Complex Microsatellites Research Articles

Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance.

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

Analysis and Profiling of Leishmania major Expressed Sequence Tags

BackgroundLeishmania genome projects involving specific species and strains are resulting in a rapid accumulation of full and partial expressed DNA sequences. Expressed sequence tags (ESTs) collected from public databases can be mined for both structural and functional genomics' motifs. AimIn this study we mined L. major EST that were available from the online NCBI database, for simple sequence repeats (SSRs), which can be used in the developing of simple and complex microsatellites, as well as to assess their distributions. MethodsIn this study, we acquired a total of 2,191 ESTs of the parasite species L. major expressed in both stages (amastigote and promastigote) that were mined using deterministic text search algorithms as implemented in the MISA script. After sequence reduction (joining overlapping fragments) using CAP3, we mined a total of 1448 ESTs (305 from amastigote, and 1211 from promastigote stages). ResultsThe frequencies of identified mono, di, tri, tetra, and complex SSRs are about 30%, 46%, 4%, 1%, and 19% respectively. Principal components analysis showed that the complex repeat motifs are the most abundant SSR in the amastigote stage, while the mono-repeats are the most abundant in the promastigote stage.Comparative sequence analyses of identified and stage specific SSRs, showed that the proportion of differentially expressed fragments (after reduction) in amastigote is 54%, which is statistically lower (p-value <0.001) than those differentially expressed fragments in promastigote (about 74%). Further analysis suggests that the majority of the EST-SSRs code for signal peptides in the parasite trans-membrane region.Furthermore, functional domain marker (FDM-SSR) analysis of these identified SSR-ESTs revealed their potential role in the leishmania metabolism. The protein PDIa is expressed in the amastigote stage only, while the EF-hand domain, the GrpE nucleotide exchange factor SHERP, 40S ribosomal protein S3, Metallo-peptidase family M24, and PQ loop repeat are all expressed in the promastigote stage only.

In silico genome-wide identification and analysis of microsatelliterepeats in the largest RNA virus family (Closteroviridae)

Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life, including viruses. Members of the family Closteroviridae are the largest RNA viruses and severely affect different agricultural crops worldwide, including1397645907citrus, grapevine, and vegetables. Here we identified and systematically analyzed the nature and distribution of both simple and complex microsatellites present in the complete genome of 36 species belonging to Closteroviridae. Our results showed, in all analyzed genomes, that neither genome size nor GC content had any influence on number, relative abundance, or relative density of microsatellites. For each genome, dinucleotide repeats were found to be highly predominant and AT/TA and AG/GA were the two most abundant dinucleotide repeat motifs. Repeats larger than trinucleotide were relatively rare in these viral genomes. Comparative study of occurrence, abundance, and density of microsatellites among available RNA and DNA viral genomes indicated that simple repeats were less abundant in genomes of Closteroviridae. To our knowledge, this is the first analysis of microsatellites occurring in the largest viral genome that infects plants. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.

Genome wide survey and analysis of microsatellites in Tombusviridae family

Microsatellites are small repetitive sequences found in all kingdoms of life including viruses. Members of the Tombusviridae family severely affect growth of wide range of plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 47 species of Tombusviridae family. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, dinucleotide repeats followed by mononucleotide repeats were found to be highly predominant. Mononucleotide repeats were found to be underrepresented in majority of Tombusviridae genomes. Poly G and Poly C repeats were more abundant as compared to poly A or poly T nucleotides. TG/GT and AG/CA was the most abundant dinucleotide repeat motif observed in Tombusviridae genomes. Repeats larger than trinucleotide were never found in these viral genomes. Comparative study of relative abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were lower than many RNA virus genomes. To our knowledge, this is the first analysis of microsatellites occurring in Tombusviridae genomes. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.

Screening and characterization of RAPD markers in viscerotropic Leishmania parasites.

Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5′ end transversions, and presence of inter– and intra– taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers, to develop molecular diagnostics assays to characterize and differentiate VL causing agents.

Genome wide survey and analysis of small repetitive sequences in caulimoviruses

Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life including viruses. Members of the Caulimoviridae family severely affect growth of vegetable and fruit plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 44 species of Caulimoviridae. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, mono- and dinucleotide repeats were found to be highly predominant and are overrepresented in genome of majority of caulimoviruses. AT/TA and GAA/AAG/AGA was the most abundant di- and trinucleotide repeat motif, respectively. Repeats larger than trinucleotide were rarely found in these genomes. Comparative study of occurrence, abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were least abundant in genomes of caulimoviruses. Polymorphic repeats even though rare were observed in the large intergenic region of the genome, indicating strand slippage and/or unequal recombination processes do occur in caulimoviruses. To our knowledge, this is the first analysis of microsatellites occurring in any dsDNA viral genome. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.

Genetic diversity based on swine leukocyte antigen complex mi-crosatellites(&lt;I&gt;SLA-MS&lt;/I&gt;) in five pig populations

The genetic diversity of swine leukocyte antigen complex (SLA) was studied among Guangdong local pigs, Huanan wild boars (S.s. chirodontus) and introduced pigs, which aimed at providing a theoretical foundation for further pig anti-disease resistance breeding. Pietrain pigs, Duroc pigs, Large black-white pigs, Lantang pigs, and Huanan wild boars were genotyped by employing 18 microsatellites in swine leukocyte antigen complex (SLA-MS). The result showed that the average diversity in SLA II was higher (He=0.628, PIC=0.581) than that in SLA I (He=0.530, PIC=0.474) and in SLA III (He=0.526, PIC=0.458). The molecular diversity indices (MDI) of Huanan wild boars was the highest(0.716), followed by Lantang pigs (0.614), Large black-white pigs (0.559), Pietrain pigs (0.550) and Duroc pigs (0.507). As a whole, the genetic diversity of Huanan wild boars was the highest over Guangdong native pigs and introduced pigs. Large black-white pigs and Duroc pigs had ever happened a severe bottleneck by comparison with the Garza-Williamson index (GWI) in Huanan wild boar. From the genetic distance, one clade was that Lantang pigs were first clustered with Huanan wild boar, and then grouped together with Large black-white pigs; another clade was that Pietrain pigs were independently clustered with Duroc pigs in the NJ tree. The results would establish the foundation for pig conservation of germplasm resource, disease resistance breeding, and multiplicative strains.

MSDB: A User-Friendly Program for Reporting Distribution and Building Databases of Microsatellites from Genome Sequences

Microsatellite Search and Building Database (MSDB) is a new Perl program providing a user-friendly interface for identification and building databases of microsatellites from complete genome sequences. The general aims of MSDB are to use the database to store the information of microsatellites and to facilitate the management, classification, and statistics of microsatellites. A user-friendly interface facilitates the treatment of large datasets. The program is powerful in finding various types of pure, compound, and complex microsatellites from sequences as well as generating a detailed statistical report in worksheet format. MSDB also contains other two subprograms: SWR, which is used to export microsatellites from the database to meet user's requirements, and SWP, which is used to automatically invoke R to draw a sliding window plot for displaying the distribution of density or frequency of identified microsatellites. MSDB is freely available under the GNU General Public license for Windows and Linux from the following website: http://msdb.biosv.com/.

Association between major histocompatibility complex microsatellites, fecal egg count, blood packed cell volume and blood eosinophilia in Pelibuey sheep infected with Haemonchus contortus

The objective of this study was to assess the correlation among traits associated with resistance or susceptibility to Haemonchus contortus infestation and to evaluate the participation of the ovine major histocompatibility complex (MHC) in Pelibuey sheep, a prevalent breed in tropical and sub-tropical regions in Mexico and elsewhere. Association among the fecal egg count (FEC), blood packed cell volume (PCV), antibody (AB) levels, serum proteins (SP) and blood eosinophil count (EOS) was assessed in 52 lambs experimentally infected with H. contortus, and the participation of the MHC was evaluated using polymorphisms in three microsatellites, located at the class I (OMHC1) and class II (OLADRB1, OLADRB2) regions of the MHC. Spearman correlation analysis among the traits showed a negative association ( P < 0.01) between FEC and PCV (−0.35), EOS (−0.50), SP (−0.30) and AB (−0.57), and a positive correlation of antibodies with EOS (0.50). The homozygotes for the OMHC1-188 and OLADRB2-282 alleles were associated with a reduction in FEC (−813 and −551, respectively). Conversely, the OMHC1-200 and OMHC1-206 alleles were associated with an increase in FEC (1704 and 1008, respectively). Furthermore, the OLADRB1-482 allele was associated with an increase of 163 EOS by allele copy, while the OMHC1-200 allele showed a reduction of 95 EOS in homozygotes. The associations among microsatellite MHC loci and the remaining variables were not significant. These results reinforce the evidence that MHC polymorphisms have an important role in parasite resistance or susceptibility in Pelibuey sheep and could be used as genetic markers to assist selection and improve parasite resistance to H. contortus.

Patterns of molecular evolution of microsatellite loci in pepper (Capsicum spp.) revealed by allele sequencing

A total of 28 fragments from five microsatellite loci containing simple to highly complex repeat motifs were amplified from a number of Capsicum accessions and subsequently cloned and sequenced. In addition to variation in the number of repeats, allelic differences were found, especially in the more complex microsatellites, that are the consequences of various mutations including base substitutions, insertions/deletions, and rearrangements resulting in 21 distinct alleles. A number of the observed allelic differences were in part not revealed by the use of standard DNA-sizing technologies. The possible mutation and evolution mechanisms and the consequences of using complex and/or compound microsatellite markers for evolutionary, diversity, and taxonomical studies are discussed.

A Comprehensive Survey of Human Y-Chromosomal Microsatellites

We have screened the nearly complete DNA sequence of the human Y chromosome for microsatellites (short tandem repeats) that meet the criteria of having a repeat-unit size of > or = 3 and a repeat count of > or = 8 and thus are likely to be easy to genotype accurately and to be polymorphic. Candidate loci were tested in silico for novelty and for probable Y specificity, and then they were tested experimentally to identify Y-specific loci and to assess their polymorphism. This yielded 166 useful new Y-chromosomal microsatellites, 139 of which were polymorphic, in a sample of eight diverse Y chromosomes representing eight Y-SNP haplogroups. This large sample of microsatellites, together with 28 previously known markers analyzed here--all sharing a common evolutionary history--allowed us to investigate the factors influencing their variation. For simple microsatellites, the average repeat count accounted for the highest proportion of repeat variance (approximately 34%). For complex microsatellites, the largest proportion of the variance (again, approximately 34%) was explained by the average repeat count of the longest homogeneous array, which normally is variable. In these complex microsatellites, the additional repeats outside the longest homogeneous array significantly increased the variance, but this was lower than the variance of a simple microsatellite with the same total repeat count. As a result of this work, a large number of new, highly polymorphic Y-chromosomal microsatellites are now available for population-genetic, evolutionary, genealogical, and forensic investigations.

Microsatellites in the HLA region: 1999 update.

In this third update of a series of reviews on microsatellites in the HLA region or close to it we report 155 microsatellites, corresponding to 51 newly described markers, in addition to the 103 reported in the 1997 and 1998 reviews. This work is based both on a literature review and on data publicly available in molecular databases on the internet (http://www.gdb.org; http://bioinfo.weizmann.ac.il/cards/; http://cedar.genetics.soton.ac.uk/) up to September 1999. Thanks to numerous studies involving major histocompatibility complex (MHC) microsatellites, documentation on HLA region is proposed, including information on microsatellites described through MHC sequence projects and presenting documented location, polymorphism and amplification condition, together with additional information on previously described microsatellites when available and information on data in the literature regarding gametic associations between HLA region loci and alleles and microsatellite alleles. As basic information are presented various documents: i) a table showing the following characteristics of the 155 microsatellites: name, localisation, polymorphism, primer sequences, reference; ii) an integrated map of some HLA region genes and the 155 microsatellites considered; and iii) a summary table on HLA and microsatellites association patterns. In addition, an overview on HLA microsatellite analysis application is presented, with a special focus on disease genetics studies in the form of recent references where the use of microsatellites of the HLA region was a key tool. This review aims at providing the human immunogenetics community with a tool for helping optimal choice of microsatellites to be used in various studies.