mallet genomics 

Genomics and speciation

The diversity of life on our planet is generated by the process of speciation, evolutionary splitting into divergent groups that can coexist in a state of nature. The changes at genomic level that cause speciation are still obscure. This is a time to jettison preconceived ideas, and to absorb what new data can tell us.

Today, these data will frequently include whole genome sequences. Heliconius melpomene is the first butterfly species to have its genome both sequenced and mapped to chromosomes, by the Heliconius Genome Consortium (led by two former postdocs, Chris Jiggins and Owen McMillan). The new genome has considerably enhanced already active work on understanding the developmental genetics and evolution of mimicry, on the conservation of genomic structure (synteny), and on the evolution of olfactory and chemosensory genes, as well as on speciation. The Heliconius genome is only the second member of the Lepidoptera to be sequenced and mapped to chromosomes. The Lepidoptera is an important group with 180,000 species described, around 10% of the planet's known species. The genome is one of the key ENSEMBL genomes now used for comparative genomics purposes in many different fields.

a, Maps of the 21 Heliconius chromosomes (colour) and of the 28 Bombyx chromosomes (grey) based on positions of 6,010 orthologue pairs demonstrate highly conserved synteny and a shared n = 31 ancestor. Dotted lines within chromosomes indicate major chromosomal fusions. The major differences in chromosome number are explained by ten fusions on the Heliconius lineage (to give n=21 pairs of chromosomes), and three on the Bombyx lineage (n=28), both from the Lepidoptera modal karyotype of n=31.

b, Maximum-likelihood tree showing expansions of chemosensory protein (CSP) genes in the two butterfly genomes.
From Fig. 2 of Heliconius Genome Consortium 2012

In spite of considerable conservation of synteny, we now realize that a single reference sequence in the genus is not enough. One problem is that separate species, and even colour pattern races within species may differ in indels or highly divergent regions that could be important in developmental switching. These are hard to find using just a single reference sequence. Therefore, the Consortium's next project is to sequence 16 genomes from across the genus. This will considerably improve reference mapping (for instance, in the Heliconius erato group), as well as improving our understanding of genomic evolution in the Lepidoptera, and in general.

The Heliconius melpomene genome on ENSEMBL
The Heliconius genome browser and downloadable complete genome

How to sequence a genome on a tight budget: the case of Heliconius

The international group now known as the Heliconius Genome Consortium was conceived in around 2000, first meeting that year as a symposium at the Association of Tropical Biologists meeting at Bloomington, Indiana. In 2004 we put in the first white paper to NHGRI to sequence Heliconius. However, this was not chosen for funding. By 2009 next-generation sequencing became readily feasible, and the Consortium decided to go it alone. In 2009, we drew up plans to sequence the Heliconius melpomene genome at a meeting in Harvard University. Nine laboratories each committed $15,000 to the enterprise, and the main sequencing work was carried out for us by Baylor. We were very fortunate that many other people and groups worldwide contributed analyses, assembly and annotations. By 2011 we had a draft genome, and in 2012 our paper was published in Nature.

For further details of the Heliconius Genome consortium, see:

The laboratories contributing to the Heliconius Genome Consortium

(alphabetical order)
Richard ffrench-Constant, University of Exeter, Cornwall Campus
Chris Jiggins, Cambridge University
Mathieu Joron, Muséum d'Histoire Naturelle, Paris
Marcus Kronforst, University of Chicago
James Mallet, formerly University College London; now at Harvard University
W. Owen McMillan, Smithsonian Tropical Research Institute, Panamá
Sean Mullen, Boston University
Robert Reed, Cornell University, and Adriana Briscoe, University of California, Irvine (both then at UC Irvine)