Systematics & phylogenomics
of the marine red algal class
Fl id
Florideophyceae
h
from west Pacific Ocean
Showe--Mei Lin1*, LiShowe
Li-Chia Liu1, Chien
Chien--Ming Chen2
Tsang--Huang Shih2 & Tun
Tsang
Tun--Wen Pai2
1Institute of Marine Biology
2Department of Computer Science & Engineering
National Taiwan Ocean University
Seaweed applications– as foods
• Greens:
Ulva, Caulerpa
Gelidium http://www.comnews.gio.gov.tw/
• Browns
B
:
Laminaria,
g
Sargassum
• Reds:
Gelidium
Porphyra
Gracilaria
Grateloupia
Eucheuma/Betaphycus
http://colly.suko
n.idv.tw/ &
http://www.yiji.
com/
(from “Seaweeds
“Sea eeds net of Taiwan”)
Tai an”)
http://blog.roodo.com/magulis/archives/5693075.html
Biofuels//bioethenols
Biofuels
Gracilaria firma
(W Taiwan)
(W.
T i
)
Sargassum
g
(E. Taiwan)
http://www.flickr.com/photos/roamover/1477269020/
Ulva (W. Taiwan)
Other applications
• Alcohol drinks
• Health foods
• Cosmetic &
Makeup
• Medicine &
antivirus
ti i drugs
d
Info source: Taiwan’sFisheries
Algal
g fluo-protein
p
cake
From: rugbyball.myweb.hinet.net/scpo/image/cake2.gif
Research Institute
http://www.tfrin.gov.tw/friweb/
The diversity of seaweeds in Taiwan
Petercladiella
• Taiwan,
T i
bisected by the
tropic of Cancer,
both tropical
and subtropical ;
Dictyota
• High
g diversityy
of marine
macroalgae:
macroalgae
Greens: ~110
Greens:
~110 spp.
Browns:~
Browns
:~90
90 spp.
Reds:: ~400
Reds
~400 spp.
spp.
~ 600 species in
Eucheuma
total
Caulerpa
Marine flora in
N.E. Taiwan
Keelung (Spring
marine flora)
海膜
Dermonema
Halymenia ceylanica
Porphyra
What are red algae？
• Absence anyy
flagellate stages;
• Accessory
photosynthetic
pigments –
phycobilins;
• Presence of pit
plugs;
• Unique sexual
reproductive
structures –
carpogonia &
carposporophytes
Spermatangia
(Lin & Hommersand 2007)
(From Graham et al. 2009)
(Lin et al. 2004)
Origins of red algae
- evolved from
cyanobacteria-like
ancestors based on
the endosymbiosis
theory.
theory
(Adopt from Delwiche 1999)
Unique features of
red algae
Animal cell
C t ki
Cytokinensis
i (細胞質分裂)
Pitt p
plugs
ugs (蛋白質孔連結)
Plant cell
Red algae from southern Taiwan
Corallines
(calcified
red
d algae)
l )
Zellera tawallina
Kappaphycus
Gracilaria edulis
Triphases of Life Cycle History
Systematics of red algae
C mparative cyst
Comparative
cystocarp
carp devel
development
pment
Subfamily
Delesserioideae
Subfamily
Phycodryoideae
Subfamily
Nitophylloideae
Lin et al. (2001): three-subfamily system
Systematics of red algae -
DNA sequence
s
analyses
l s s
Lin et al. (2001): three-subfamily system
Why we need many gene
sequences for red algal
systematics?
Whittaker’s
Whittaker s five kingdom system
Based on differences in nutrition
•
•
•
•
Plantae were
mostly multicellular
autotrophs
t t h
Animalia
multicellular
heterotrophs
Fungi multicellular
saprotrophs, that is
nitrogen rich
nitrogen-rich
sources;
Protista and
Monera included
Monera,
unicellular and
simple cellular
colonies.
browns
greens
(Evolution 2007 Cold Spring Harbor Laboratory Press)
Tree of Life – Three Domains
Woese
(1977)
defined
Archaea by
phylogenetic
h l
ti
taxonomy of
16S
ribosomal
RNA
Phylogenomic
approaches
Red
algae
:phylogenetic
analysis of
genome-wide
sets of
conserved genes
2nd endosymbiosis of
the red algal lineage
Koonin EV: The origin
g &
early evolution of
eukaryotes in the light of
phylogenomics.
p
y g
Genome
Biology 2010, 11:209.
Direct vs. Indirect
cystocarp
development
(Lin et al
al.
2002, 2003,
2004, 2007,
2010, 2011)
rbcL phylogeny
of foliose Graicilaria from Taiwan
G. huangi
Genome information of Gracilaria
Blade-form
1 Ch
1.
Chromosome
number (1N)
ca 24-30
ca.
24 30
2. Genome size –
unknown (150200 Mb estimated
based on a similar
genus Chondrus);
3. ca. 10,000
coding genes
(1N).
From Yabu & Yamamoto (1988)
Terete-form
Future works
1) To complete the characterization of three
t
transcriptomes
i t
off Gracilaria
G il i (Solexa
(S l
d t
datasets)；
t )；
2)
To complete searching conserved genes as single
copy for phylogenomic studies;
3) Functional analyses: i.e. life history, cell division,
floridean starch (related to glycogen),
glycogen) ontology
development related pathway etc…
4) To perform another 454 run for G.
G spinulosa
(suggested from the Solexa data, but depending
upon if any research funding available);
5) Speciation machenism from a genome-wide
comparison among the species with different types
off cystocarp
t
development.
d
l
t
Acknowledgments
•
National Science Council ((Taiwan, R.O.C.))
•
Center of Excellence for Marine
Bioenvironment and Biotechnology
(NTOU)
•
Seaweed Lab members at Institute of
Marine Biology (NTOU)
Thanks for y
your attention