monarch is a national treasure in Mexico, home of the butterfly’s overwintering sites, we are hopeful that a sequenced and annotated genome would increase the potential for collaborations on monarch biology between the Reppert laboratory and groups at the National Autonomous University of Mexico in Mexico City. We have a great interest in using the genome to foster such long-term outreach activities between the United States and Mexico.

Monarch butterflies are science educators. Monarch butterfly migration offers an unparalleled educational resource. It captivates thousands of school children in North America each year, and has inspired many young minds to choose careers in science. Moreover, the monarch butterfly is a commonly used science “tool” in the classroom. Non-profit organizations, like Monarch Watch and Journey North, use this natural resource to help promote science education.  

Conservation is necessary. A better understanding of the mechanisms behind monarch butterfly migration may well aid in the preservation of this spectacular phenomenon, currently threatened by the loss of the butterflies’ mountainous habitat in central Mexico. Monarch migration also drives a unique ecosystem at the overwintering grounds, which needs protection.

Butterflies enrich our lives. It has been said that butterflies are “a metaphor for life.” These delicate, graceful creatures capture our imagination and inspire all aspects of human endeavor—from science to sculptures, and from preservation to poetry. As the novelist and lepidopterist Vladimir Nabokov once mused, “My pleasures are the most intense known to man: writing and butterfly hunting.” Understand butterflies, and we understand ourselves.

Genomic resources for the monarch butterfly are already paying off. We have established a brain expressed sequence tag (EST) library with the aid of the Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign. The library, which is instrumental for gene discovery, consists of approximately 10,000 annotated transcript tags that are being used with microarray technology to examine differences in gene expression between “summer” and migratory butterflies. We are also using a candidate gene approach, based on the library sequences and on information about potentially relevant gene products deduced from studies in other migratory and foraging species. The library has already proven its utility by revealing a new clock gene in monarchs, which has been found to exist in many non-drosophilid insects. This novel gene, called insect cryptochrome 2, has not only contributed to our understanding of a novel clockwork mechanism in monarch butterflies, but has fundamentally changed our view of the evolution of circadian clock mechanisms in general.

Genomic resources will contribute to monarch population genetics. We are also scrutinizing the monarch EST database for single nucleotide polymorphisms (SNPs), which serve as important genetic markers (Zhu et al., 2008). We expect that the monarch EST library will yield more than 15,000 putative SNPs, and predict that more than 500 genes will have double SNPs. These SNPs, placed in the context of genome structure, will be useful for analyzing population substructure and distribution rates between Eastern and Western monarch populations in North America, as well as between naturally occurring migrating (North American) and nonmigrating (South American) subspecies.  SNP data will also be helpful for identifying genes that are evolving under natural selection.

The monarch genome must be sequenced. Developing more comprehensive genomic resources for the monarch butterfly—in particular by sequencing and annotating the entire genome—is a fundamental step in harnessing this system to address important issues in contemporary biology. The Reppert laboratory has been studying monarch butterfly biology and migration for the past eight years.  Our research accomplishments are substantial in this area (see Publications), and we feel we are on the brink of making major discoveries about the genetic basis of butterfly migration and the remarkable navigational capabilities of the monarch butterfly. To continue to develop the monarch as a model system for study of migration, navigation, and circadian clocks, we need to sequence its genome.