COMPLEX ADAPTIVE TRAITS

COMPLEX ADAPTIVE TRAITS
Newsletter
24
Vol. 3 No. 10 2012
2 Gb
2 kb 5 kb
200 bp 500 bp 800 bp
paired-end
10 kb 20 kb mate-pair
16,307
N50
81 kb
14 Gb
PacBio
100x
(
100 bp)
1.6 Gbp
N50
de novo
287 kb
RNA-seq
45,469
130
RNA-seq
QTL
RNAi
de novo genome sequencing
contig
N50
16 kb scaffold
N50
21 kb
AFLP
QTL
AFLP
AFLP
RNA-seq
scaffold(
6.5 kb)
scaffold
(
1.6 kb)
scaffold
1.6 kb
1
scaffold
scaffold
Fosmid
scaffold
3
Illumina MiSeq
QTL
(PRC2)
PRC2
PRC2
Class2 KNOX
Sakakibara et al. 2013. Science
Aoyama et al. 2012. Development
(1) Aoyama, T., Hiwatashi, Y., Shigyo, M., Kofuji, R., Kubo, M., Ito, M., and Hasebe, M. (2012).
AP2-type transcription factors determine stem cell identity in the moss Physcomitrella patens.
Development 139, 3120-3129.
(2) Sakakibara, K., Ando, S., Yip, H.K., Tamada, Y., Hiwatashi, Y., Murata, T., Deguchi, H.,
Hasebe, M., and Bowman, J.L. (2013). KNOX2 genes regulate the haploid-to-diploid
morphological transition in land plants. Science 339, 1067-1070.
(
:
(
)
)
(AM
(
)
)
AM
4
5
7
AM
(1) AM
Rhizophagus irregularis DAOM197198
90Mb
AM
AM
Sclerocystis pubescens)
Endogone
(Endogone pisiformis
30Mb
AM
RNA-seq
RNA-seq
(2)
tricot
(3)
(ii)
(iii)
24
adaptive dynamics
(i)
(iv)
RNA-seq
Suzaki T, Ito M, and Kawaguchi M. Genetic basis of cytokinin and auxin functions during root
nodule development. Frontiers in Plant Science, 4, 42 (2013)
Fujita H, and Kawaguchi M. Pattern formation by two-layer Turing system with complementary
synthesis. Journal of Theoretical Biology, 322, 33-45 (2013)
Takahara M, Magori S, Soyano T, Okamoto S, Yoshida C, Yano K, Sato S, Tabata S, Yamaguchi K,
Shigenobu S, Takeda N, Suzaki T, Kawaguchi M. TOO MUCH LOVE, a novel kelch
repeat-containing F-box protein, functions in the long-distance regulation of the
legume-Rhizobium symmbiosis. Plant Cell Physiology Rapid paper 54, 433-47 (2013)
Murakami Y, Yokoyama H, Fukui R and Kawaguchi M. Downregulation of NSP2 expression in
developmentally young regions of Lotus japonicus roots in response to rhizobial Inoculation. Plant
Cell Physiol. 54, 518-27 (2013)
Suzaki, T. and Kawaguchi, M. Grafting analysis indicates that malfunction of TRICOT in the root
causes a nodulation-deficient phenotype in Lotus japonicus. Plant Signaling & Behavior, in press.
Suzaki, T, Ito, M, and Kawaguchi, M. Induction of localized auxin response during spontaneous
nodule development in Lotus japonicus. Plant Signaling & Behavior, in press.
Suzaki, T, Kim, C.S, Takeda, N, Szczyglowski, K. and Kawaguchi, M. TRICOT encodes an
AMP1-related carboxypeptidase that regulates root nodule development and shoot apical meristem
maintenance in Lotus japonicus. Development 140, 353-361 (2013)
Suzaki T, Yano K, Ito M, Umehara Y, Suganuma N, and Kawaguchi M. Positive and negative
regulation of cortical cell division during root nodule development in Lotus japonicus is
accompanied by auxin response. Development 139, 3397-4006 (2012)
Hakoyama T, Oi R, Hazuma K, Suga E, Adachi Y, Kobayashi M, Akai R, Sato S, Fukai E, Tabata
S, Shibata S, Wu GJ, Hase Y, Tanaka A, Kawaguchi M, Kouchi H, Umehara Y, Suganuma N. The
SNARE Protein SYP71 Expressed in Vascular Tissues is Involved in Symbiotic Nitrogen Fixation
in Lotus japonicus Nodules. Plant Physiol. 160, 897-905 (2012)
Chen J, Moreau C, Liu Y, Kawaguchi M, Hofer J, Ellis N and Chen R Conserved genetic
determinant of motor organ identity in Medicago truncatula and related legumes. Proc. Natl. Acad.
Sci. USA 109, 11723-8 (2012)
Juan Pascual-Anaya
23
(
BGI
Sanger Institute, ensembl
33
)
(Pelodiscus sinensis)
ZW
ZW
DNA(
)
short
insert libraries(170bp, 500bp, 800b) long insert libraries(2Kbp, 5Kbp, 10Kbp, 20Kbp, 40Kbp)
DNA
depth
105x
Customized SOAPdenovo
2.1Gbp N50
scaffold :3Mbp
RNAseq
( mRNA
:146.7Gb)
(18188
)
(DDBJ/NCBI/ENSEMBL)
2012
7
(http://asia.ensembl.org/Pelodiscus_sinensis/Info/Index )
(
)
1-to-1 orthologous genes
11602
9
mRNA
RNAseq
22M
/
73% 10M
(15000
(
[
]
miRNA
)
mRNA
(TK23)
)
(gastrula)
(Nagashima et al. Science 2009)
Wnt
Wnt
(
)
(1) Nagashima, H., Kuraku, S., Uchida, K., Ohya, K. Y., Narita, Y., Kuratani, S. (2012) Body plan
of turtles: an anatomical, developmental and evolutionary perspective. Anat. Sci. Int. 87, 1-13
(2) Oisi, Y., Ota, K.G., Kuraku, S., Fujimoto, S., Kuratani, S. (2012) Craniofacial development of
hagfishes and the evolution of vertebrates. Nature. 493(7431):175-80
(3) Hirasawa, T., Kuratani, S. (2013) A new scenario of the evolutionary derivation of the
mammalian diaphragm from shoulder muscles. J.Anat. in press
(4) Wang, Z., Pasvual-Anaya, J., Zadissa, A., Li, W., Niimura, Y., Huang, Z., Li, C., White, S.,
Xiong, Z., Fang, D., Wang, B., Ming, Y., Chen, Y., Zheng, Y., Kuraku, S., Pignatelli, M., Herrero,
J., Beal, K., Nozawa, M., Li, Q., Wang, J., Zhang, H., Yu, L., Shigenobu, S., Wang, J., Liu, J.,
Flicek, P., Searle, S., Wang, J., Kuratani, S., Yin, Y., Aken, B., Zhang, G., Irie, N. (2013) The draft
genomes of soft-shell turtle and green sea turtle yield insights into the development and
evolution of the turtle–specific body plan. Nature Genet. in press
1,+
1, *
3.
2,*
+
3,#
*
1,#
1.
2.
#
(1)
DNJ D-AB1
10
RNA-Seq
Suc1
DNJ
D-AB1
(2)
spli
Bt
Bmacj6
(3)
RNA-seq
RNA-seq
Bmacj6
(1) Daimon, T., Fujii, T., Yago, M., Hsu, Y.-F., Nakajima, Y., Fujii, T., Katsuma, S., Ishikawa, Y.,
and Shimada, T. (2012) Female sex pheromone and male behavioral responses of the bombycid
moth Trilocha varians: comparison with those of the domesticated silkmoth Bombyx mori.
Naturwissenschaften 99: 207-215.
(2) Daimon, T., Fujii, T., Fujii, T., Yokoyama, T., Katsuma, S., Shinoda, T., Shimada, T., and
Ishikawa, Y. (2012), Reinvestigation of the sex pheromone of the wild silkmoth, Bombyx
mandarina: The effects of bombykal and bombykyl acetate. J. Chem. Ecol. 38: 1031-1035.
(3) Fujii, T., Banno, Y., Abe, H., Katsuma, S., and Shimada, T. (2012) A homolog of the human
Hermansky-Pudluck Syndrome-5 (HPS5) gene is responsible for the oa larval translucent mutants
in the silkworm, Bombyx mori. Genetica 140: 463-468.
(4) Ito, K., Kidokoro, K., Katsuma, S., Shimada, T., Yamamoto, K., Mita, K., and Kadono-Okuda,
K. (2012) Positional cloning of a gene responsible for the cts mutation of the silkworm, Bombyx
mori. Genome 55: 493-504.
(5) Katsuma, S. and Shimada, T. (2012) Comparative studies of Bombyx mori nucleopolyhedrovirus
infection in BmN4 cell lines maintained in different laboratories. J. Insect Biotechnol. Sericol. 81:
7-12.
(6) Hori, T., Kiuchi, T., Shimada, T., Nagata, M., and Katsuma, S. (2013) Silkworm plasmatocytes
are more resistant than other hemocyte morphotypes to Bombyx mori nucleopolyhedrovirus
infection. J. Invertebr. Pathol. 112: 102-104.
(7) Wang, L., Kiuchi, T., Fujii, T., Daimon, T., Li, M., Banno, Y., Katsuma, S., and Shimada, T.
(2013) Reduced expression of the dysbindin-like gene in the Bombyx mori ov mutant exhibiting
mottled translucency of the larval skin. Genome 56: 101-108.
(8) Fujii, T., Abe, H., Kawamoto, M., Katsuma, S., Banno, Y., and Shimada, T. (2013) Albino (al)
is a tetrahydrobiopterin (BH4)-deficient mutant of the silkworm Bombyx mori. Insect Biochem. Mol.
Biol. (in press).
(9) Wang, L., Kiuchi, T., Fujii, T., Daimon, T., Li, M., Banno, Y., Kikuta, S., Kikawada, T.,
Katsuma, S., and Shimada, T. (2013) Mutation of a novel ABC transporter gene is responsible for
the failure to incorporate uric acid in the epidermis of ok mutants of the silkworm, Bombyx mori.
Insect Biochem. Mol. Biol. (in press).
$
RNA
seq
[1]
[2]
[3]
mRNA
[4]
[1] Illumina
Burkhorderia sp.
Allpaths-LG
[2]
SPIA
RNA-seq
24 Scaffold
Scaffold
Gap
total RNA
HiSeq
Ribosomal RNA
[3] RNA-seq
[4] 23
DEG
50
web
TbT
DEG elimination strategy;
DEGES
DEG
TbT
TCC
[1]
scaffolding
fosmid
RS
[2] miRNA
100
10
DEGES
20 kb
scaffolding
siRNA,
rRNA
non-coding RNA
RNA
[3] 5
RNA-seq
RNA-seq
[4] TCC
40 kb
PacBio
Contig
RNA
miRNA
R
A
DEGES
3
A
Kadota K., Nishiyama T., Shimizu K. A normalization strategy for comparing tag count data.
Algorithms Mol. Biol. 7:5. (2012).
Nishiyama T., Miyawaki K., Ohshima M., Thompson K., Nagashima A., Hasebe M., Kurata T.
Digital gene expression profiling by 5'-end sequencing of cDNAs during reprogramming in the
moss Physcomitrella patens. PLoS One. 7:e36471. (2012).
Hojo M., Maekawa K., Saitoh S., Shigenobu S., Miura T., Hayashi Y., Tokuda G., Maekawa H.
Exploration and characterization of genes involved in the synthesis of diterpene defence secretion in
nasute termite soldiers. Insect Mol. Biol. 21:545-557 (2012)
Shigenobu, S. and Stern, D. Aphids evolved novel secreted proteins for symbiosis with bacterial
endosymbiont. Proc. Royal Soc. B 280: 20121952 (2013).
Ryo Tabata, Takehiro Kamiya, Shuji Shigenobu, Katsushi Yamaguchi, Masashi Yamada,
Mitsuyasu Hasebe, Toru Fujiwara, Shinichiro Sawa. Identification of an EMS-induced causal
mutation in a gene required for boron-mediated root development by low-coverage genome
re-sequencing in Arabidopsis. Plant Signaling & Behavior. 8: e22534 (2013)
Takahara M, Magori S, Soyano T, Okamoto S, Yoshida C, Yano K, Sato S, Tabata S, Yamaguchi K,
Shigenobu S, Takeda N, Suzaki T, Kawaguchi M. TOO MUCH LOVE, a Novel Kelch
Repeat-Containing F-box Protein, Functions in the Long-Distance Regulation of the
Legume-Rhizobium Symbiosis. Plant Cell Physiol. (2013).
Tokuda G, Elbourne LDH, Kinjo Y, Saitoh S, Sabree Z, Hojo M, Yamada A, Hayashi Y,
Shigenobu S, Bandi C, Paulsen IT, Watanabe H, Lo N. Maintenance of essential amino acid
synthesis pathways in the Blattabacterium cuenoti symbiont of a wood-feeding cockroach. Biol.
Lett. 9, 20121153 (2013).
`
Rickettsiella
Rickettsiella
1,425 ,
RNA
38.3%, coding content 89%
grylli, Coxiella, Legionella
Serratia
B
biotin
thiamine
6
Rickettsiella
11
5500 SOLiD
50 bp
4.5
leads
1,576,143 bp
,
RNA
42 , GC
Rickettsiella
Hamiltonella,
Gly Glu
RNA-Seq
mRNA
TbT
P < 0.01
54
Rickettsiella
Regiella
Hamiltonella
Rickettsiella
Rickettsiella
Rickettsiella
Proc.
Natl. Acad. Sci. USA
Rickettsiella
RNAi
siRNA
(1) Futahashi R., Kurita R., Mano H., Fukatsu T. (2012) Redox alters yellow dragonflies into red.
Proc. Natl. Acad. Sci. USA 109: 12626-12631.
(2)
2012
- 2012 7 10
http://www.aist.go.jp/aist_j/press_release/pr2012/pr20120710/pr20120710.html
4
scaffoldN50
145kb
3.6Mb
775kb
RNAseq
gene model
25
BBP4,5
yellow
ebony
BBP4, 5
4
(1.3Mb)
BBP
1cM
33
SNP12
33
SNP
5
A
B
2
RNAseq
heterogenic
HPLC MS
Ze
Ze
siRNA
3
1
EMST
siRNA
(Electroporation Mediated Somatic Transgenesis)
Ze
Wnt1
EMST
siRNA
Wnt1
K
4
p, Ze, ms, K
EMST
3
H
25
H
EMST
p
RNAseq
H
Futahashi R., Shirataki, H., Narita, T., Mitak, K. and Fujiwara, H. (2012) Microarray-based
Comprehensive Analysis for Stage-specific Larval Camouflage Pattern-associated Genes in the
Swallowtail Butterfly, Papilio xuthus. BMC Biol. 10, e46.
Shirai, H., Kamimura, M. Yamaguchi, J., Imanishi, S., Kojima, T. and Fujiwara, H. (2012)
Two adjacent cis-regulatory elements are required for ecdysone response of ecdysone receptor
(EcR) B1 transcription. PLoS One 7 (11) e49348.
Ando, T. and Fujiwara, H. (2013) Electroporation mediated somatic transgenesis for rapid
functional analysis in insects. Development, 140, 454-458.
2013
2013
67
64
216-221
177-179
2
2
2
2
1
Tetrahymena thermophila
2
2
[1] Importin-β
23
importin-β
importin-β GFP
GFP
importin-β
importin-β
[2]
GFP
GFP
30
16
29
2
(1) Iwamoto, M., Asakawa, H., Ohtsuki, C., Osakada, H., Koujin, T., Hiraoka, Y., and Haraguchi, T.
(2013) Monoclonal antibodies recognize Gly-Leu-Phe-Gly repeat of nucleoporin Nup98 of
Tetrahymena, yeasts, and humans. Monoclon. Antib. Immunodiagn. Immunother. 32: 81–90.
(1)
Nup98
2013-061612
2013
3
25
QTL
2
F2
Haplochromis chilotes
H. sauvagei
mapping
SNP
7
3
Illumina Hiseq2000
Pundamilia nyererei
SNP
SNP
QTL
2
1
3cM
V1R
LWS
Hot
Spot
V1R
SNP
3
SNP
F2
186
genotyping
307
QTL
3
H. chilotes
RNAseq
H. sauvagei
2
AmnSINE1
5
AS071
AS021
AS071
Fgf8
3
AS071
3
3
Nakanishi et al. 2011
fgf8
SINE
Nakanishi et al.
wnt8b
AS071
sprouty2
AS021
satb2
AS021
AS021
AS021
SINE
SINE
SINE
SINE
AS021
AS021
2
SINE
indel
AS021
AS021
SINE
satb2
Ota T, Nikaido M, Suzuki H, Hagino-Yamagishi K, Okada N. (2012) Characterization of V1R
receptor (ora) genes in Lake Victoria cichlids. GENE 499:273–279.
Nikaido M, Suzuki H, Toyoda A, Fujiyama A, Hagino-Yamagishi K, Kocher TD, Carleton KL,
Okada. (2013) Lineage specific expansion of V2R receptor (OlfC) genes in cichlids may contribute
to diversification in amino acid detection. Genome Biol. Evol.5: 711-722.
Nakanishi A, Kobayashi N, Suzuki-Hirano A, Nishihara H, Sasaki T, Hirakawa M, Sumiyama K,
Shimogori T, Okada N. (2012) A SINE-Derived Element Constitutes a Unique Modular Enhancer
for Mammalian Diencephalic Fgf8. PLoS One 7:e43785.
Polypedilum vanderplanki
DNA
LEA
Polypedilum nubifer
de novo
264kb
N50
Roche 454 GS FLX
92
EST(
Sanger
N50
28.3kb
76
Fosmid
)
17,824 17,224
)
GC
(
0.34 0.49
75%
DNA
(ROS)
D.
melanogaster
C. elegans
ARId (Anhydrobiosis-related Island)
ARId
ARId
ROS
DNA
COI
ITS1
P. nubifer
4,450
Drosophila yakuba
Drosophila sylvestris
P.vanderplanki
3,920
(1) Furuki T, Shimizu T, Chakrabortee S, Yamakawa K, Hatanaka R, Takahashi T, Kikawada T,
Okuda T, Mihara H, Tunnacliffe A, Sakurai M (2012) Effects of Group 3 LEA protein model
peptides on desiccation-induced protein aggregation Biochimica et Biophysica Acta - Proteins &
Proteomics 1824(7):891-897
(2) Mukae K, Cornette R, Gusev O, Hatanaka R, Okuda T, Kikawada T (2012) Elucidation of
mechanisms underlying desiccation tolerance with exhaustive gene analysis
58(1):73-76
Fgf10
Fgf10
Fgf10
R2
387bp
R31C2
531bp
R212L2
R3
Fgf10KO
Fgf10KO/ 212L2
Fgf10
R212L2
Fgf10KO/
31C2
R31C2
Hox
Fgf10
Hox
R2
Hoxb-6
Wnt
R212ab
Hoxa-9
Hox6
53
R2
Fgf10
Hox9
Fgf10
AbdB
Hox
R3
Fgf10
Hox
Fgf10
R3
Fgf10
R3
Fgf10
Fgf10
R3
R3
Fgf10
R3
R3
Fgf10
R3
Hox
R3
in vitro
Fgf10
Hox
Hox
R3
Hox
Hox
-
Fgf10
Hox
Fgf10
R3
Fgf10
R3
Fgf10BAC
Watanabe, Y., et al. (2012). "Fibroblast growth factor 10 gene regulation in the second heart field
by Tbx1, Nkx2-5, and Islet1 reveals a genetic switch for down-regulation in the myocardium." Proc
Natl Acad Sci U S A 109(45): 18273-18280.
Yamamoto-Shiraishi, Y and Kuroiwa A. “Wnt and BMP signaling cooperate with Hox in the
control of Six2 expression in limb tendon precursor.” Dev. Biol. In press (2013) doi:
10.1016/j.ydbio.2013.02.023.
A
I
9
85
2
3 Gbp
Acropora digitifera
Symbiodinium minutum
B1
Montastraea faveolata
(
1.5 Gbp)
(
A
C)
B
B
1
(
615 Mbp)
B
42,000
19
2
DNA
5snRNAs (U2, U4, U5, U6)
3
14
DNA
(4) RNA
3
(1)
B
40%
(2)
regulator of chromosome condensation
family protein (RCC1)
86
52
dinoflagellate/viral nucleoprotein(DVNP)
19
(3)
TSS
(4)
5’
GT
18,000
B
GC GA
80%
Koyanagi et al., 2013
DNA
(1)
(SLTS)
RNA
SLTS
SLTS
TSS
(2)
1,300Mb
2,200Mb
90X
B
(3)
C
A
2,700Mb
(4)
A,B,C
RNA
(1) Koyanagi, R., Takeuchi, T., Hisata, K., Gyoja, F., Shoguchi, E., Satoh, N., Kawashima, T.
MarinegenomicsDB: An integrated genome viewer for community-based annotation of genomes.
Zool. Sci. in press.
2
(1)
24
ANGIE
2
ANGIE
6
[Kalinka
et al. Nature 2010]
ANGIE
D. melanogaster
D. simulans
D. melanogaster
D. virillis
(2)
D. melanogaster
D. virillis
[Izawa and Sese, 2013]
RNA-seq ChIP-seq
http://lab.se-se.jp/recot/
Web
”Highly accessed”
2013
3
31
Akiko Izawa and Jun Sese. (2013) RECOT: a tool for the coordinate transformation of
next-generation sequencing reads for comparative genomics and transcriptomics. Source Code for
Biology and Medicine 2013, 8:6.
RIL
Miyakojima MG-20
33
35
DNAseq
SNPs
CM0010_330.r2.m
(Gifu B-129)
55
70
SNPs
(Chr.1_58.4cM- Chr.1_61.8cM)
QTL
RIL
Chr1
DNA
chr.1
SNP
LjRacGTPase activating protein 1
RIL
LjRacGTPase
RIL
DNA
RIL
RIL
RIL
F6, F7
E1, E2(GIGANTEA)
PHYA, PHYB, PHYE, E1, GIGANTEA
GIGANTEA
Flowering Locus Ta
E1
GIGANTEA
RT-PCR
association
association
(1). Ishibashi, N., Setoguchi, H. 2012. Polymorphism of DNA sequences of cryptochrome genes is
not associated with the photoperiodic flowering of wild soybean along a latitudinal cline. Journal of
Plant Research (in press) DOI:10.1007/s10265-011-0470-6
(2). Ikeda, H., Carlsen, T., Fujii, N., Brochmann, C., Setoguchi, H. 2012. Evolution of an alpine
endemic plant at the arctic-alpine range periphery following Pleistocene climatic oscillations.
New Phytologist 194: 583-594. DOI: 10.1111/j.1469-8137.2012.04061.x
QTL
DNA
HiSeq2000 180 bp 500 bp
188× PacBio RS
SOAPdenovo, SGA, ALLPATHS-LG
109 120Mb scaffold
51k
scaffold
HiSeq2000
PacBio
34×
121k
N50
1000 4000
HiSeq2000
LSC PacBioToCA
SGA
castaneum, Drosophila melanogaster, Apis melifera, Caenorhabditis elegans
BLAST
castaneum
9833
66
D. melanogaster
23849
10570
51
C. elegans
31234
32
RAD
HiSeq2000
Tribolium
50
T.
A. melifera
QTL
DNA
DNA
14
17Gb
PstI
HiSeq2000
RAD
134
Restriction site Associated
36
QTL
Ornstein-Uhlenbeck model
2013
PacBio
RAD
RAD
QTL
scaffold
2013
RNAseq
RNAi
Konuma, J., S. Chiba & T. Sota (2013) Quantitative genetic analysis of subspecific differences in
body shape in the snail-feeding carabid beetle Damaster blaptoides. Heredity 110: 86-93.
Sota, T., J. Konuma, M. Fujiwara & E. Shoguchi (2013) Genome sizes of three species in the
subtribe Carabina (Coleoptera: Carabidae). Entomological Science 16: 122-124.
(
)
1.
1.5
larval RNAi
RNA
RNAi
cDNA
larval RNAi
RNA
Illumina HiSeq 2000
447.8
de novo
12.7
70%
Tribolium castaneum
doublesex
dsx RNAi
dsx
RNAi
RNA-seq
RNA-seq
larval RNAi
1000
HiSeq 2000
918 Mb
PacBio RS
Cornette
Illumina
Ito, Y., Harigai, A., Nakata, M., Hosoya, T., Araya, K., Oba, Y., Ito, A., Ohde, T., Yaginuma, T. and
Niimi, T. (2013) The role of doublesex in the evolution of exaggerated horns in the Japanese
rhinoceros beetle. EMBO Rep., in press.
(Hemerocallis fulva)
(H. citrina)
HiSeq2000(Illumina)
RNA-seq
2
2
(S,M,L)
3
HiSeq2000(Illumina)
read
357,976 Contig
347,801 Contig
(
Total RNA
100bp
18
Trinity De novo Assembly
749.4507bp N50 1257
769.0918bp N50 1314
Contig
484,881 Contig
)
3
Contig
Contig
723.6247 bp N50
1154
RSEM
read
R
TCC(1.0.0)
L
S, M, L
DEGs
2876 contig
2280 contig
2977 contig
1581 contig
1523 contig
1346 contig
S
M
Blast nr
―
M
R2R3MYB family
Zeaxanthin epoxidase
Anthocyanin 2
Neoxanthin synthase
(Violaxanthin, Neoxanthin)
F2
F2
delphinidin
3-O-rutinoside
RT-PCR
F3’h (
F3'5'h ), Dfr, Ans, 3gt, Rt
F2
F3’h (
F3’h (
F3'5'h ), Dfr, 3gt
F3'5'h ), Dfr, 3gt
R2R3MYB family
F2
Anthocyanin 2
(1) Shun K Hirota, Kozue Nitta, Yuni Kim, Aya Kato, Nobumitsu Kawakubo, Akiko A Yasumoto,
Tetsukazu Yahara. (2012) Relative role of flower color and scent on pollinator attraction:
experimental tests using F1 and F2 hybrids of daylily and nightlily. PLoS ONE 7(6):e39010.
doi:10.1371/journal.pone.0039010
(2) Tomotaka Matsumoto, Akiko A. Yasumoto, Kozue Nitta, Tetsukazu Yahara, Hidenori
Tachida.(2013) Difference in flowering time as an isolating barrier. Journal of Theoretical Biology
317: 161-167. doi: 10.1016/j.jtbi.2012.10.001
[
]
1000
2500
6
CE-MS
6
100
MutS
5
5
1
PacBio
ChIP-Seq
[
]
MDS42
33
4
31
11
44
5 20
454FLX
A
B
A
B
4
Cefixime, Enoxacin,
Chloramphenicol, Amikacin
(1)
,
,
,
,
(
),
p.19-29(2011)
(2)“Epigenetic feedback regulation accelerates adaptation and evolution”, C. Furusawa, K. Kaneko,
PLoS One, in press
(
)
(
:
)
(
)
(
)
(Trunk-Ground
Anolis sagrei,
Anolis homolechis,
27-29
)
34
30-31
Anolis allogus,
Anolis mesteri
(1).
3
TRP
TRPA1
A. allogus
32
TRP
TRP
TRPM8
3
TRPA1 TRPM8
TRPA1
Patch-Clamp
(2).
3
5
)
2
(Illumina HiSeq2000)
homolechis RNAseq
(
4
26
(A. sagrei A. allogus)
RNAseq
A. sagrei A. allogus A. homolechis
WAD-ranking
33
3
:
A.
POMC
3
A. allogus
TRP
(
3)
Dermokine
A. allogus
RNAseq
TRP
(1) Cadis Diaz, A., Nagata, N., Katabuchi M., Diaz L.M., Echenique-Diaz, L.M., Akashi, H.D.,
Makino, T. and Kawata, M. (2013) Relative importance of habitat use, range expansion, and
speciation in local species diversity of Anolis lizards in Cuba. Ecosphere, in press
Drosophila prolongata
D. prolongata
D. prolongata
D. prolongata
D.
melanogaster
D. prolongata
D. prolongata
D. kurseongensis
KB866
D. prolongata
D. prolongata
D. prolongata
sensory bias
D. prolongata
RNAseq
D. prolongata
D. prolongata
D. prolongata
RNAseq
ENU mutagenesis
D. prolongata
D. prolongata
white
yellow
Juliane K. Ishida
(Phtheirospermum japonicum)
(1)
de novo
RNASeq
de novo assembly
RNA
58,000
Gene Ontology
hydrolase
2,6-dimethoxy-p-benzoquinone (DMBQ)
DMBQ
12
48
1577 contigs
30
DMBQ
1
8
qRT-PCR
(2)
6
RNAi
RNAi
10%
cDNA
(3)
RNASeq
1) Yoshida, S., Kameoka, H., Tempo, M., Akiyama, K., Umehara, M., Yamaguchi, S., Hayashi, H.,
Kyozuka, J., Shirasu, K. (2012) The D3 F-box protein is a key component in host strigolactone
responses essential for arbuscular mycorrhizal symbiosis. New Phytologist 196, 1208-1216.
2) Yoshida, S., Shirasu, K. (2012) Plants that attack plants: molecular elucidation of plant
parasitism. Curr. Opin. Plant Biol. 15, 708-713.
3) Den Herder, G., Yoshida, S., Antolín-Llovera, M., Ried, M., Parniske, M. (2012) Lotus
japonicus E3 ligase SEVEN IN ABSENTIA4 destabilizes the symbiosis receptor-.like kinase
SYMRK and negatively regulates rhizobial infection. Plant Cell, 24, 1691-1707
Pax1
Alx1
Alx1
Alx1
VEGF
Alx1
10
NGS
Alx1 VEGF
in silico
Pax1
tcf2
Tbx1
Pax1
tcf21
hybridization
foxA2
Pax1
tcf21
Double in situ
Pax1
Tbx1
Tbx1
Tbx1
Pax1 Tbx1
Pax1
Pax1
Tbx1
Pax1
Pax1/9
Pax9
Pax1
Tbx1
Tbx1
Pax1/9
Pax9
Heterochronic Activation of VEGF Signaling and the Evolution of the Skeleton in Echinoderm
Pluteus Larvae. Yoshiaki Morino, Hiroyuki Koga, Kazunori Tachibana, Eiichi Shoguchi, Masato
Kiyomoto and Hiroshi Wada. Evolutuion and Development 14: 428-436 (2012)
10.1111/j.1525-142X.2012.00563.x
COMPLEX ADAPTIVE TRAITS Newsletter Vol. 3 No. 10
COMPLEX ADAPTIVE TRAITS Newsletter
URL http://staff.aist.go.jp/t-fukatsu/SGJHome.html