SUCEST SUCEST: Felipe Rodrigues da Silva Embrapa Recursos Genéticos e Biotecnologia o projeto genoma da cana-de-açúcar

SUCEST

SUCEST:SUCEST:

Felipe Rodrigues da Silva

Embrapa Recursos Genéticos e Biotecnologia

o projeto genoma da cana-de-açúcar.

SUCEST

Crescimento do GenBank

14.396

3.841

11.101

2.0091.160

652

0

3000

6000

9000

12000

15000

18000

1980 1983 1986 1989 1992 1995 1998 2001

ano

pa

res

de

ba

se

(m

ilh

õe

s)

Volume de dados disponíveis publicamente

SUCEST

Crescimento do GenBank

0,680338

14.396

3.841

11.101

2.009

1.160652

0,1

1

10

100

1000

10000

100000

1980 1983 1986 1989 1992 1995 1998 2001

ano

pa

res

de

ba

se

(m

ilh

õe

s)

Volume de dados disponíveis publicamente

http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html

SUCEST

Genomas completos de organismos

http://wit.integratedgenomics.com/GOLD/

Genomas completos (totais não cumulativos)

2 3 7 7 9 18

1.3 Gb

0

3

6

9

12

15

18

1995 1996 1997 1998 1999 2000ano

ge

no

ma

s

1

10

100

1000

10000

mil

hõ

es

de

ba

se

s

genomas

Mb

SUCEST

SUCEST

SUCEST

SOPÃOde letrinhas...

A

AA

A

A

A

AA

A

A

T TT T

T TT

T

T

TT

G

G

GG

G

G

G

G

G

C

C

C

C

C

C

C

C

CC

C

A

AA

A

A

A

AA

A

A

T TT T

T TT

T

TT

G

G

GG

GG

C

C

C

C

C

C

C

C

CC

C

A

AA

A

A

A

AA

A

A

TT TT

TTT

T

T

TT

G

G

GG

G

G

G

G

G

C

C

C

C

C

C

C

C

CC

C

AA

A

AA

AA

A

A

T TT

T TT

T

T

T

G

G

GG

G

G

G

G

C

C

C

C

C

C

C

CC

A

AA

A

A

A

AA

A

A

T TT T

T TT

T

T

TT

G

G

GG

G

G

G

G

G

C

C

C

C

C

C

C

C

CC

C

SUCEST

Cana-de-açúcar

• Cultivada em mais de 90 países

• Ocupando cerca de 20 milhões de hectares

• Família das Gramíneas (Poace)

http://apps.fao.org

SUCEST

A cana-de-açúcar no Brasil

• 25% da produção mundial

• 300 milhões de tons.

• 5 milhões de hectares plantados

• 14.5 milhões de tons. de açúcar

• 15.3 bilhões de litros de álcool

• 350 industrias

• 50 mil produtores

• 1.4 milhões de empregos direto

• 3.6 milhões de empregos indiretos

SUCEST

Origem e tamanho

• Saccharum officinarum

2n = 80

Saccharum spontaneum

2n = 64 ou 2n = 112

10 – 25%

X

S. berberi, S. sinence, S. robustum

conjunto não-reduntante = 930 Mbp

Sorgo = 760 Mbp

Arroz = 430 Mbp

• 2C = 7.440 Mbp 2n = 100-130

D'Hont, A. and Glaszmann, J. C. 2001. Proc Int Soc Sugarcane Technol 24: 556-559.

SUCEST

Projeto Genoma

Seqüenciamento Completo do Genoma– Região Gênica e Região Intergênica

Estrutural

FuncionalEST – Expressed Sequence Tag

–Regiões que codificam proteínas (Genes)

SUCEST

Seqüenciamento Completo

...ATGTTGGGCCACAGTTGACCATTGAAACTGGTTGACCATTGAAACTGACCTTGACGTAACGTGGTA....

Genomic DNA

Biblioteca de BACs

Mapa físico

BAC a ser seqüenciado

Clones Shotgun

Seqüência

...ATGTTGGGCCACAGTTGACCATTGAAACTGACCTTGACGTAACGTGGTA... Montagem

SUCEST

EST – Expressed Sequence Tag

Clonagem em E. coliSeqüenciamento

ACCTGATGGCATTTCCATCAAGCTGACCTGGAAATCGTTGGCCDNA gene Bgene A

Proteína NH2 COOHNH2 COOH

3´5´mRNA

Dogma Central da Biologiainserçãoem vetor

cDNA

SUCEST

SUCEST

• Total de Entradas 1,528,715• Homo sapiens 967,015 (63,4%)

• Plantas (total) 73,087 (4.8%)

• Mus musculus + domesticus (camundongo) 306,544• Caenorhabditis elegans 72,521• Arabidopsis thaliana 36,173• Drosophila melanogaster 27,625• Oryza sativa (arroz) 25,844• Rattus sp. (rato) 20,311• Brugia malayi (nematoide parasita) 13,641• Toxoplasma gondii 10,671• Emericella nidulans 5,787• Schistosoma mansoni 3,659• Trypanosoma brucei rhodesiense 3,519• Danio rerio (zebrafish) 3,373• Saccharomyces cerevisiae 3,042• Zea mays (milho) 1,783• Leishmania major 1,692

• Saccharum sp. 495• Outros ~ 20,000

GenBank - dbEST Março de 1998

http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html

SUCEST

Os Objetivos do projeto SUCEST

• Identificar 50.000 genes únicos

(ou seqüenciar 300.000 ESTs)

• Desenvolver um Banco de Dados para a cana-de-açúcar

• Disponibiilizar este Banco de Dados para grupos de Data Mining

• Análise funcional dos ESTs

SUCEST

O Cronograma

Data Meta

Jul/1999 Distribuição dos Primeiros Clones

Dec/1999 20,000 ESTs

Jul/2000 60,000 ESTs

Dec/2000 100,000 ESTs

Jul/2001 140,000 ESTs

Dec/2001 180,000 ESTs

Jul/2002 220,000 ESTs

Dec/2002 260,000 ESTs

Jul/2003 300,000 ESTs

SUCEST

As Bibliotecas de cDNATecidos / Órgãos

– Raiz

– Meristema

– Caule

– Sementes

– Flores

– Cartucho da Folha

– Zona de Transição Folha-Raiz

– Gema Lateral

– Calli

– Plântulas imaturas

– Plântulas infectadas com Herbaspirillum rubrisubalbicans

– Plântulas infectadas com Gluconacetobacter diazotroficans

Variedades

– SP80-3280

– SP70-1143

– SP80-87432

– RB 845298

– RB 805028

– PB5211 X P57150-4

SUCEST

Os Laboratórios de Seqüenciamento

USP (SP)(3)

BIOINFORMATICAUNICAMP (CA)

UNESP (BT)(2)

ESALQ (PI)(3)

USP (RP)(1)

UNAERP (RP)(1)

UMC (MC)(1)

UNIVAP (SJ)(1)

UNESP (JB)(2)

UFSCAR (AR)(1)

UFSCAR (SC)(1)

USP (SC)(1)

UNESP (RC)(1)

IAC (CA)(1)

IAC (CO)(1)

UNICAMP (CA)(1)

RIO DE JANEIROPERNAMBUCO ALAGOAS

ABI 377-96

SUCEST

EST – Expressed Sequence Tag

Clonagem em E. coliSeqüenciamento

ACCTGATGGCATTTCCATCAAGCTGACCTGGAAATCGTTGGCCDNA gene Bgene A

Proteína NH2 COOHNH2 COOH

3´5´mRNA

Dogma Central da Biologiainserçãoem vetor

cDNA

291.689 reads260.352 clones

266.016 clones

SUCEST

Limpeza das seqüências

• remoção de seqüências ribossômicas

• remoção de seqüências de vetor

• remoção da região de poliA

• corte por qualidade

• eliminação das derrapagens

SUCEST

poliA

AGGGGAGAATTTATGATCCCCTAGTACACCCGGCAGGACCGGTCCGGAATTCCCCGGTCGACCCAC GCGTCCGCTACAACAACAGCAGCAGCTTCCATTTACCTTGTCGGCTGTTGCAACCGCTGCTGCCTA CCACCAGCAACTACAGCTGCTACCAGTTAACCCATTGGCACTGGCTAACCCATTGGCTGCTGCCTT CCTGCAGCAGCAACAATTGCTGCCATTCAACCAGATGTCTTTGATGAACCCTGCCTTGTCGTGGTA GCAACCCATCGTTGGAGGTGCCATCTTCTAGAATACAAATGAGTTGTACTTGATAACAATGTTCTT GTGTCGGCGTGTGCAACTTCCCAGAAATAATCAATACATTGATTGAGATTTANAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAATATAATTAAAATAAAAAAATTTATAAAAAAAAAAAAATAATT TTTTTTTATAAAAAATAAATATAAAATAAAAAGGGGGGGCCGTTTTAAAGGAACAAAGTTTAAGAC CGGGGGTATGAAAGGGAAAATTTTTTTATATAGGGCCCCAAAATTAAATACATGGGCCGGTGTTAA CAACGGCGGGAGGGAAAAAACCTGGGGGTTACCAATTTAAAGCCGTGGAAAAAATCCCTTTTTTCA AGTGGGGTAAAAAGAAAAGGCCCCACCCATCGCCCTTCCAAAAATTGCCCCCCTTAAAGGAAAAAG GACACCCCCTTTTGGGCGCATATAACCGGGGGGGTGGGGGTACCCCCAAGGGAACTTATATTTTTC AGGCCTCATAGCCCTTTTTTTTTTTTTTTTTTTTTTTTTCAAGGTAGCGGGTTTCCCAGGAAAATT AAAAGGGGGGTCCTTTTGGGTAATAATGTTTTN

SUCEST

poliA

AGGGGAGAATTTATGATCCCCTAGTACACCCGGCAGGACCGGTCCGGAATTCCCCGGTCGACCCAC GCGTCCGCTACAACAACAGCAGCAGCTTCCATTTACCTTGTCGGCTGTTGCAACCGCTGCTGCCTA CCACCAGCAACTACAGCTGCTACCAGTTAACCCATTGGCACTGGCTAACCCATTGGCTGCTGCCTT CCTGCAGCAGCAACAATTGCTGCCATTCAACCAGATGTCTTTGATGAACCCTGCCTTGTCGTGGTA GCAACCCATCGTTGGAGGTGCCATCTTCTAGAATACAAATGAGTTGTACTTGATAACAATGTTCTT GTGTCGGCGTGTGCAACTTCCCAGAAATAATCAATACATTGATTGAGATTTANAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAATATAATTAAAATAAAAAAATTTATAAAAAAAAAAAAATAATT TTTTTTTATAAAAAATAAATATAAAATAAAAAGGGGGGGCCGTTTTAAAGGAACAAAGTTTAAGAC CGGGGGTATGAAAGGGAAAATTTTTTTATATAGGGCCCCAAAATTAAATACATGGGCCGGTGTTAA CAACGGCGGGAGGGAAAAAACCTGGGGGTTACCAATTTAAAGCCGTGGAAAAAATCCCTTTTTTCA AGTGGGGTAAAAAGAAAAGGCCCCACCCATCGCCCTTCCAAAAATTGCCCCCCTTAAAGGAAAAAG GACACCCCCTTTTGGGCGCATATAACCGGGGGGGTGGGGGTACCCCCAAGGGAACTTATATTTTTC AGGCCTCATAGCCCTTTTTTTTTTTTTTTTTTTTTTTTTCAAGGTAGCGGGTTTCCCAGGAAAATT AAAAGGGGGGTCCTTTTGGGTAATAATGTTTTN

SUCEST

Quality trimming

CGGAAGACTGGAGTCGTCGCTGCGGCACCGGTCCGGAATTCCCGGGTCGACCCACGCGTCCGGCCG CCGCCACCGCATCCCTTGCAGCCCCAATCCCCCACGGCGACCATGGCCGGCGCGCAGGAGTCCCTG TCCCTGGTGGGCACGATGCGTGGCCACAACGGCGAGGTGACGGCGATCGCCACCCCGATCGACAAC TCGCCGTTCATCGTCTCCTCCTCCCGCGACAAGTCCGTGCTGGTGTGGGACCTGCAAAACCCGGTC CACTCCACCCCGGAATCCGGCGCCACCGCCGACTACGGCGTCCCCTTCCGCCGCCTCACCGGCCAC TCCCACTTCGTCCAGGACGTCGTCCTCAGCTCCGACGGCCAGTTCGCCCTCTCCGGCTCCTGGGAC GGCGAGCTCCGCCTCTGGGACCTCTCCACCGGCGTCACCACCCGCCGCTTCGTCGGCCACGAGAAG GACGTCCTCTCCGTCGCCTTCTCCGTCGACAACCGCCAGATCGTCTCCGCGTCCCGCGACAAGACC ATCAAGCTCTGGAACACCCTCGGTGAGTGCAAGTACACCATTGGTGGCGACCTCGGCGGCGGGGAG GGCCACAACGGGTGGGTCTCCTGCGTCAGGTTCTTCCCCAACACCTTTCAGGCCACCATTGTCTCC GGATTCTGGGACCGCACCGTCAGGTCTGGAACCTTACCAACTGCAAGCTGCGATGCACTCTCGATG CCCACGCGGCTATGTTAACGCCGTCGCC

ACGTX: <10 ACGTX: >=10 and <15ACGTX: >=15 and <20ACGTX: >=20 and <25ACGTX: >=25 and <30ACGTX: >=30

754 bases

SUCEST

Quality trimming

CGGAAGACTGGAGTCGTCGCTGCGGCACCGGTCCGGAATTCCCGGGTCGACCCACGCGTCCGGCCG CCGCCACCGCATCCCTTGCAGCCCCAATCCCCCACGGCGACCATGGCCGGCGCGCAGGAGTCCCTG TCCCTGGTGGGCACGATGCGTGGCCACAACGGCGAGGTGACGGCGATCGCCACCCCGATCGACAAC TCGCCGTTCATCGTCTCCTCCTCCCGCGACAAGTCCGTGCTGGTGTGGGACCTGCAAAACCCGGTC CACTCCACCCCGGAATCCGGCGCCACCGCCGACTACGGCGTCCCCTTCCGCCGCCTCACCGGCCAC TCCCACTTCGTCCAGGACGTCGTCCTCAGCTCCGACGGCCAGTTCGCCCTCTCCGGCTCCTGGGAC GGCGAGCTCCGCCTCTGGGACCTCTCCACCGGCGTCACCACCCGCCGCTTCGTCGGCCACGAGAAG GACGTCCTCTCCGTCGCCTTCTCCGTCGACAACCGCCAGATCGTCTCCGCGTCCCGCGACAAGACC ATCAAGCTCTGGAACACCCTCGGTGAGTGCAAGTACACCATTGGTGGCGACCTCGGCGGCGGGGAG GGCCACAACGGGTGGGTCTCCTGCGTCAGGTTCTTCCCCAACACCTTTCAGGCCACCATTGTCTCC GGATTCTGGGACCGCACCGTCAGGTCTGGAACCTTACCAACTGCAAGCTGCGATGCACTCTCGATG CCCACGCGGCTATGTTAACGCCGTCGC


753 bases

SUCEST

Quality trimming

CGGAAGACTGGAGTCGTCGCTGCGGCACCGGTCCGGAATTCCCGGGTCGACCCACGCGTCCGGCCG CCGCCACCGCATCCCTTGCAGCCCCAATCCCCCACGGCGACCATGGCCGGCGCGCAGGAGTCCCTG TCCCTGGTGGGCACGATGCGTGGCCACAACGGCGAGGTGACGGCGATCGCCACCCCGATCGACAAC TCGCCGTTCATCGTCTCCTCCTCCCGCGACAAGTCCGTGCTGGTGTGGGACCTGCAAAACCCGGTC CACTCCACCCCGGAATCCGGCGCCACCGCCGACTACGGCGTCCCCTTCCGCCGCCTCACCGGCCAC TCCCACTTCGTCCAGGACGTCGTCCTCAGCTCCGACGGCCAGTTCGCCCTCTCCGGCTCCTGGGAC GGCGAGCTCCGCCTCTGGGACCTCTCCACCGGCGTCACCACCCGCCGCTTCGTCGGCCACGAGAAG GACGTCCTCTCCGTCGCCTTCTCCGTCGACAACCGCCAGATCGTCTCCGCGTCCCGCGACAAGACC ATCAAGCTCTGGAACACCCTCGGTGAGTGCAAGTACACCATTGGTGGCGACCTCGGCGGCGGGGAG GGCCACAACGGGTGGGTCTCCTGCGT


618 bases

SUCEST

Resultado de blastX

>gi|1346109|sp|P49027|GBLP_ORYSA GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN (GPB-LR) (RWD) pir||T03764 protein RWD - rice dbj|BAA07404.1| (D38231) RWD [Oryza sativa] Length = 334

Score = 315 bits (798), Expect = 4e-85 Identities = 150/170 (88%), Positives = 156/170 (91%) Frame = +1

Query: 109 MAGAQESLSLVGTMRGHNGEVTAIATPIDNSPFIVSSSRDKSVLVWDLQNPVHSTPESGA 288 MAGAQESL L G M GHN VTAIATPIDNSPFIVSSSRDKS+LVWDL NPV + E Sbjct: 1 MAGAQESLVLAGVMHGHNDVVTAIATPIDNSPFIVSSSRDKSLLVWDLTNPVQNVGEGAG 60

Query: 289 TADYGVPFRRLTGHSHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHEKDV 468 ++YGVPFRRLTGHSHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGH+KDVSbjct: 61 ASEYGVPFRRLTGHSHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHDKDV 120

Query: 469 LSVAFSVDNRQIVSASRDKTIKLWNTLGECKYTIGGDLGGGEGHNGWVSC 618 LSVAFSVDNRQIVSASRD+TIKLWNTLGECKYTIGGDLGGGEGHNGWVSCSbjct: 121 LSVAFSVDNRQIVSASRDRTIKLWNTLGECKYTIGGDLGGGEGHNGWVSC 170

read trimmado

SUCEST

Resultado de blastX

>gi|1346109|sp|P49027|GBLP_ORYSA GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN (GPB-LR) (RWD) pir||T03764 protein RWD - rice dbj|BAA07404.1| (D38231) RWD [Oryza sativa] Length = 334

Score = 352 bits (893), Expect(2) = e-100 Identities = 168/192 (87%), Positives = 175/192 (90%) Frame = +1

Query: 109 MAGAQESLSLVGTMRGHNGEVTAIATPIDNSPFIVSSSRDKSVLVWDLQNPVHSTPESGA 288 MAGAQESL L G M GHN VTAIATPIDNSPFIVSSSRDKS+LVWDL NPV + E Sbjct: 1 MAGAQESLVLAGVMHGHNDVVTAIATPIDNSPFIVSSSRDKSLLVWDLTNPVQNVGEGAG 60

Query: 289 TADYGVPFRRLTGHSHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHEKDV 468 ++YGVPFRRLTGHSHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGH+KDVSbjct: 61 ASEYGVPFRRLTGHSHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHDKDV 120

Query: 469 LSVAFSVDNRQIVSASRDKTIKLWNTLGECKYTIGGDLGGGEGHNGWVSCVRFFPNTFQA 648 LSVAFSVDNRQIVSASRD+TIKLWNTLGECKYTIGGDLGGGEGHNGWVSCVRF PNTFQ Sbjct: 121 LSVAFSVDNRQIVSASRDRTIKLWNTLGECKYTIGGDLGGGEGHNGWVSCVRFSPNTFQP 180

Query: 649 TIVSGFWDRTVR 684 TIVSG WDRTV+Sbjct: 181 TIVSGSWDRTVK 192

read inteiro

SUCEST

Determinação do limiar de qualidade

Quality window parameters

-300

-250

-200

-150

-100

-50

0

50

100

150

200

0 2 4 6 8 10 12 14 16

bases bellow threshold

dis

tan

ce fr

om

bla

st h

it en

d

quality threshold

20

10

16

18

14

12

9

quality threshold

SUCEST

Quality trimming



754 bases

SUCEST

Quality trimming

CGGAAGACTGGAGTCGTCGCTGCGGCACCGGTCCGGAATTCCCGGGTCGACCCACGCGTCCGGCCG CCGCCACCGCATCCCTTGCAGCCCCAATCCCCCACGGCGACCATGGCCGGCGCGCAGGAGTCCCTG TCCCTGGTGGGCACGATGCGTGGCCACAACGGCGAGGTGACGGCGATCGCCACCCCGATCGACAAC TCGCCGTTCATCGTCTCCTCCTCCCGCGACAAGTCCGTGCTGGTGTGGGACCTGCAAAACCCGGTC CACTCCACCCCGGAATCCGGCGCCACCGCCGACTACGGCGTCCCCTTCCGCCGCCTCACCGGCCAC TCCCACTTCGTCCAGGACGTCGTCCTCAGCTCCGACGGCCAGTTCGCCCTCTCCGGCTCCTGGGAC GGCGAGCTCCGCCTCTGGGACCTCTCCACCGGCGTCACCACCCGCCGCTTCGTCGGCCACGAGAAG GACGTCCTCTCCGTCGCCTTCTCCGTCGACAACCGCCAGATCGTCTCCGCGTCCCGCGACAAGACC ATCAAGCTCTGGAACACCCTCGGTGAGTGCAAGTACACCATTGGTGGCGACCTCGGCGGCGGGGAG GGCCACAACGGGTGGGTCTCCTGCGT


618 bases

SUCEST

Quality trimming



base 684

SUCEST

Quality trimming


719 bases

antes dif. homol. dif. depois

618 - 66 684 + 35 719

SUCEST

Determinação do limiar de qualidade

Quality window parameters

-300

-250

-200

-150

-100

-50

0

50

100

150

200

0 2 4 6 8 10 12 14 16

bases bellow threshold

dis

tan

ce fr

om

bla

st h

it en

d

quality threshold

20

10

16

18

14

12

9

quality threshold

SUCEST

Exemplo de derrapagem

SUCEST

todos os reads291,689 reads

864.5 ±186.3 comprimento médio399.5 ±161.3 # médio bases >= 20/read

283,216 reads

remoção de ribossômicos

283,216 reads

busca de vetores

275,436 reads

corte de vector + poliA

273,728 reads

corte por qualidade

273,728 reads

corte de vetores em extremidade

258,107 reads

corte de derrapagens

256,101 reads

corte de poliA em extremidade

reads trimados237,954 reads

642.6 ±139.8 avg. read size397.8 ±120.1 avg bases >= 20/read

remoção de seqs de baixa qualidade

SUCEST

cluster size

(reads) HS X phrap X CAP3 X HS

total

common

1 32202 13731 18535 11634 16838 14296 10744

2 12440 5617 9207 4869 7665 4852 3792

3 6752 2402 5192 2151 4193 1984 1441

4 4225 1239 3329 1145 2709 992 697

5 2856 676 2360 700 1872 521 344

6 2098 442 1806 482 1452 354 231

7 1582 288 1362 317 1115 220 144

8 1245 202 1091 242 862 153 99

9 974 156 913 186 720 113 72

10 776 105 752 143 634 74 44

11 639 76 607 99 511 54 30

12 492 71 547 99 429 46 32

13 437 47 454 90 400 40 25

14 366 42 391 40 341 26 13

15 306 31 390 50 295 18 11

16 273 25 279 35 275 18 8

17 225 15 273 23 235 11 4

18 177 11 227 15 191 5 2

19 124 6 177 18 176 5 3

>=20 1192 40 1814 87 2228 23 12

total 69381 25222 49706 22425 43141 23805 17748

SUCEST

Discrepância interna

SUCEST

Discrepância interna

SUCEST

Teste de consistência interna

0

1

2

3

4

5

6

7

8

9

0 10 20 30 40 50 60 70 80

% of discrepancy in reads

% o

f d

isc

rep

an

t re

ad

s

hs (204k)

old-trim (219k)

SUCEST


0

1

2

3

4

5

6

7

8

9

0 10 20 30 40 50 60 70 80


% o

f d

isc

rep

an

t re

ad

s

hs (204k)

phrap (218k)

cap3 (221k)

SUCEST


0

1

2

3

4

5

6

7

8

9

0 10 20 30 40 50 60 70 80


% o

f d

isc

rep

an

t re

ad

s

hs (204k)

phrap (218k)cap3 (221k)

old-trim (219k)

SUCEST

Teste de consistência externa

0,00000

0,00005

0,00010

0,00015

0,00020

75 80 85 90 95 100

% identity

% p

oss

ible

mat

ches

hsold-trim

SUCEST


0,00000

0,00005

0,00010

0,00015

0,00020

75 80 85 90 95 100

% identity

% p

ossib

le m

atc

hes

cap3phraphs

SUCEST


0,00000

0,00005

0,00010

0,00015

0,00020

75 80 85 90 95 100

% identity

% p

oss

ible

mat

ches

cap3phraphsold-trim

SUCEST

Números totais

Total sequences 291,689

cDNA clones sequenced (5’or 3’) 260,352

5’ end sequences 259,325

3’ end sequences 32,364

Total high-quality sequences 237,954

Success index (%) 81.6

Average insert size (bp) 1,250

Average sequence size (bp) 864 / 642

Bases with phred quality = 20/read 399

SUCEST

Números totais

Trotal sequences analyzed 237,954

Number of contigs 26,803

Number of singletons 16,338

Number of sugarcane assembled sequences (SAS) 43,141

Number of assembled sequences matching to known genes 27,833 (64.5%)

Number of clones with full length inserts 14,409 (

SUCEST

Contribuição específica

por biblioteca

Número de

ESTs SAS contigs singletons % contribuição

AD1 8,137 1,474 1,200 3.4

AM1 5,991 841 664 1.9

AM2 6,629 982 705 2.3

CL6 3,511 595 467 1.4

FL1 8,412 1,753 1,465 4.1

FL3 5,714 840 667 1.9

FL4 7,289 1,082 886 2.5

FL5 5,115 861 744 2.0

FL8 3,362 378 337 0.9

HR1 5,070 717 519 1.7

LB1 3,699 459 369 1.1

LB2 5,402 790 650 1.8

LR1 6,653 984 819 2.3

LR2 2,329 299 254 0.7

LV1 3,068 384 327 0.9

RT1 4,227 569 484 1.3

RT2 5,819 942 728 2.2

RT3 4,356 614 478 1.4

RZ1 2,012 205 175 0.5

RZ2 3,177 385 301 0.9

RZ3 6,528 929 752 2.1

SB1 7,407 1,313 1,132 3.0

SD1 4,459 792 642 1.8

SD2 4,099 857 632 2.0

ST1 4,359 645 523 1.5

ST3 4,519 507 418 1.2

• 47% dos SAS são formados

por reads oriúndos de uma

única biblioteca

• 38% dos SAS tecido-especícos

são singletons

SUCEST

Classificação funcional

SUCEST

Porcentagem por órgão

Functional Category AD/HR AM/LB CL FL LV RT SD ST X±sd

Amino acid metabolism 6.0 4.0 5.9 4.2 3.9 7.3 4.6 4.9 5.1±1.2

Bioenergetics 17.3 12.6 17.5 12.6 12.0 21.9 16.9 15.8 15.8±3.3

Cellular communication/ Signal transduction

10.7 11.1 9.8 11.0 10.1 10.8 7.9 11.8 10.4±1.2

Cellular dynamics 18.5 19.7 15.0 19.1 18.6 18.3 15.1 20.1 18.1±2.0

DNA metabolism 2.5 3.8 2.4 3.8 4.8 2.2 1.8 1.7 9±1.1

Lipid, fatty-acid and isoprenoid metabolism

4.0 3.5 3.2 3.8 3.7 4.4 4.6 3.5 3.8±0.5

Mobile genetic elements 1.5 1.3 2.0 1.4 1.0 1.1 0.7 1.1 1.3±0.4

Nitrogen, sulphur and phosphate metabolism

0.9 0.7 0.8 0.6 0.7 1.7 0.7 0.7 0.9±0.3

Nucleotide metabolism 2.5 2.5 3.1 2.5 2.2 2.4 2.2 2.6 2.5±0.3

Plant grow and development 3.8 3.4 4.5 3.5 3.4 4.0 2.9 4.1 3.7±0.5

Protein metabolism 16.9 18.7 17.2 18.4 21.7 16.5 20.5 16.5 18.3±1.9

RNA metabolism and transcription

6.7 7.2 7.1 6.8 6.8 5.6 5.0 6.4 6.5±0.8

Secondary metabolism 6.1 3.9 5.2 4.5 4.0 8.4 5.5 6.8 5.5±1.5

Storage proteins 0.2 0.1 0.2 0.1 0.1 0.3 5.7 0.2 0.9±1.9

Stress response 14.7 12.7 14.4 12.8 13.4 17.6 17.8 15.7 14.9±2.0

Transport 8.5 6.7 6.3 7.1 6.7 8.0 9.2 7.8 7.5±1.0

Putative proteins 15.2 16.2 15.8 16.8 15.1 14.0 12.7 15.8 15.2±1.3

Unable to classify 6.3 6.1 6.4 6.7 6.3 5.8 5.3 6.3 6.1±0.4

SUCEST

SAStecido- específicas

Número

de ESTs Melhor hit biblioteca

360 (Y17556) alpha kafirin [Sorghum bicolor] SD

103 (A23207) zein zA1 [Zea mays] SD

42 (AF232008) beta-glucosidase aggregating factor precursor [Zea mays] RT

24 (AC007789) putative low molecular early light-inducible protein [Oryza sativa] SD

22 (AP002820) putative peroxidase [Oryza sativa] RT

19 (X56337) alpha-amylase [Oryza sativa] CL

18 (AP000374) cyclopropane fatty acid synthase [Arabidopsis thaliana] FL

SUCEST

• Total de Entradas 1,528,715• Homo sapiens 967,015 (63,4%)

• Plantas (total) 73,087 (4.8%)

• Mus musculus + domesticus (camundongo) 306,544• Caenorhabditis elegans 72,521• Arabidopsis thaliana 36,173• Drosophila melanogaster 27,625• Oryza sativa (arroz) 25,844• Rattus sp. (rato) 20,311• Brugia malayi (nematoide parasita) 13,641• Toxoplasma gondii 10,671• Emericella nidulans 5,787• Schistosoma mansoni 3,659• Trypanosoma brucei rhodesiense 3,519• Danio rerio (zebrafish) 3,373• Saccharomyces cerevisiae 3,042• Zea mays (milho) 1,783• Leishmania major 1,692

• Saccharum sp. 495• Outros ~ 20,000


SUCEST

• Total de Entradas 7,692,809• Homo sapiens 3,369,459 (43.8%)

• Plantas (total) 1,099,102 (14.3 %)

• Glycine max (soja) 160,500• Arabidopsis thaliana 113,000• Medicago truncatula (barrel medic) 112,458• Lycopersicon esculentum (tomate) 107,226• Zea mays (milho) 86,999• Oryza sativa (arroz) 72,657• Hordeum vulgare (cevada) 68,480• Chlamydomonas reinhardtii 64,973• Sorghum bicolor 62,642• Triticum aestivum (trigo) 58,141• Pinus taeda (loblolly pine) 34,896• Lotus japonicus 27,078• Solanum tuberosum (batata) 26,177• Gossypium arboreum 20,978• Sorghum propinquum 17,974• Mesembryanthemum (ice plant) 14,033• Gossypium hirsutum (algodão) 9,438• Secale cereale 8,123• Saccharum sp. 495• Outras Plantas (67 spp.) 32.834


SUCEST

• Total de Entradas 12,845,578• Homo sapiens 4,691,979 (36.5%)

• Plantas (total) 2,279,170 (17.4 %)

• Glycine max (soja) 284,714 • Triticum aestivum (trigo) 256,593 • Hordeum vulgare (cevada) 240,882 • Zea mays (milho) 180,587 • Arabidopsis thaliana 174,624 • Medicago truncatula (barrel medic) 170,500 • Lycopersicon esculentum (tomate) 148,346• Chlamydomonas reinhardtii 130,324 • Oryza sativa (arroz) 108,429 • Solanum tuberosum (batata) 94,420 • Sorghum bicolor 84,712 • Lactuca sativa (alface) 68,188 • Pinus taeda (loblolly pine) 60,226 • Physcomitrella patens 50,250 • Helianthus annuus (girassol) 44,961• Gossypium arboreum (algodão) 38,894 • Lotus japonicus 32,096 • Sorghum propinquum 21,387 • Saccharum sp. 495• Outras Plantas (78 spp.) 88.542

GenBank - dbEST Setembro de 2002

http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html

SUCEST

Genetics and Molecular Biology1. The libraries that made SUCEST

2. Bioinformatics of the sugarcane EST project

3. Trimming and clustering sugarcane ESTs

4. The sugarcane signal transduction (SUCAST) catalogue: prospecting signal transduction in sugarcane

5. In silico characterization and expression analyses of sugarcane putative sucrose non-fermenting-1 (SNF1) related kinases

6. Identification of 14-3-3-like protein in sugarcane (Saccharum officinarum)

7. A search for homologues of plant photoreceptor genes and their signaling partners in the sugarcane expressed sequence tag (Sucest) database

8. Phylogenetic relationships between Arabidopsis and sugarcane bZIP transcriptional regulatory factors

9. Identification of sugarcane cDNAs encoding components of the cell cycle machinery

10. Dissecting the sugarcane expressed sequence tag (SUCEST) database: unraveling flower-specific genes

11. Molecular chaperone genes in the sugarcane expressed sequence database (SUCEST)

12. Oxidative stress response in sugarcane

13. In silico differential display of defense-related expressed sequence tags from sugarcane tissues infected with diazotrophic endophytes

14. Mechanisms of sugarcane response to herbivory

15. Base excision repair in sugarcane

19. Preliminary analysis of microsatellite markers derived from sugarcane expressed sequence tags (ESTs)

20. Sequence polymorphism from EST data in sugarcane: a fine analysis of 6-phosphogluconate dehydrogenase genes

21. A search for markers of sugarcane evolution

22. Sugarcane genes related to mitochondrial function

23. Mitochondrial and chloroplast localization of FtsH-like proteins in sugarcane based on their phylogenetic profile

24. Patterns of expression of cell wall related genes in sugacane

25. Expression of sugarcane genes induced by inoculation with Gluconacetobacter diazotrophicus and Herbaspirillum rubrisubalbicans

26. Identifying sugarcane expressed sequences associated with nutrient transporters and peptide metal chelators

27. Prospecting sugarcane genes involved in aluminum tolerance

28. N-glycosylation in sugarcane

29. Sugarcane expressed sequences tags (ESTs) encoding enzymes involved in lignin biosynthesis pathways

30. Biosynthesis of secondary metabolites in sugarcane

31. Identification of sugarcane genes involved in the purine synthesis pathway

32. A new member of the chalcone synthase (CHS) family in sugarcane

33. Classification. expression pattern and comparative analysis of sugarcane expressed analysis of sugarcane expressed sequences tags (ESTs) encoding glycine-rich proteins (GRPs)

34. Identification. classification and expression pattern analysis of sugarcane cysteine proteinases

35. Identification of metalloprotease gene families in sugarcane

36. Sugarcane phytocystatins: Identification. classification and expression pattern analysis

16. DNA repair-related genes in sugarcane expressed sequence tags (ESTs)

17. Distribution of DNA repair-related ESTs in sugarcane

18. Survey of transposable elements in sugarcane expressed sequence tags (ESTs)

SUCEST

Genetics and Molecular Biology

http://www.sbg.org.br/revista24_index.htm

SUCEST

Grupo do SUCEST

SUCEST

Uma parte do LBI

SUCEST

Uma parte do LBI

SUCEST

Os trimmadores

Grupo Genoma - CBMEG

Grupo Genoma - CBMEG

[email protected] http://www.lbi.ic.unicamp.br/

SUCEST

www.laerte.com.brwww.laerte.com.br

SUCEST

SUCEST

Documents

SUCEST SUCEST: Felipe Rodrigues da Silva Embrapa Recursos Genéticos e Biotecnologia o projeto genoma da cana-de-açúcar