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Information on the level and distribution of genetic variation is important for conservation plan of captive population of an endangered species such as tiger and cheetah. We assayed the frequency of microsatellites in the genomic and genic sequences of wild cats (Panthera tigris, Acinonyx jubatus) and compared it with the domestic cat (Felis catus). Frequency, relative abundance and density of microsatellites were highest in the domestic cat when compared with wild cats. The frequency of microsatellites was positively correlated with the G+C content of genomic and genic sequences. The maximum frequency of microsatellites among all three sequence sets was of di-nucleotide repeats (genomic-88.1%; genic-70.4%), whereas the hexa-nucleotide repeat represents < 0.5%. Motif conservation study among the genomic and genic sequences revealed conservation of 81.3% and 51.0% motif within the members of family Felidae. A total 40,233 primers from genic sequences were designed in order to enrich the members of family Felidae with genomic resources. The designed primers could be useful in determining the molecular genetics of population structure and individualization of a particular cat.

We used an in silico approach to survey and compare microsatellites in transcript sequences of four sequenced members of genus Fusarium. G + C content of transcripts was found to be positively correlated with the frequency of SSRs. Our analysis revealed that, in all the four transcript sequences studied, the occurrence, relative abundance and density of microsatellites varied and was not influenced by transcript sizes. No correlation between relative abundance and transcript sizes was observed. The relative abundance and density of microsatellites were highest in the transcripts of Fusarium solani when compared with F. graminearum, F. verticillioides and F. oxysporum. The maximum frequency of SSRs among all four sequence sets was of trinucleotide repeats (67.8%), whereas the dinucleotide repeat represents <1%. Among all classes of repeats, 36.5% motifs were found conserved within Fusarium species. In order to study polymorphism within Fusarium isolates, 11 polymorphic genic-SSR markers were developed. Of the 11 markers, 5 were from F. oxysporum and remaining 6 belongs to F. solani. SSR markers from F. oxysporum were found to be more polymorphic (38%) as compared to F. solani (26%). Eleven polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Fusarium., (© FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Fusarium oxysporum is a ubiquitous species complex of soil-borne plant pathogens comprising of many different formae speciales, each characterized by a high degree of host specificity. In the present investigation, we surveyed microsatellites in the available express sequence tags and transcript sequences of three formae speciales of F. oxysporum viz. melonis (Fom), cucumerium (Foc), and lycopersici (Fol). The relative abundance and density of microsatellites were higher in Fom when compared with Foc and Fol. Thirty microsatellite primers were designed, ten from each forma specialis, for genetic characterization of F. oxysporum isolates belonging to five formae speciales. Of the 30 primers, only 14 showed amplification. A total of 28 alleles were amplified by 14 primers with an average of two alleles per marker. Eight markers showed 100% polymorphism. The markers were found to be more polymorphic (47%) in Fol as compared to Fom and Foc; however, polymorphic information content was the maximum (0.899) in FocSSR-3. Nine polymorphic markers obtained in this study clearly demonstrate the utility of newly developed markers in establishing genetic relationships among different isolates of F. oxysporum., (© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

This work aimed to conduct a comparative analysis of the occurrence, relative density (RD) and abundance (RA) of simple sequence repeats (SSRs), within the genomic and transcriptomic sequences of four different isolates of Cryptococcus neoformans. Among the whole genome sequences, it was observed that the C. neoformans isolate JEC21 exhibited the most elevated RA (165.3) and RD (2471.8) of SSRs. Conversely, among the transcriptome sequences, the C. neoformans isolate KN99 displayed the greatest RA (145.5) of SSRs. Among the classes of SSRs, trinucleotide repeats exhibited a higher prevalence in both the genomic sequences (50%) and transcriptome sequences (65%) over other repeats. Motif conservation analysis among the isolates demonstrated that 41.1% of motifs were conserved among the isolates of C. neoformans. The study also found unique motifs that could potentially serve as molecular probes for the purpose of isolate identification. A total of 8117 primers were created for the isolates of Cryptococcus to enrich it with genomic resources. The genomic resources created in this study have the potential to aid in the diversity analysis and the creation of markers specific to individual isolates. [ABSTRACT FROM AUTHOR]

In this study, we evaluated the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) in the complete genome and transcriptomic sequences of the plant pathogenic species of Pythium to acquire a better knowledge of their genome structure and evolution. Among the species, P. ultimum had the highest RA and RD of SSRs in the genomic sequences, whereas P. vexans had the highest RA and RD in the transcriptomic sequences. The genomic and transcriptomic sequences of P. aphanidermatum showed the lowest RA and RD of SSRs. Trinucleotide SSRs were the most prevalent class in both genomic and transcriptomic sequences, while dinucleotide SSRs were the least prevalent. The G + C content of the transcriptomic sequences was found to be positively correlated with the number (r = 0.601) and RA (r = 0.710) of SSRs. A motif conservation study revealed the highest number of unique motifs in P. vexans (9.9%). Overall, a low conservation of motifs was observed among the species (25.9%). A gene enrichment study revealed P. vexans and P. ultimum carry SSRs in their genes that are directly connected to virulence, whereas the remaining two species, P. aphanidermatum and P. arrhenomanes, harbour SSRs in genes involved in transcription, translation, and ATP binding. In an effort to enhance the genomic resources, a total of 11,002 primers from the transcribed regions were designed for the pathogenic Pythium species. Furthermore, the unique motifs identified in this work could be employed as molecular probes for species identification. [ABSTRACT FROM AUTHOR]

Pathogenic bacteria use phase variation of surface molecules and other characteristics as a significant adaptation mechanism. Repetitive sequences made up of numerous identical repeat units can be found in many phase variable genes. Here, we investigated the frequency and distribution of long-SSRs (Simple Sequence Repeats) in 15 human pathogenic Staphylococcus, Streptococcus, and Enterococcus bacteria. Long-SSRs were found to be distributed differently in the genic and inter-genic sequences. In the genic sequences, 61.3 SSRs were discovered on average, while 16.2 SSRs were found in the intergenic regions. Staphylococcus exhibited the highest frequency of SSRs, followed by Enterococcus, and Streptococcus had the lowest frequency of SSRs. Higher A + T content was found to be the best predictor of long-SSR in these human pathogens. Tetranucleotide repeats predominated in inte-rgenic regions, while trinucleotide repeats were in the majority in genic regions. In human pathogenic Streptococcus and Staphylococcus bacteria, genus-specific encoding of amino acids by tri-nucleotide SSRs was observed. Based on the presence of SSRs in housekeeping genes, a genetic relationship between these human pathogenic bacteria was constructed and compared to a phylogeny based on the 16 S ribosomal RNA gene. [ABSTRACT FROM AUTHOR]

The occurrence of Microsatellites (SSRs) has been witnessed in most of the fungal genomes however its abundance varies across species. In the present study, we analyzed the frequency of SSRs in the whole genome and transcripts of two phyto-pathogenic (Aspergillus niger and Aspergillus terreus) and compared them with two non-pathogenic (Aspergillus nidulans and Aspergillus oryzae) Aspergillus. Higher relative abundance and relative density of SSRs were observed in the whole genome and transcript sequences of the pathogenic Aspergillus when compared to the non-pathogenic. The relative abundance and density of SSRs were positively correlated with the G+C content of transcripts. Among the different classes of SSR, the percentage of tetra-nucleotide SSRs were maximum in A. niger (36.7%) and A. oryzae (35.9%) whereas A. nidulans and A. terreus preferred tri-nucleotide SSRs (38.2 and 42.1%) in whole genome sequences. In transcripts, tri-nucleotide SSRs were the most abundant whereas di-nucleotide SSRs were the least favored. Motif conservation study among the transcripts revealed conservation of only 27% motif within Aspergillus species. Furthermore, a similar relationship among the Ascomycetes was obtained on the basis of motif conservation and conserved genes (rDNA). To analyze the diversity present within the Indian isolates of Aspergillus, primers were successfully designed for 692 motifs in A. niger and A. terreus of which 20 were selected for diversity analysis. Among all the markers amplified, 10 markers (83.3%) were polymorphic, whereas remaining two markers (16.6%) were monomorphic. Ten polymorphic markers acquired in this investigation showed the utility of recently created SSR markers in the assessment of genetic diversity among various isolates of Aspergillus. [ABSTRACT FROM AUTHOR]

The article focuses on a study for novel genic microsatellite markers from Cajanus scarabaeoides and their comparative efficiency in revealing genetic diversity in pigeonpea. Topics discussed include economic impact of pigeonpea, information on population genetic, extraction of Genomic DNA using phenol–chloroform extraction method, and analysis of population genetic structure and gene flow.

Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ~38%, whereas hexa-nuceotide repeats were the least (~10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma. [ABSTRACT FROM AUTHOR]