Next generation sequencing (NGS) is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. Here we summarize the results of the large scale development of microsatellites for 54 non-model species using NGS and show there are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilised as markers. We highlight that the heterogeneity within each group is very large. Despite this variation, we provide an indication of what number of sequences and consequent proportion of a 454 run are required for the development of 40 designable, unique microsatellite loci for a typical molecular ecological study. Finally, to address the challenges of choosing loci from the vast array of microsatellite loci typically available from partial genome runs (average for this study, 2341 loci), we provide a microsatellite development flowchart as a procedural guide for application once the results of a partial genome run are obtained.
Litoria aurea
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Baumea juncea
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Gahnia trifida
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Drymodes brunneopygia
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Virola sebifera
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Bothriocroton hydrosauri
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Paratya australiensis
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Hemicordulia tau
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Necterosoma penicillatus
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Ischnura heterstickta
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Senecio pinnatifolius
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Senecio madagascariensis
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Lantana camara
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Antechinus flavipes
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Isoodon obesulus
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Macrotis logotis
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Pelecanus conspicillatus
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Holothuria scabra
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Petaurus breviceps
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Assa darlingtoni
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Neophoca cinerea
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
BARCODE22.fa
Leipoa ocellata
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
BARCODE23.fa
Amphibolurus norrisi
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Ctenotus atlas
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
BARCODE25.fa
Mustelus antarcticus
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Gehyra variegata
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Gehyra lazolli
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Hydrophis spiralis
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Podocapus lawrencei
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Nyctophilus gouldi
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Nyctophilus geoffroyi
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Ngarawa dirga
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Austrochiltonia sp "Elizabeth"
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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unidentified hoverfly
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Microdon mutabilis
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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Sepiadarium austrinum
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF41_MID1.fna
Triglochin procera
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF42_MID2.fna
Austroplatypus incompertus
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF43_MID3.fna
Phalacrocorax fuscescens
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF44_MID4.fna
Cristiceps australis
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF45_MID5.fna
Balaustium medicagoense
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF46_MID6.fna
Gallinula mortierii
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF47_MID7.fna
Euperipatoides rowelli
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF48_MID8.fna
Aquila audax
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF50_MID10.fna
Santalum acuminatum
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF52.fna
Eremiascincus richardsonii
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF54.fna
Glaphyromorphus douglasi
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF55.fna
Epthianura albifrons
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF56.fna
Callitris verrucosa
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF57.fna
Triodia irritans
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
AF58.fna
Austrochiltonia sp "northern"
Shotgun data (in FASTA format) from Roche 454 titanium GS-FLX machine
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