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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.)

DNA sequencing was done in collaboration with our partners at Eureka Genomics (Illumina sequencing) and at Virginia Tech (Roche sequencing). Below are some of the relevant statistics for this work.

Back to our Danaus Genome Evolution Home Page.

 
 

Sequencing coverage of the Danaus plexippus genome:

A high-depth draft genome sequence has been completed and assembled (in collaboration with Robert Settlage at Virginia Bioinformatics Institute) and a gene set created. The following raw sequence provides 150x coverage in Illumina and 29x coverage in Roche/454 sequencing of this 273 MB genome:

Type
Reads
Nucleotides
Coverage
Unpaired Illumina
160,238,322
15,648,538,304
55x
Paired-end Illumina at 200 nt separation
161,783,387
15,206,131,306
54x
Mate-paired Illumina at 3 to 5 KB separation
121,315,525
11,692,157,496
41x

Unpaired Roche/454

19,277,297
6,591,793,370
23x
Paired-end Roche/454 at 8 KBseparation
3,776,390
770,770,002
2.7x
Paired-end Roche/454 at 20 KB separation
2,805,280
1,034,981,756
3.6x

In addition, we generated 115 million Illumina reads (5.4 Gb of sequence) for the transcriptome from RNA collected at many different life stages, and additional illumina sequencing targeting miRNAs (see details in the manuscript).

 
 

Features of the Danaus plexippus genome:

Genome size
273 Mb
Number of chromosomes
29 or 30
Repeat content
13.1%
G+C proportion
31.6%

Coding sequence proportion

7.5%
Number of protein-encoding genes identified
16,866
Number of protein-encoding genes with identifiable Interpro domains
10,999
Number of protein-encoding genes with assigned GO terms
11,210
Number of tRNA genes identified
431
Number of types of miRNA genes identified
116
 
 

Download Danaus plexippus datasets:

Download the version 1 scaffolds in FASTA format here.

Download the version 1 scaffolds plus the version 0 unscaffolded contigs in FASTA format here.

Download the version 2 scaffolds in FASTA format here.

Download the nucleotide sequences of the OGS1.0 gene set here.

Download the amino acid sequences of the OGS1.0 gene set here.

 
 

Search, view, or browse for Danaus plexippus genes of interest:

Access the "genome browser" here where all genome features are mapped on a depiction of the genome.

Enter your nucleotide or amino acid sequence here to search for matches to the Danaus plexippus genome, gene set, ESTs, or inferred protein sequences using several variants of BLAST.

Search for particular genes of Danaus plexippus by keyword (e.g., "kinase") here.

Search for particular genes of Danaus plexippus by InterProScan domains or Gene Ontology terms here.

Browse microRNAs (miRNAs) here.