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The Daphnia pulex cDNA sequencing project 

A major goal of the Daphnia Genome Project is the production and sequencing of full-length cDNA that are used to (1) create the Daphnia Gene Encyclopedia, (2) annotate the Daphniagenome sequence and (3) produce probes for the third generation microarray. This phase of the project involves researchers from Indiana University, the University of New Hampshire, the Joint Genome Institute and Dartmouth College.  This project is funded by the National Science Foundation Biocomplexity grant and by the US Department of Energy. The diversity of cDNA libraries reflect our need to enrich these resources with genes that are transcribed under ecologically relevant conditions.

The results of the cDNA efforts 

Table 1. The Daphnia pulexcDNA libraries supporting genomic research activities. cDNA clones were sequenced from both ends, except for library Log52 that was sequence only from the 5' end. Clone diversity is calculated by dividing the # of clusters (including clusters of 1 EST) by the # of clones. This estimate is inflated, especially for non-normalized libraries, by ignoring clones containing organelle transcripts (6% to 45% of ESTs are mitochondrial, depending on library). By contrast, the normalized libraries typically contain between <1% and 10% organelle ESTs.  All Daphniaisolates are from a naturally inbred population located witin an ephemeral pond a few meters from the Pacific coast in Oregon. The pond is found north of Florence on the east side of highway 101 at milepost 201 in Douglas County.  Log52 and Log50 are initial candidates for the genome sequencing project (a first time sequence pass was obtained from Log50) while the Chosen One libraries were created from the same clone whose genome was sequenced, assembled and soon to be annotated.

Daphnia pulex library ID

Date Created

Condition, Developmental Stage

# Arrayed Clones

# Sequenced Clones

# Nuclear ESTs

# Clusters†

# Clones†

% Clone Diversity

% Organelle ESTs

Non-normalized

 

 

 

 

 

 

 

 

 

Log52

26-Jun-03

Unchallenged, mixed

10,000

1,648

1,414

804

1,435

56

9.0

Log50-1

18-Mar-04

Hypoxia, adult

2,304

2,304

3,355

1,039

1,823

57

10.6

Log50-2

18-Mar-04

Hypoxia, juvenile

3,840

3,840

5,567

1,524

3,033

50

12.7

Log50-3

1-Apr-04

Low dose UV exposure, mixed

2,304

2,304

2,620

1,013

1,433

71

23.6

Log50-4§

1-Apr-04

High dose UV exposure, mixed

2,304

384

450

188

243

77

22.9

Log50-5

5-Mar-04

Unchallenged, juvenile

1,536

1,152

1,580

553

827

67

16.7

Log50-6

19-Jul-04

Low dose cadmium, mixed

2,688

2,688

4,048

1,209

2,170

56

12.8

Log50-7

19-Jul-04

Low dose arsenic, mixed

4,224

4,224

6,370

1,867

3,399

55

14.6

Log50-8

19-Jul-04

Low dose zinc, mixed

4,224

4,224

6,817

1,535

3,709

41

6.5

Log50-9

19-Jul-04

High dose mixed metals, mixed

4,608

4,608

7,185

1,863

3,770

49

14.4

Log50-10§

22-Jun-04

Unchallenged, mixed

3,840

384

390

159

232

69

14.6

Log50-11§

18-Dec-03

Unchallenged, mixed

4,992

384

405

167

238

70

30.0

Log50-12

8-Sep-04

Invertebrate (Chaoborus) predation, adult

4,608

4,608

6,542

2,034

3,511

58

17.7

Log50-13

8-Sep-04

Food starvation, juvenile

2,304

2,304

2,826

924

1,378

67

18.3

Log50-14

8-Sep-04

Food starvation, adult

2,304

2,304

2,684

860

1,291

67

23.1

Log50-15§

8-Sep-04

Microcystis fed, juvenile

2,304

384

307

150

175

86

44.8

Log50-16§

8-Sep-04

Microcystis fed, adult

2,304

384

368

164

208

79

39.2

Log50-17

8-Sep-04

Fish predation, juvenile

3,840

3,840

4,750

1,548

2,638

59

22.5

Log50-18§

8-Sep-04

Fish predation, adult

2,300

384

425

177

249

71

20.3

Log50-19§

8-Sep-04

Methyl Farnesoate hormone, juvenile

2,300

384

413

170

227

75

31.7

Log50-20

8-Sep-04

Methyl Farnesoate hormone, adult

3,840

3,840

4,833

1,323

2,604

51

11.8

Total

 

 

76,808

51,718

72,179

 

34,593

 

 

Daphnia pulex library ID

Date Created

Condition, Developmental Stage

# Arrayed Clones

# Sequenced Clones

# Nuclear ESTs

# Clusters†

# Clones†

% Clone Diversity

% Organelle ESTs

Normalized

 

 

 

 

 

 

 

 

 

Log50-21

22-Jun-04

Unchallenged, mixed

3840

5376

8962

3413

4762

72

0.7

Chosen One-1§

7-Feb-06

Females, juvenile

384

384

211

98

121

96

8.0

Chosen One-2

7-Feb-06

Females, adult

3456

3456

5313

2252

2821

84

1.5

Chosen One-3

7-Feb-06

Males, adult

4224

4224

5425

2168

2883

83

21.7

Chosen One-4

10-Apr-06

Low dose nickel, mixed

4224

4224

6484

2865

3599

86

0.5

Chosen One-5

10-Apr-06

Low dose copper, mixed

4224

4224

6852

2963

3685

85

1.3

Chosen One-6

10-Apr-06

Acid stress pH 6.0, mixed

3840

3840

6626

2870

3514

86

0.5

Chosen One-7

10-Apr-06

High salinity, mixed

3840

3840

6121

2645

3275

85

2.6

Chosen One-8

4-Apr-06

Fullerene nanoparticle, mixed

4224

4224

5643

2428

3044

84

14.1

Chosen One-9

11-May-06

Bacterial infection, mixed

3456

3456

5639

2553

2935

90

1.1

Chosen One-10

2-May-06

High dose mixed metals, mixed

3840

3840

4398

2030

2452

91

3.5

Chosen One-11

2-May-06

Low dose mixed metals, mixed

3456

3456

5407

2447

2967

89

0.8

Chosen One-12

11-May-06

Low dose monomethylarsenic III, mixed

4224

4224

6274

2768

3387

87

4.5

Chosen One-13

10-May-06

Titanium dioxide nanoparticle, mixed

4224

4224

5742

2490

3037

86

3.4

Chosen One-14

10-May-06

Microcystis fed, mixed

3072

3072

4734

2052

2522

86

8.1

Chosen One-15

10-May-06

Calcium starvation, mixed

3840

3840

5309

2278

2887

84

11.1

Total

 

 

58,368

59,904

89,140

 

47,891

 

 

§ Libraries failing stringent quality control checks and were therefore excluded from high throughput EST sequencing.
† These numbers are of clusters and clones of nuclear genes only.

Clones are individual cDNA isolates from the libraries, ESTs are sequences that passed stringent quality control measures, and clusters are assembled ESTs into overlapping sets that represent unique nuclear protein coding loci. 

Match the sequence IDs to the developmental and ecological conditions under investigation from cDNA libraries

LIBRARY/SEQUENCE NAME

TYPE†

SEX

STAGE

IN VIVO CONDITIONS

TISSUES FROM

CANA_Daphnia_pulex_Log50_Library_14

Standard

Mixed

Adult

Stressed by starvation

Jim Haney, University of New Hampshire

CANB_Daphnia_pulex_Log50_Library_13

Standard

Mixed

Juvenile

Stressed by starvation

Jim Haney, University of New Hampshire

CANC_Daphnia_pulex_Log50_Library_5

Standard

Female

Juvenile

Standard laboratory conditions

Joseph Shaw, Dartmouth College

CANF_Daphnia_pulex_Log50_Library_10

Standard

Female

Mixed

Standard laboratory conditions

Joseph Shaw, Dartmouth College

CANG_Daphnia_pulex_Log50_Library_11

Standard

Female

Mixed

Standard laboratory conditions

Joseph Shaw, Dartmouth College

CANH_Daphnia_pulex_Log50_Library_21

Normalized

Female

Mixed

Standard laboratory conditions

Joseph Shaw, Dartmouth College

CANI_Daphnia_pulex_Log50_Library_18

Standard

Mixed

Adult

Stressed by exposure to fish predator (Lepomis macrochirus)

Jim Haney, University of New Hampshire

CANN_Daphnia_pulex_Log50_Library_17

Standard

Mixed

Juvenile

Stressed by exposure to fish predator (Lepomis macrochirus)

Jim Haney, University of New Hampshire

CANO_Daphnia_pulex_Log50_Library_1

Standard

Mixed

Adult

Stressed by hypoxia

Jim Haney, University of New Hampshire

CANP_Daphnia_pulex_Log50_Library_2

Standard

Mixed

Juvenile

Stressed by hypoxia

Jim Haney, University of New Hampshire

CANS_Daphnia_pulex_Log50_Library_3

Standard

Mixed

Mixed

Stressed by low dose exposure to UV

Michael Pfrender, Utah State University

CANT_Daphnia_pulex_Log50_Library_4

Standard

Mixed

Mixed

Stressed by high dose exposure to UV

Michael Pfrender, Utah State University

CANU_Daphnia_pulex_Log50_Library_7

Standard

Female

Mixed

Stressed by exposure to arsenic (1348 ug/L of As as sodium arsenite)

Joseph Shaw, Dartmouth College

CANW_Daphnia_pulex_Log50_Library_6

Standard

Female

Mixed

Stressed by exposure to cadmium (20 ug/L of Cd as cadmium chloride)

Joseph Shaw, Dartmouth College

CANX_Daphnia_pulex_Log50_Library_8

Standard

Female

Mixed

Stressed by exposure to zinc (200 ug/L of Zn as zinc chloride)

Joseph Shaw, Dartmouth College

CANY_Daphnia_pulex_Log50_Library_20

Standard

Female

Adult

Exposed to Methyl Farnesoate hormone

Brian Eads, Indiana University

CANZ_Daphnia_pulex_Log50_Library_19

Standard

Female

Juvenile

Exposed to Methyl Farnesoate hormone

Brian Eads, Indiana University

CAOA_Daphnia_pulex_Log50_Library_16

Standard

Mixed

Adult

Stressed by exposure to Microcystis

Darren Bauer, University of New Hampshire

CAOB_Daphnia_pulex_Log50_Library_15

Standard

Mixed

Juvenile

Stressed by exposure to Microcystis

Darren Bauer, University of New Hampshire

CAOC_Daphnia_pulex_Log50_Library_9

Standard

Female

Mixed

Stressed by metal exposure, high concentrations (20 ug Cd/L; 200 ug Zn/L; 1348 ug As/L) pooled into this single sample

Joseph Shaw, Dartmouth College

CAOF_Daphnia_pulex_Log50_Library_12

Standard

Mixed

Adult

Stressed by exposure to invertebrate predator (Chaoborus americanus)

Jim Haney, University of New Hampshire

CBIA_Daphnia_pulex_Chosen_One_Library_1

Normalized

Strictly Female

Juvenile (4 days old)

Standard laboratory conditions

Jacqueline Lopez, Indiana University

CBIB_Daphnia_pulex_Chosen_One_Library_2

Normalized

Strictly Female

Adult (10 days old) with embryos in brooding chamber

Standard laboratory conditions

Jacqueline Lopez, Indiana University

CBIC_Daphnia_pulex_Chosen_One_Library_3

Normalized

Strictly Male

Adult (10 days old)

Standard laboratory conditions

Jacqueline Lopez, Indiana University

CUCS_Daphnia_pulex_Log50_Library_14

Normalized

Mixed

Adult

Stressed by starvation

Jim Haney, University of New Hampshire

CUCW_Daphnia_pulex_Log50_Library_13

Normalized

Mixed

Juvenile

Stressed by starvation

Jim Haney, University of New Hampshire

CBNN_Daphnia_pulex_Chosen_One_Library_4

Normalized

Female

Adults plus neonates up to third instar

Stressed by exposure to nickle (200 ug/L of Ni as nickle chloride)

Joseph Shaw, Dartmouth College

CBNO_Daphnia_pulex_Chosen_One_Library_5

Normalized

Female

Adults plus neonates up to third instar

Stressed by exposure to copper (5 ug/L of Cu as copper sulphate)

Joseph Shaw, Dartmouth College

CBNP_Daphnia_pulex_Chosen_One_Library_6

Normalized

Female

Adults plus neonates up to third instar

Stressed by acid (pH 6.0)

Joseph Shaw, Dartmouth College

CBNS_Daphnia_pulex_Chosen_One_Library_7

Normalized

Female

Adults plus neonates up to third instar

Stressed by salt (750 mg/L of sodium chloride)

Joseph Shaw, Dartmouth College

CBNT_Daphnia_pulex_Chosen_One_Library_8

Normalized

Female

3 day old neonates

Stressed by exposure to nanoparticles (Fullerene)

Rebecca Klaper, University of Wisconsin-Milwaukee

CBTO_Daphnia_pulex_Chosen_One_Library_9

Normalized

Female

Mixed including parthenogenetics and sexuals

Stressed by bacterial infection

Thomas Little, University of Edinburgh

CBTP_Daphnia_pulex_Chosen_One_Library_10

Normalized

Female

Adults plus neonates up to third instar

Stressed by mixed metals exposure, high concentrations (20 ug Cd/L; 200 ug Zn/L; 1348 ug As/L)

Joseph Shaw, Dartmouth College

CBTS_Daphnia_pulex_Chosen_One_Library_11

Normalized

Female

Adults plus neonates up to third instar

Stressed by mixed metals expsoure, low concentrations (1 ug Cd/L; 50 ug Zn/L; 500 ug As/L)

Joseph Shaw, Dartmouth College

CBTT_Daphnia_pulex_Chosen_One_Library_12

Normalized

Female

Adults plus neonates up to third instar

Stressed by exposure to monomethylarsenic III (100 ug/L of As as diiodo-MMAIII)

Joseph Shaw, Dartmouth College

CBTU_Daphnia_pulex_Chosen_One_Library_13

Normalized

Female

5 day old neonates

Stressed by exposure to nanoparticles (Titanium Dioxide)

Rebecca Klaper, University of Wisconsin-Milwaukee

CBTW_Daphnia_pulex_Chosen_One_Library_14

Normalized

Female

Adults plus neonates up to third instar

Stressed by exposure to Microcystis

Darren Bauer, University of New Hampshire

CBTX_Daphnia_pulex_Chosen_One_Library_15

Normalized

Female

Adults plus neonates up to third instar

Stressed by calcium starvation (1 mg/L of Ca)

Joseph Shaw, Dartmouth College

† Standard libraries were created by Darren Bauer and Kelley Thomas at the Hubbard Center for Genome Studies ; Normalized libraries were created by Zach Smith and John Colbourne at The Center for Genomics and Bioinformatics; Sequencing was performed by Erika Lindquist at the Joint Genome Institute.

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