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Evolutionary Interpretation of the Genome of the Monarch Butterfly, Danaus plexippus

Scientists at Genome Project Solutions played a leadership role in the sequencing and interpretation of the genome of the monarch butterfly, Danaus plexippus.

The results were reported in:  Zhan, S., Merlin, C., Boore, J. L., and Reppert, S. M.  2011 The monarch butterfly genome yields insights into long-distance migration. Cell 147: 1171-1185.  (Published manuscript here.)

Abstract from this manuscript:  We present the draft 273 Mb genome of the migratory monarch butterfly (Danaus plexippus) and a set of 16,866 protein-coding genes. Orthology properties suggest that the Lepidoptera are the fastest evolving insect order yet examined. Compared to the silkmoth Bombyx mori, the monarch genome shares prominent similarity in orthology content, microsynteny, and protein family sizes. The monarch genome reveals a vertebrate-like opsin whose existence in insects is widespread; a full repertoire of molecular components for the monarch circadian clockwork; all members of the juvenile hormone biosynthetic pathway whose regulation shows unexpected sexual dimorphism; additional molecular signatures of oriented flight behavior; microRNAs that are differentially expressed between summer and migratory butterflies; monarch-specific expansions of chemoreceptors potentially important for long-distance migration; and a variant of the sodium/potassium pump that underlies a valuable chemical defense mechanism.The monarch genome enhances our ability to better understand the genetic and molecular basis of long-distance migration.

Read our news articles about this project here and here.

Read popular press reports at Scientific American, US News and World Report,, Biology News Net, Healthfinder, Science News, Science Daily, Science Centric, Science Newsline, and White Coat Notes.


What is inside this site?

Go to THIS PAGE to see statistics on the genome sequencing, assembly, and gene modeling and download various analyses and datasets.

The genomes below, including that of Danaus plexippus, have been analyzed by the PHRINGE ("Phylogenetic Resources for the Interpretation of Genomes") pipeline. Briefly described, PHRINGE creates a graph with all inferred protein sequences as nodes, with edges formed from distance scores calculated from their full length alignments, then clusters these into gene families using a method that considers the evolutionary relationships among the organisms, then performs a phylogenetic analysis on each. This allows the most accurate possible assignment of orthologous and paralogous relationships, inference of retained gene function, and reconstruction of gene duplications and losses. Users can see the multiple sequence alignments and phylogenetic trees of all genes, compare intron-exon structures, and see the relative arrangements of homologs across all genomes. See a summary of the PHRINGE method, details of the PHRINGE pipeline, or an explanation of why it is important to use evolutionary analysis to find orthologs.

Every gene of each animal has a "Detail Pages" with information such as its position, length, and intron-exon structure, the most similar sequences, with links, and the clusters (at various phylogenetic depths) to which it has been assigned by PHRINGE. Find a Detail Page by gene ID number, often obtained by searching for a particular gene or by clicking on any particular gene box on a Synteny Page. The cluster ID of each Detail Page is linked to the corresponding "Cluster and Compare Page".  See an arbitrarily chosen example here.

Every cluster of homologous genes has a "Cluster and Compare Page" with information such as the multiple sequence alignment, comparison of intron-exon structures, and the phylogeny of the member genes. Find a Cluster and Compare Page from the cluster IDs on a Detail Page of any member gene. See an arbitrarily chosen example here.

"Synteny Pages" show an overview of the relative physical arrangements of homologous genes for specified portions of specified genomes. Connecting lines are red if there has been an inversion. Mouse over gene boxes for more information. Click on any gene box to go to the corresponding Detail Page. See an arbitrarily chosen example here.

Click on any numeral in the "details" column of the table above to see which cluster levels this taxon is found and a comparison of the numbers of members of each gene family among all considered genomes.

Organisms Currently Being Compared
Organism Details Group
Sequenced by Genome home Publication
Homo sapiens Chordata
GRC Homo IHGSC (2004) Nature 431: 931-45
Caenorhabditis elegans Nematoda
Sanger, Washington U Caenorhabditis CESC (1998) Science 282: 2012-18
Daphnia pulex Arthropoda, Crustacea
JGI Daphnia Colbourne, et al., (2011) Science 331: 555-61
Ixodes scapularis Arthropoda, Chelicerata
Broad, JCVI Ixodes

in preparation.

Pediculus humanus Arthropoda, Insecta, Hemiptera
JCVI Pediculus Kirkness, et al., (2010) PNAS 107: 12168-73
Tribolium castaneum Arthropoda, Insecta, Coleoptera
Baylor U Tribolium Richards, et al. (2008) Nature 452: 949-55
Pogonomyrmex barbatus Arthropoda, Insecta, Hymenoptera
PBGSC Pogonomyrmex Smith, et al., (2011) PNAS 108: 1-6
Apis mellifera Arthropoda, Insecta, Hymenoptera
Baylor U Apis HGSC (2006) Nature 443: 931-49
Drosophila melanogaster Arthropoda, Insecta, Diptera
Celera, BDGC Drosophila Myers, et al., (2000) Science 287: 2196-2204
Anopheles gambiae Arthropoda, Insecta, Diptera
IAGP Anopheles Holt, et al., (2002) Science 298: 129-49
Bombyx mori Arthropoda, Insecta, Lepidoptera
ISGC Bombyx Xia, et al. (2004) Science 306: 1937-40
Danaus plexippus Arthropoda, Insecta, Lepidoptera
This project This project Zhan, et al. (2011) Cell 147: 1171-1185.
Tree of the animals in this analysis with cluster levels and taxon IDs