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Historically, many population genetics studies have utilized microsatellite markers sampled at random from the genome and presumed to be selectively neutral. Recent studies, however, have shown that microsatellites can occur in transcribed regions, where they are more likely to be under selection. In this study, we mined microsatellites from transcriptomes generated by 454-pyrosequencing for three vertebrate species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the occurrence of microsatellites across species; (ii) whether particular gene ontology terms were over-represented in genes that contained microsatellites; (iii) whether repeat motifs were located in untranslated regions or coding sequences of genes; and (iv) in silico polymorphism. Microsatellites were less common in tiger salamanders than in either lake sturgeon or kangaroo rats. Across libraries, trinucleotides were found more frequently than any other motif type, presumably because they do not cause frameshift mutations. By evaluating variation across reads assembled to a given contig, we were able to identify repeat motifs likely to be polymorphic. Our study represents one of the first comparative data sets on the distribution of vertebrate microsatellites within expressed genes. Our results reinforce the idea that microsatellites do not always occur in noncoding DNA, but commonly occur in expressed genes. Key words: 454 pyrosequencing, repeat motif, genomics, coding region. Historiquement, plusieurs etudes de genetique des populations ont employe des marqueurs microsatellites choisis au hasard dans le genome et presumes neutres. Des travaux recents ont cependant montre que les microsatellites sont parfois situes dans des regions transcrites ou ils sont plus susceptibles d'etre sous selection. Dans ce travail, les auteurs ont identifie des microsatellites au sein de transcriptomes generes par pyrosequen^age 454 chez trois especes de vertebres : l'esturgeon jaune (Acipenserfulvescens), la salamandre tigree (Ambystoma tigrinum) et le rat-kangourou (Dipodomys spectabilis). Les auteurs ont evalue : (i) l'abondance des microsatellites chez les trois especes; (ii) la frequence relative des termes d'ontologie genique au sein des genes contenant des microsatellites; (iii) la presence des motifs repetes au sein de regions codantes ou non-traduites; et (iv)le polymorphisme in silico. Les microsatellites etaient moins abondants chez la salamandre tigree que chez l'esturgeon jaune ou le rat-kangourou. Dans l'ensemble des librairies, les repetitions trinucleotidiques etaient plus frequentes que tout autre motif repete, vraisemblablement parce qu'elles n'entrainent pas de changement de cadre de lecture. En evaluant la variation pour les sequences assemblees au sein d'un meme contig, les auteurs ont pu identifier des motifs repetes vraisemblablement polymorphes. Cette etude represente l'un des premiers jeux de donnees permettant de comparer la distribution des microsatellites au sein de genes exprimes chez les vertebres. Ces resultats confirment que les microsatellites ne sont pas tous situes au sein de l'ADN non-codant, mais qu'ils sont frequemment rencontres au sein de genes exprimes. [Traduit par la Redaction] Mots-cles: pyrosequencage 454, motif repete, genomique, region codante., Introduction Microsatellites are short nucleotide motifs such as [(AC).sub.n] or [(GATA).sub.n] that are repeated in tandem (Litt and Luty 1989; Weber and May 1989). Despite their apparent ubiquity among eukaryotes, [...]

To optimize conservation efforts, it is necessary to determine the risk of extinction by collecting reliable population information for a given species. We developed eight novel, polymorphic microsatellite markers and used these markers in conjunction with twelve existing markers to measure genetic diversity of South Korean populations of leopard cat (Prionailurus bengalensis), a species for which population size and habitat area data are unknown in the country, to assess its conservation status. The average number of alleles and the observed heterozygosity of the species were 3.8 and 0.41, respectively, and microsatellite diversity was lower than the average genetic diversity of 57 populations of 12 other felid species, and lower than that of other mammal populations occurring in South Korea, including the raccoon dog (Nyctereutes procyonoides), water deer (Hydropotes inermis), and endangered long-tailed goral (Naemorhedus caudatus). Furthermore, analysis of genetic structure in the national leopard cat population showed no clear genetic differentiation, suggesting that it is not necessary to divide the South Korean leopard cat population into multiple management units for the purposes of conservation. These results indicate that the genetic diversity of the leopard cat in South Korea is unexpectedly low, and that the risk of local extinction is, as a result, substantial. Thus, it is necessary to begin appropriate conservation efforts at a national level to conserve the leopard cat population in South Korea. [ABSTRACT FROM AUTHOR]