Comparative Lactation Biology MamExp: an interactive gene expression browser for collaborative comparative lactation genomics Christophe Lefèvre , ITRI, BioDeakin, GTP Deakin University Kevin Nicholas Julie Sharp Karensa Menzies Pragati Sharma Sanjana Kuruppath Amit Kumar Philip Church James Stillman Shannu Palamuru VPAC Adam Wong Zoology Uni.Melbourne Matthew Digby John Arnould Sonia Mailer Cate Pooley Kylie Cane Elizabeth Pharo Coralie Reich Alison DeLeo Elie Khalil Danny Topcic Joly kwek Rachael O’Dowd Amelia Brennan Karensa Menzies Maurice Ling V.B.C, monash David Powell Yvan Strahm Torsten Seeman Reprogen Uni. Sydney Keith L. Macmilland Paul A Sheehy Peggy Rismiller, University of Adelaide, SA Katherine Belov, Faculty of Veterinary Science, University of Sydney, NSW platypus genome consortium
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Comparative Lactation BiologyMamExp: an interactive gene expression browser
for collaborative comparative lactation genomics
Christophe Lefèvre , ITRI, BioDeakin, GTP Deakin University
Kevin Nicholas
Julie Sharp
Karensa Menzies
Pragati Sharma
Sanjana Kuruppath
Amit Kumar
Philip Church
James Stillman
Shannu Palamuru
VPAC
Adam Wong
Zoology Uni.Melbourne
Matthew Digby
John Arnould
Sonia Mailer
Cate Pooley
Kylie Cane
Elizabeth Pharo
Coralie Reich
Alison DeLeo
Elie Khalil
Danny Topcic
Joly kwek
Rachael O’Dowd
Amelia Brennan
Karensa Menzies
Maurice Ling
V.B.C, monash
David Powell
Yvan Strahm
Torsten Seeman
Reprogen Uni. Sydney
Keith L. Macmilland
Paul A Sheehy
Peggy Rismiller, University of Adelaide, SA
Katherine Belov, Faculty of Veterinary Science, University of Sydney, NSW platypus genome consortium
Exploring lactation diversity
Comparative genomics & transcriptomics of the lactation system
Molecular interface between mother and child
Evolution/adaptation of the lactation programfrom echidna and wallaby to man...
Comparative lactation biology:
Mammalian diversity…
GENETIC RESOURCES - biodiversity approach
GENETIC RESOURCES - biodiversity approach
Using comparative genomics
Mammal evolution:
fossil dating
Mining 200 Million years of lactation …
Mammal evolution: Mammalian super-tree
The delayed rise of present-day mammals. Olaf R. P. et al. Nature Vol 446 | 29 March 2007
Mammal evolution: Mammalian super-tree
The delayed rise of present-day mammals. Olaf R. P. et al. Nature Vol 446 | 29 March 2007
Mammal evolution: Mammalian super-tree
The delayed rise of present-day mammals. Olaf R. P. et al. Nature Vol 446 | 29 March 2007
Research Platforms
Genomics
Bioinformatics
Proteomics Bioactives
metabolics
Lactation
program
gene discoverygene regulation
gene evolution
sequencing
Genome analysis
sequencing
Expression microarray
Protein prediction
signal prediction
Function prediction
Web query interface generate dynamic annotation (php scripts)
Gene index sequence annotation Bio-activity prediction gene expression regulation
EST-PAC a web package for EST annotation and protein sequence predictionYvan Strahm , David Powell and Christophe Lefèvre. Source Code for Biology and Medicine 2006, 1:2
Percentage identity
humandog
Distribution of similarity between assembled seal
EST’s
Using estpac…
Lefevre, C. M., Sharp, J. A., & Nicholas, K. R. (2010)Annual review of human genomics
Evolution of lactation
Monotreme
lactation
Monotreme lactation- short gestation period of 21-23 days
- egg incubation for 10-12 days
- lactation 120 to 200 days
milk is delivered to a highly altricial young.
Method
Milk cell cDNA sequencing
EST assembly
EST & contig annotation
Genome mapping
Contig clustering
EST to contig mapping (expression)
Comparative genomics
BLG
CSN2
CSN2b
C6orf58
?
CSN3
50%
8%
10%
23%
91%
Platypus milk cDNA library
87 ESTs (after removal of 20% rRNA +10% low quality)
1667 ESTs 58 genes
-Milk cell sequencing identifies milk protein sequences
-Milk cell gene expression
-High level of major milk protein
-Overall similar profiles in echidna and platypus
-Consistent with other mammals
-C8orf58:
-new monotreme milk protein ?
- alpha, beta, kappa and beta like caseins in echidna
- alpha-casein in platypus?
- gap in the platypus genome sequence
- CSN1 cDNA sequence confirmed by PCR
Caseins• three classes of phosphorylated micelles forming caseins:
- Related to Ca binding protein involved in bone and dentition
- alpha-caseins (CSN1s1, and CSN1s2 in bovine milk) . precipitated by very low calcium concentrations. have the highest phosphate content. no discernable secondary structure . the least conserved caseins
- Beta-casein: CSN2. precipitated by moderate calcium concentrations . have some secondary structure . moderately conserved
- kappa-caseins: CSN3. insensitive to calcium. essential for micelle formation. most conserved caseins
• rapidly evolving cluster of lactation specific genes • single CSN1 in marsupial• short exons, all in-frame• splice variants common in eutherians• phosphorylation motif straddle exon junction