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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/).