Billie Swalla - Transcriptome sequencing reveals heterochronic shift of chordate gene networks in molgulid ascidians
Billie J. Swalla
Transcriptome Sequencing Reveals
Heterochronic Shift of
Chordate Gene Networks
in Molgulid Ascidians
Swalla et al. 2001
hetero = other
chronos = time
Haekel – 1875
de Beer – 1930 “Embryos and Ancestors”
Gould – 1997 “Ontogeny and Phylogeny”
“Few Evolutionary concepts have generated
more confusion and controversy than
heterochrony” McKinney, 1999
Evolution and Development of
1. Changes in gene expression in
2. Downstream structural genes
become pseudogenes (muscle)
3. Heterochrony - changes in timing
of gene activation
4. Gene Loss
and invariant cleavage.
Some species have
The cell lineage is very
similar in Ciona, Phallusia,
Halocythia roretzi &
Two Species of Closely
Related Ascidians and a
Molgula oculata has a head, tail,
and otolith - chordate embryo.
M. occulta egg X M. oculata sperm
has a head, short tail, and otolith.
Molgula occulta lacks chordate
features - head, tail, and otolith.
Swalla and Jeffery, 1996
(convergence & extension)
Jiang and Smith, 2007
Notochord Gene Network
Davidson and Christiaen, Cell (2006)
Molgula oculata notochord
(40 cells, converged & extended)
Molgula occulta no notochord
(20 cells, not converged & extended)
(20 cells, converged & extended)
Swalla and Jeffery, 1996
Heterochronic shift of metamorphosis genes in
Gene Species Cleavage Gastrula/
Tailbud Larva Juvenile
META-2 C. intestinalis
Echinonectin C. intestinalis
50/168 genes show early differential expression in Molgula compared to C.
M. occulta transgenic NoTrlc
Alberto Stolfi & Lionel Christiaen
Both tail and tailless species contain the majority of
known notochord genes
Digital Normalization performs as well or slightly better
than raw read assembly
Metamorphosis genes are expressed much earlier than
in other ascidian species
Early onset of Metamorphosis may be a pre-adaptation
to evolution of a tailless embryo
Thanks to Beacon!!
1. Great colleagues!!
2. Revived an exciting research program
that benefited greatly from genomics
3. Leadership opportunities and support for
4. Graduate student support for travel
University of Washington Michigan State University
• Dr. Titus Brown
• Dr. Kanchan Pavangadka
• Elijah Lowe
• Dr. Billie J. Swalla
• Dr. Charlotte Konikoff
• Kristin Andrykovich
• Kelly Hennessey
• Max Maliska
• Lauren Vandepas
New York University
Dr. Lionel Christiaen
Dr. Alberto Stolfi
96/98 Sanger-sequenced Molgulid genes
contained by global assembly.
69% of M. oculata transcripts found (BLASTX
1e-12) in Ciona proteome.
55% of M. occulta transcripts => Ciona.
How do we evaluate assembly?
Query: 1MDSSNRSHPNAHLQYHTDYNYPPFRRVMLAAVKEGLYHPRLPSLRRMDMDTATHKLPDEH 60
Sbjct: 50 MDSSNRSHPNAHLQYHTDYNYPPFRKVMLAAVKEGLYHPRLPSLRRMDMDTATHKLPDEH 229