Frequency and Distribution of Microsatellites in the Genome of Filamentous Fungus,Neurospora crassa

A total of 38.0 Mb of publicly available DNA sequence in Neurospora crassa was researched for mono- to hexanucleotide simple sequence repeats (SSR or microsatellite) to determine the type, size and frequency. A total of 14 788 SSRs were observed in the whole genomic DNA sequence, about one every 2.57 kb, with the criteria of SSR length >15 bp and 80% matches. The most abundant microsatellite was trinucleotide repeat, the number was 4 729, followed by hexanucleotide and mononucleotide repeats, the numbers were 2 940 and 2 489 respectively, and the least abundance was dinucleotide repeat, only 691 were found. Among the 10 082 ORFs, 4 094 SSRs were harbored in 2 373 ORF (no intron) of the organism. One thousand and fifty six ORFs harbored only one SSR. Similar with other organisms, tri- and hexanucleotide repeats were predominant in ORFs, 54.1 and 48.8% of tri- and hexanucleotide repeats were distributed in ORF region. The density of these two motifs was overpresented in coding regions, because ORF region and coding region constitutes only 46 and 38.3% of genomic sequence, respectively. Upstream and downstream 300 bp of regulatory regions were high density regions of SSRs, particularly density of pentanucleotide SSR in upstream region was as high as five times of average density in genomic DNA, density of di- and tetranucleotide SSR was also more than two times of average density. The density of penta-, tetra-, di- and mononucleotide SSRs was relatively higher than average density. There were 47 SSRs in mitochondria 64 840 bp DNA sequence, their distribution is similar with genomic DNA sequence. These results suggested that SSRs were clustered in regulatory regions of genomic DNA.

Development and utility of EST-SSR markers in Ulva prolifera of the South Yellow Sea

Ulva species can grow rapidly in nutrient-rich habitats causing green tides and marine fouling. A more complete understanding of the reasons behind these outbreaks is urgently required. Accordingly, this study attempts to use microsatellite markers based expressed sequence tag（EST） to analyze the genetic variation of several Ulva prolifera populations in the South Yellow Sea of China. Two hundred and thirty-eight SSRs were identified from 8 179 unique ESTs（6 203 newly sequenced and 1 976 downloaded from NCBI database） and 37 primer pairs were successfully designed according to the ESTs; 11 pairs were selected to detect the genetic diversity and relationship of 69 attached U. prolifera samples and 13 free-floating samples collected from coastal and off-coast areas of the South Yellow Sea. The results of cross-species transferability showed that six of the 11 EST-SSR primers could give good amplification in other five Ulva species and the average allele number was 4.67. Genetic variation analysis indicated that all 82 U. prolifera samples were clearly divided and most samples collected from the same site clustered together as a group in the dendrogram tree produced by unweighted pair-group mean analysis（UPGMA） method and the cluster results showed some consistency with the geographical origins. In addition, 13 free-floating samples（except HT-001-2） were grouped as a single clade separated from the attached samples.

Analysis of Genetic Polymorphic SSR Markers in Germplasm Resources of the Natural Colored Cotton

Short sequence repeats(microsatellite,SSR) and expressed sequence tags-SSR(EST-SSR) markers were employed to analyze the genetic diversity of natural colored cotton varieties.About

Genetic diversity and population structure of Prochilodus costatus and Prochilodus argenteus preceding dam construction in the Paraopeba River,Sao Francisco River Basin,Minas Gerais,Brazil

Curimat?-pioa (Prochilodus costatus) and curimat?-pacu (Prochilodus argenteus) are migratory fish species endemic to the S?o Francisco River Basin in Brazil. Both species play important roles in local fisheries and ecology in the Paraopeba River. A dam was recently constructed on this river and to help in the development and conservation programs, we characterized the genetic variation of both species before dam construction. Complex hypervariable repeats micro-satellite was used to asses genetic variation for both species within and between the five collection sites in order to detect population substructuring. Nucleotide substitutions and insertion/deletion polymorphisms (indels) resulted in 35 P. costatus haplotypes (sample size = 89) and 22 P. argenteus haplotypes (sample size = 32). Significant genetic diversity and population differentiation was detected between five sampling sites for both species. Therefore, each of the five sites should be regarded as a group comprising significant genetic differences in species conservation and maintenance plans. Comparing these results to genetic diversity measures after dam construction will be critical for future management in this region.

Genetic differentiation between and within Northern Native American language groups:an argument for the expansion of the Native American CODIS database

The National Research Council recommends that genetic differentiation among subgroups of ethnic samples be lower than 3%of the total genetic differentiation within the ethnic sample to be used for estimating reliable random match probabilities for forensic use.Native American samples in the United States’Combined DNA Index System(CODIS)database represent four language families:Algonquian,Na-Dene,Eskimo-Aleut,and Salishan.However,a minimum of 27 Native American language families exists in the US,not including language isolates.Our goal was to ascertain whether genetic differences are correlated with language groupings and,if so,whether additional language families would provide a more accurate representation of current genetic diversity among tribal populations.The 21 short tandem repeat(STR)loci included in the Globalfiler^(■)PCR Amplification Kit were used to characterize six indigenous language families,including three of the four represented in the CODIS database(i.e.Algonquian,Na-Dene,and Eskimo-Aleut),and two language isolates(Miwok and Seri)using major population genetic diversity metrics such as F statistics and Bayesian clustering analysis of genotype frequencies.Most of the genetic variation(97%)was found to be within language families instead of among them(3%).In contrast,when only the three of the four language families represented in both the CODIS database and the present study were considered,4%of the genetic variation occurred among the language groups.Bayesian clustering resulted in a maximum posterior probability indicating three genetically distinct groups among the eight language families and isolates:(1)Eskimo,(2)Seri,and(3)all other language groups and isolates,thus confirming genetic subdivision among subgroups of the CODIS Native American database.This genetic structure indicates the need for an increased number of Native American populations based on language affiliation in the CODIS database as well as more robust sample sets for those language families.