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Table 2 Results of DIRS1-like retrotransposon detection and clustering

From: Eukaryote DIRS1-like retrotransposons: an overview

Higher taxon

Species

Copy number

Family number

Min

Max

Reference

 

Danio rerio *

2091

14

1

1157

a

 

Gasterosteus aculeatus

21

4

1

12

b

Actinopterygii

Oryzias latipes

6

1

-

-

c

 

Takifugu rubripes *

7

1

-

-

d

 

Tetraodon nigroviridis *

8

2

1

7

b

Amoebozoa

Dictyostelium discoideum *

16

1

-

-

[51]

 

Acantheamoeba sp.

1

1

-

-

e

Amphibia

Xenopus tropicalis *

692

81

1

38

[52]

Annelida

Capitella sp. I

5

2

1

4

f

Blastocladiomycota

Allomyces macrogynus

21

6

1

10

b

Cephalochordata

Branchiostoma floridae

15

11

1

3

[53]

Chlorophyta

Chlamydomonas reinhardtii

11

5 (3)

1

4

[54]

 

Volvox carteri

36

6 (4)

2

13

[55]

Cnidaria

Nematostella vectensis *

60

21 (1)

1

7

[48]

Crustacea

Daphnia pulex *

100

39

1

5

[56]

Echinodermata

Strongylocentrotus purpuratus *

4

4

-

-

e

Haptophytes

Emiliana huxleyi

1

1

-

-

f

Hemichordata

Saccoglossus kowalevskii *

240

8 (1)

1

175

e

Heterolobosea

Naegleria gruberi

7

6

1

2

[57]

 

Bombyx mori

6

2

3

3

[58]

Hexapoda

Nasonia vitripennis *

37

18

1

4

e

 

Tribolium castaneum *

1

1

-

-

e

Mucoromycotina

Mucor circinelloides

3

2

1

2

f

 

Phycomyces blakesleeanus *

28

13

1

5

f

 

Rhizopus oryzae *

24

11

1

4

[59]

Mollusca

Aplysia californica

39

7

2

10

b

 

Lottia gigantea

44

22 (1)

1

5

f

Nematoda

Caenorhabditis briggsae $

1

1 (1)

-

-

g

 

Pristionchus pacificus $

4

3 (3)

1

2

g

Petromyzontida

Petromyzon marinus

2

2

-

-

g

Sauropsida

Anolis carolinensis

775

42

1

319

b

Urochordata

Oikopleura dioica *

4

2

1

3

h

  1. For each species, the number of sequences detected using ReDoSt and the number of families obtained with the MCL program are given. When they are informative, the minimum (Min) and the maximum (Max) numbers of sequences included in a family are provided. Species in which the presence of DIRS1-like elements was previously reported (cf. Table 1) are indicated with an asterisk. In the family number column, numbers in brackets indicate the number of families that we characterized as PAT-like elements. The two Nematoda species that comprise only PAT-like elements are indicated with a dollar. The clustering was performed on all sequences detected in the 32 species. The families shared by several species are represented several times in the table.
  2. Notes: a: The zebrafish genome sequencing project at the Sanger Institute (http://www.sanger.ac.uk/Projects/D_rerio/) funded by the Wellcome Trust. b: The Broad Institute of Harvard and MIT ( http://www.broadinstitute.org/). c: The National Institute of Genetics and the University of Tokyo (http://medakagb.lab.nig.ac.jp/Oryzias_latipes/index.html). d: The Institute of Molecular and Cell Biology (http://www.fugu-sg.org/). e: The Baylor College of Medicine Human Genome Sequencing Center (http://www.hgsc.bcm.tmc.edu/project-species-x-organisms.hgsc). f: The U.S. Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/genome-projects/). g: The Genome Institute at Washington University School of Medicine in St. Louis (ftp://genome.wustl.edu/pub/organism/). h: The Genoscope (http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/).
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BMC Genomics

ISSN: 1471-2164

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