Microsatellite libraries

NEOF has supported the isolation of markers from 125 species:

Off
39 birds 28 insects 22 mammals
7 flowering plants 7 fishes 6 amphibians
6 reptiles 2 crustaceans 2 molluscs
4 other invertebrates 1 cephalopod 1 algae

 Microsatellite libraries created

Mammals

  • Snow leopard, Panthera uncial (Miseq)
  • African golden wolf, Canis anthus (Miseq)
  • , Crocuta crocuta
  • , 
  • Pine marten, Martes martes (Miseq)
  • American mink, Neovison vison (Miseq)
  • Rabbit, Oryctolagus cuniculus
  • Royal pika, Ochotona roylei (Miseq)
  • , Lepilemur edwardsi
  • , Tamiasciurus hudsonicus
  • , Hylopetes phayrei
  • , Menetes berdmorei
  • , Hylopetes lepidus
  • , Rhinolophus ferrumequinum
  • , Kerivoula papillosa
  • Fawn leaf-nosed bat, Hipposideros cervinus
  • Grey long-eared bat, Plecotus austriacus (454)
  • Water shrew, Neomys fodiens
  • Pyreanean desman, Galemys pyrenaicus (Miseq)
  • , Acomys dimiditus (454)
  • , Muscardinus avellanarius (454)

Birds

Passerines:

  • , Passer domesticus
  • Zebra finch, Taeniopygia guttata (isolated via genome sequence)
  • , Chloebia gouldiae
  • , Parus caeruleus
  • , Acrochephalus sechellensis
  • Great reed warbler, Acrocephalus arundinaceus
  • , Pica pica
  • Azure-winged magpie, Cyanopica cyanus
  • , Malurus cyaneus
  • , Emberiza schoeniclus
  • , Notiomystis cincta
  • Seychelles flycatcher, Terpsiphone corvina
  • , Acanthisitta chloris
  • t, Saxicola rubicola (MiSeq)
  • , Merops apiaster (Miseq)

Non-passerines:

  • , Clamator glandarius
  • , Alectura lathami
  • Chicken, Gallus gallus
  • , Branta bernicla hrota
  • , Struthio camelus
  • Mauritius pink pigeon Columba mayeri
  • , 
  • , Aethia pygmaea
  • , Charadrius alexandrinus
  • , Oceanodroma leucorhoa
  • , hybrid Pterodroma arminjoniana spp (454)
  • , Pterodroma heraldica (454)
  • , Eudyptes chrysolophus
  • , Onychoprion fuscatus (Miseq)
  • Great bustard, Otis tarda
  • , Burhinus oedicnemus
  • Common pheasant, Phasianus colchicus (Miseq)
  • Monk parakeet, Myiopsitta monachus (Miseq)

Birds of prey:

  • , Pandion haliaetus
  • Turkey vulture, Cathartes aura
  • Black vulture, Coragyps atratus
  • Reunion harrier, Circus maillardi
  • , Bubo bubo
  • Pygmy falcon, Polihierax semitorquatus (Miseq)

Fishes

  • , Rhodeus sericeus
  •  (Mackerel icefish), Champsocephalus gunnari
  •  (no common name)
  • , Cetorhinus maximus
  • Flapper skate, Dipturus intermedia (Miseq)
  • Blue skate, Dipturus flossada (Miseq)
  • Porbeagle shark, Lamna nasus (Miseq)

Reptiles

  • Skink, Gongylomorphus (4 species)
  • Bojer's skink, Gongylomorphus bojerii
  • Orange tailed skink, Gongylomorphus spp
  • , Podarcis muralis (454)
  • , Phelsuma guimbeaui guimbeau

Amphibians

  • , Triturus cristatus
  • , Triturus vulgaris
  •  (Gymnophiona), Boulengerula uluguruenis
  • Guatemala spike-thumb frog, Plectrohyla guatemalensis (Miseq)
  • Honduras spike-thumb frog, Plectrohyla dasypus (Miseq)
  • Copan brook frog, Duellmanohyla soralia (Miseq)

Molluscs

  • , Hydrobia ulvae
  • Shining ramshorn snail, Segmentina nitida (Miseq)

Insects

  • , Hemideina maori
  • , Gryllus bimaculatus
  • ., Coccotrypes dactyliperda
  • , Coccotrypes carpophagus
  • , Polycentropus flavomaculatus
  • Stalk-eyed fly, Diasemopsis meigenii
  • , Cimex lectularius
  • , Arctia caja
  • , Parnassius apollo nevadensis
  • , Microstigmus nigrophthalmus
  • Chalcid parasitic oak gallwasp (3 species)
  • Heathland solitary wasp, Ammophila pubescens
  • Tropical hover wasp, Liostenogaster flavolineata
  • , Lasioglossum malachurum
  • Red mason bee, Osmia bicornis (isolated via genome sequence)

, Aedes taeniorhynchus
Mosquito sp., Sabethes sp.
Dance flies (multiple species)
12 species of dance fly (Diptera:Empididae) across three genera (Rhamphomyia (n=5), Empis(n=4) and Hilara (n=3)): Rhamphomyia longicauda, R. crassirostris, R. tibiella, R. longipes, R. nigripennis, Empis aestiva, E. tessellata, E. nigripes, E. stercorea, Hilara maura, H. chorica, H. interstincta

Crustaceans

  • Ostracod, Eucypris virens
  • White-clawed crayfish, Austropotamobius pallipes 

Cephalopods

  • , Nautilus pompilius (MiSeq)

Other Invertebrates

  • , 
  • Ascidian, Diplosoma listerianum
  • , Eunicella verrucosa
  • , Alcyonium digitatum

Flowering plants

  • Elder-flowered orchid, Dactylorhiza sambucina
  • Green-winged orchid, Orchis morio
  • , Ficus sycomorus
  • , Cirsium acaule
  • , Sium latifolium (MiSeq)
  • Quaking-grass, Briza media
  • Blue sedge, Carex flacca

Algae

  • Red alga sp., Gracilariopsis longissima

Sequencing methods

454 - indicates the clones were sequenced using 454 sequencing at the University of Liverpool.

MiSeq - indicates an Illumina paired-end library was created using 1µg of repeat-enriched genomic DNA and by following the standard protocol of the SureSelect Library Prep Kit, ILM (Agilent Technologies Inc. Santa Clara, California) and DNA sequencing was conducted using a MiSeq Benchtop Sequencer (Illumina Inc., San Diego, California) by the 91̽»¨ Diagnostics Genetics Service, 91̽»¨ Children's Hospital.

Other libraries were created using Sanger sequencing and a consensus sequence created from the forward and reverse sequences.

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