Billie J. Swalla
bjswalla@u.washington.edu
Transcriptome Sequencing Reveals
Heterochronic Shift of
Chordate Gene Networks
...
Tunicates
mbulacraria Chordata
Cephalochordates
Modified from
Swalla et al. 2001
Xenoturbella
Heterochrony
http://www.bio.miami.edu/dana/dox/heterochrony.html
Allometric
Growth
Differential
growth in
organs and
body ...
Heterochrony
hetero = other
chronos = time
Haekel – 1875
de Beer – 1930 “Embryos and Ancestors”
Gould – 1997 “Ontogeny and...
C. Titus Brown
Evolution and Development of
Tailless Ascidians
1. Changes in gene expression in
regulatory genes
2. Downstream structural...
Molgula clades
Solitary ascidians
have determinant
and invariant cleavage.
Some species have
colored cytoplasms.
(Boltenia villosa)
The c...
Two Species of Closely
Related Ascidians and a
Hybrid Larva
Molgula oculata has a head, tail,
and otolith - chordate embry...
Notochord formation
(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 & extende...
Digital normalization
Digital normalization
Lowe, Swalla, Brown, in preparation
Digi Norm assembly vs Raw
read assembly
37 1713623
Digi Norm Raw
2446C. intestinalis
M. occulta
64 1513646
Digi Norm Raw
2...
Stage specific express
Lowe, Swalla, Brown, in preparation
Notochord gene expression
similar to tailed species
Prickle
Veeman, M., et al., 2007
•Planar cell
polarity (PCP)
pathway
•Involved in
convergence and
extension
Prickle expressed in
notochord cells
Mita et al Zool. Sci., 2010
M. occulta gastrulation Ciona intestinalis
Satoh Nature R...
Hybrid notochord genes allele
specific differential express
Notochord Gene Network
Davidson and Christiaen, Cell 2006
Ascidian Metamorphosis
Heterochronic shift of metamorphosis genes in
Molgula
Gene Species Cleavage Gastrula/
Neurula
Tailbud Larva Juvenile
META-...
Ascidian Development
Heterochronic Shift in
Molgulidae Development
*79 genes
examined
across of six
species
Billie Swalla, Nadine Peyriéras, Alberto Stolfi
M. occulta F+ 12 hatching
M. occulta transgenic NoTrlc
Alberto Stolfi & Lionel Christiaen
Summary
 Both tail and tailless species contain the majority of
known notochord genes
 Digital Normalization performs as...
Thanks to Beacon!!
1. Great colleagues!!
2. Revived an exciting research program
that benefited greatly from genomics
meth...
2012 Swalla Lab
Acknowledgements
University of Washington Michigan State University
• Dr. Titus Brown
• Dr. Kanchan Pavangadka
• Elijah Lo...
 96/98 Sanger-sequenced Molgulid genes
contained by global assembly.
 69% of M. oculata transcripts found (BLASTX
1e-12)...
Mapping => quantitation
Reference transcriptome required.
Assembly contig lengths
M. oculata M. occulta
Lowe, Swalla, Brown, in preparation
Tailless allele has high
expression in hybrids PCP
pathway
Billie Swalla - Transcriptome sequencing reveals heterochronic shift of chordate gene networks in molgulid ascidians
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Billie Swalla - Transcriptome sequencing reveals heterochronic shift of chordate gene networks in molgulid ascidians

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  • Billie Swalla - Transcriptome sequencing reveals heterochronic shift of chordate gene networks in molgulid ascidians

    1. 1. Billie J. Swalla bjswalla@u.washington.edu Transcriptome Sequencing Reveals Heterochronic Shift of Chordate Gene Networks in Molgulid Ascidians
    2. 2. Tunicates mbulacraria Chordata Cephalochordates Modified from Swalla et al. 2001 Xenoturbella
    3. 3. Heterochrony http://www.bio.miami.edu/dana/dox/heterochrony.html Allometric Growth Differential growth in organs and body parts Paedomorphy Retention of juvenile structures
    4. 4. Heterochrony 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
    5. 5. C. Titus Brown
    6. 6. Evolution and Development of Tailless Ascidians 1. Changes in gene expression in regulatory genes 2. Downstream structural genes become pseudogenes (muscle) 3. Heterochrony - changes in timing of gene activation 4. Gene Loss
    7. 7. Molgula clades
    8. 8. Solitary ascidians have determinant and invariant cleavage. Some species have colored cytoplasms. (Boltenia villosa) The cell lineage is very similar in Ciona, Phallusia, Halocythia roretzi & Molgula oculata.
    9. 9. Two Species of Closely Related Ascidians and a Hybrid Larva 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
    10. 10. Notochord formation (convergence & extension) Jiang and Smith, 2007
    11. 11. Notochord Gene Network Davidson and Christiaen, Cell (2006)
    12. 12. Molgula oculata notochord (40 cells, converged & extended) Molgula occulta no notochord (20 cells, not converged & extended) Hybrid notochord (20 cells, converged & extended) Notochord Formation in Molgulids Swalla and Jeffery, 1996
    13. 13. Digital normalization
    14. 14. Digital normalization Lowe, Swalla, Brown, in preparation
    15. 15. Digi Norm assembly vs Raw read assembly 37 1713623 Digi Norm Raw 2446C. intestinalis M. occulta 64 1513646 Digi Norm Raw 2398C. intestinalis M. oculata Lowe, Swalla, Brown, in preparation
    16. 16. Stage specific express Lowe, Swalla, Brown, in preparation
    17. 17. Notochord gene expression similar to tailed species
    18. 18. Prickle Veeman, M., et al., 2007 •Planar cell polarity (PCP) pathway •Involved in convergence and extension
    19. 19. Prickle expressed in notochord cells Mita et al Zool. Sci., 2010 M. occulta gastrulation Ciona intestinalis Satoh Nature Reviews Genetics 4, 2003
    20. 20. Hybrid notochord genes allele specific differential express
    21. 21. Notochord Gene Network Davidson and Christiaen, Cell 2006
    22. 22. Ascidian Metamorphosis
    23. 23. Heterochronic shift of metamorphosis genes in Molgula Gene Species Cleavage Gastrula/ Neurula Tailbud Larva Juvenile META-2 C. intestinalis M. oculata M. occulta M. tectiformis Echinonectin C. intestinalis M. oculata M. occulta M. tectiformis 50/168 genes show early differential expression in Molgula compared to C. intestinalis Larval development
    24. 24. Ascidian Development
    25. 25. Heterochronic Shift in Molgulidae Development *79 genes examined across of six species
    26. 26. Billie Swalla, Nadine Peyriéras, Alberto Stolfi
    27. 27. M. occulta F+ 12 hatching
    28. 28. M. occulta transgenic NoTrlc Alberto Stolfi & Lionel Christiaen
    29. 29. Summary  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
    30. 30. Thanks to Beacon!! 1. Great colleagues!! 2. Revived an exciting research program that benefited greatly from genomics methods 3. Leadership opportunities and support for female faculty 4. Graduate student support for travel and courses.
    31. 31. 2012 Swalla Lab
    32. 32. Acknowledgements 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
    33. 33.  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 MDSSNRSHPNAHLQYHTDYNYPPFR+VMLAAVKEGLYHPRLPSLRRMDMDTATHKLPDEH Sbjct: 50 MDSSNRSHPNAHLQYHTDYNYPPFRKVMLAAVKEGLYHPRLPSLRRMDMDTATHKLPDEH 229
    34. 34. Mapping => quantitation Reference transcriptome required.
    35. 35. Assembly contig lengths M. oculata M. occulta Lowe, Swalla, Brown, in preparation
    36. 36. Tailless allele has high expression in hybrids PCP pathway

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