Mining Of Microsatellites Research Articles

SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions

BackgroundTandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs we have Satellite repeats, that is divided into macrosatellites, minisatellites, and microsatellites, being the last two of specific interest because they can identify polymorphisms between organisms due to their instability. Currently, most mining tools focus on Simple Sequence Repeats (SSR) mining, and only a few can identify SSRs in the coding regions.ResultsWe developed a microsatellite mining software called SATIN (Micro and Mini SATellite IdentificatioN tool) based on a new sliding window algorithm written in C and Python. It represents a new approach to SSR mining by addressing the limitations of existing tools, particularly in coding region SSR mining. SATIN is available at https://github.com/labgm/SATIN.git. It was shown to be the second fastest for perfect and compound SSR mining. It can identify SSRs from coding regions plus SSRs with motif sizes bigger than 6. Besides the SSR mining, SATIN can also analyze SSRs polymorphism on coding-regions from pre-determined groups, and identify SSRs differentially abundant among them on a per-gene basis. To validate, we analyzed SSRs from two groups of Escherichia coli (K12 and O157) and compared the results with 5 known SSRs from coding regions. SATIN identified all 5 SSRs from 237 genes with at least one SSR on it.ConclusionsThe SATIN is a novel microsatellite search software that utilizes an innovative sliding window technique based on a numerical list for repeat region search to identify perfect, and composite SSRs while generating comprehensible and analyzable outputs. It is a tool capable of using files in fasta or GenBank format as input for microsatellite mining, also being able to identify SSRs present in coding regions for GenBank files. In conclusion, we expect SATIN to help identify potential SSRs to be used as genetic markers.

Genomic Microsatellite Mining and Characteristic Analysis of Gobiidae Fish

Genomic Microsatellite Mining and Characteristic Analysis of Gobiidae Fish

Profile microsatellite mining of whole genome sequencing and transcriptomic assembly in dwarf and tall areca nut (Areca catechu) in Indonesia

Abstract. Romadhon MR, Sobir, Suwarno WB, Matra DD. 2024. Profile microsatellite mining of whole genome sequencing and transcriptomic assembly in dwarf and tall areca nut (Areca catechu L.) in Indonesia. Biodiversitas 25: 1081-1088. Areca nut (Areca catechu L.) has high diversity in fruit shape and flowering time. Two superior varieties are commonly cultivated in Indonesia, namely Betara areca nut (tall) and Emas areca nut (dwarf). Molecular level diversity from genomic and transcriptome of areca nut data is available at NCBI, but not yet for Indonesian areca nut. The research compared the results of SSR with two method approaches to detect genetic diversity in the plants accurately. This study aimed to compare the SSR motifs of Betara areca nut and Emas areca nut varieties from whole genome sequencing and transcriptome assembly. The research was conducted at the Leuwikopo Seed Centre Laboratory of the IPB University, Bogor, Indonesia. The methods used are Whole Genome Sequencing (WGS) and transcriptome assembly. A total number of identified SSRs from WGS approach from Betara areca nut of 95 SSRs and Emas areca nut of 95 SSRs, while Betara areca nut SSRs from transcriptome assembly of 466 SSRs and Emas areca nut of 357 SSRs. The percentage of contigs and transcripts from Betara areca nut containing SSR was 7.43% and 4.22%, respectively, while Emas areca nut was 8.06% and 2.04%, respectively. AT is the dominant SSR motif in WGS, while the GA motif dominates the transcriptome assembly results.

Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks

BackgroundMicrosatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. ResultsThe total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. ConclusionThe current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.

EasySSR: a user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison.

Microsatellites, also known as SSRs or STRs, are polymorphic DNA regions with tandem repetitions of a nucleotide motif of size 1-6 base pairs with a broad range of applications in many fields, such as comparative genomics, molecular biology, and forensics. However, the majority of researchers do not have computational training and struggle while running command-line tools or very limited web tools for their SSR research, spending a considerable amount of time learning how to execute the software and conducting the post-processing data tabulation in other tools or manually-time that could be used directly in data analysis. We present EasySSR, a user-friendly web tool with command-line full functionality, designed for practical use in batch identifying and comparing SSRs in sequences, draft, or complete genomes, not requiring previous bioinformatic skills to run. EasySSR requires only a FASTA and an optional GENBANK file of one or more genomes to identify and compare STRs. The tool can automatically analyze and compare SSRs in whole genomes, convert GenBank to PTT files, identify perfect and imperfect SSRs and coding and non-coding regions, compare their frequencies, abundancy, motifs, flanking sequences, and iterations, producing many outputs ready for download such as PTT files, interactive charts, and Excel tables, giving the user the data ready for further analysis in minutes. EasySSR was implemented as a web application, which can be executed from any browser and is available for free at https://computationalbiology.ufpa.br/easyssr/. Tutorials, usage notes, and download links to the source code can be found at https://github.com/engbiopct/EasySSR.

Genome-Wide Survey and Analysis of Microsatellites in Waterlily, and Potential for Polymorphic Marker Development.

Waterlily (Nymphaeaceae), a diploid dicotyledon, is an ornamental aquatic plant. In 2020, the complete draft genome for the blue-petal waterlily (Nymphaea colorata) was made available in GenBank. To date, the genome-wide mining of microsatellites or simple sequence repeats (SSRs) in waterlily is still absent. In the present study, we investigated the characteristics of genome-wide microsatellites for N. colorata and developed polymorphic SSR markers across tropical and hardy waterlilies. A total of 238,816 SSRs were identified in 14 N. colorata chromosomes with an average density of 662.60 SSRs per Mb, and the largest number of SSRs were present on chromosome 1 (n = 30,426, 705.94 SSRs per Mb). The dinucleotide was the most common type, and AT-rich repeats prevail in the N. colorata genome. The SSR occurrence frequencies decreased as the number of motif repeats increased. Among 2442 protein-coding region SSRs, trinucleotides, accounting for 63.84%, were the most abundant. Gene ontology terms for signal transduction (e.g., GO: 0045859 and GO: 0019887) and the lipoic acid metabolism (ko00785,) were overrepresented in GO and KEGG enrichment analysis, respectively. In addition, 107,152 primer pairs were identified, and 13 novel polymorphism SSR markers were employed to distinguish among nine waterlily cultivars, of which Ny-5.2 and Ny-10.1 were the most informative SSR loci. This study contributes the first detailed characterization of SSRs in N. colorata genomes and delivers 13 novel polymorphism markers, which are useful for the molecular breeding strategies, genetic diversity and population structure analysis of waterlily.

Automating microsatellite screening and primer design from multi-individual libraries using Micro-Primers

Analysis of intra- and inter-population diversity has become important for defining the genetic status and distribution patterns of a species and a powerful tool for conservation programs, as high levels of inbreeding could lead into whole population extinction in few generations. Microsatellites (SSR) are commonly used in population studies but discovering highly variable regions across species’ genomes requires demanding computation and laboratorial optimization. In this work, we combine next generation sequencing (NGS) with automatic computing to develop a genomic-oriented tool for characterizing SSRs at the population level. Herein, we describe a new Python pipeline, named Micro-Primers, designed to identify, and design PCR primers for amplification of SSR loci from a multi-individual microsatellite library. By combining commonly used programs for data cleaning and microsatellite mining, this pipeline easily generates, from a fastq file produced by high-throughput sequencing, standard information about the selected microsatellite loci, including the number of alleles in the population subset, and the melting temperature and respective PCR product of each primer set. Additionally, potential polymorphic loci can be identified based on the allele ranges observed in the population, to easily guide the selection of optimal markers for the species. Experimental results show that Micro-Primers significantly reduces processing time in comparison to manual analysis while keeping the same quality of the results. The elapsed times at each step can be longer depending on the number of sequences to analyze and, if not assisted, the selection of polymorphic loci from multiple individuals can represent a major bottleneck in population studies.

Genome-wide mining of potentially-hypervariable microsatellites and validation of markers in Momordica charantia L.

Relatively large number of bitter melon microsatellite markers have been reported; however, only few resulted in successful PCR amplification and a small fraction shown polymorphisms. This limited chance of recovering polymorphic markers makes the primer screening a cost-demanding process. To test the hypothesis that microsatellites with longer motifs as well as shorter motifs repeated substantially shall have better prospects to be polymorphic, we performed a genome-wide microsatellite mining. We selected a sample of genome-wide microsatellites with prescribed motif lengths or satisfying a target repeat number, which were considered potentially-hyper variable, for primer designing and validation. Seventy five microsatellites satisfying these criteria were identified, of which 69 were validated through successful PCR amplification. Among them, 40 (53.33% of the markers identified) were polymorphic. This result showed a significantly higher success compared to our initial results of 51 (20.64%) polymorphic markers out of the 188 amplified when 247 previously reported markers were screened. The screening of two cultivars revealed that markers were efficient to identify up to three alleles. The characterization of these 69 new markers with 247 markers previously reported showed that di-nucleotide motifs were most abundant, followed by tri- and tetra-nucleotide motifs. TC motif markers were most polymorphic (12.08%) followed by AG and CT motifs (both 9.89%). Similarly, AGA (6.59%) and TATT (3.29%) were most polymorphic among the tri- and tetra-nucleotide motifs. These 69 hypervariable microsatellite markers along with 188 markers initially validated in this study shall be useful for phylogenetic analyses, studies of linkage, QTL, and association mapping in bitter melon.

RNA-Seq transcriptome analysis of Jatropha curcas L. accessions after salt stimulus and unigene-derived microsatellite mining

The small oleaginous tree of Jatropha curcas L. (physic nut) is an excellent biodiesel source whose crop could represent a good income source for farmers in tropical and semi-arid zones. However, in some areas in particular, salinity, such as many other abiotic stresses, can compromise productivity. We analyzed the root RNA-Seq transcriptome of two Brazilian J. curcas accessions after a three-hour NaCl exposition (150 mM) aiming at identifying differentially expressed genes (DEGs) useful for breeding programs. The de novo transcriptome covered 145,422 assembled transcripts (126,343 unigenes), out of which 84,589 showed at least one significant alignment to the GenBank reference genome. Differentially expressed unigenes (DEGs) of the salt-sensitive Jc171 accession (4,646) suppressed those of the salt-tolerant Jc183 (57) one. A MapMan analysis of the DEGs using Manihot esculenta Crantz genes as reference (Euphorbiaceae family) highlighted the metabolism of phytohormone, carbohydrate (CHO), lipid, amino acid, redox, and secondary metabolite in the salt-responses. RT-qPCR results of nine selected Jc183 DEGs [phenylalanine ammonia-lyase (PAL), S-adenosylmethionine-dependent methyltransferase (SAMe), S-adenosylmethionine synthase (SAM), carboxylesterase (CXE), homeobox-leucine zipper gene (HD-Zip), NAC transcription factor gene (NAC), methionine-gamma lyase (MGL), peroxidase (PX), and xyloglucan endotransglucosylase (XTH)] evaluated in 36 combinations accession/treatments validated 86.11 % of the in silico results. The data generated improved the J. curcas transcriptome based on Illumina-21 bp tags as reported before, which can benefit breeders in the improvement of salt-tolerance in J. curcas. Additionally, primer pairs successfully designed for 1,423 DEGs presenting microsatellite motifs can contribute to the development of co-dominant molecular markers, a very useful marker applied to genetic analysis.

Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra).

The complete genome sequence provides the opportunity for genome-wide and coding region analysis of SSRs in the king cobra and for cross-species identification of microsatellite markers in the Chinese cobra. In the Ophiophagus hannah genome, tetranucleotide repeats (38.03%) were the most abundant category, followed by dinucleotides (23.03%), pentanucleotides (13.07%), mononucleotides (11.78%), trinucleotides (11.49%) and hexanucleotides (2.6%). Twenty predominant motifs in the O. hannah genome were (A)n (C)n, (AC)n, (AG)n, (AT)n, (AGG)n, (AAT)n, (AAG)n, (AAC)n, (ATG)n, (ATAG)n, (AAGG)n, (ATCT)n, (CCTT)n, (ATTT)n, (AAAT)n, (AATAG)n, (ATTCT)n, (ATATGT)n, (AGATAT)n. In total, 4344 SSRs were found in coding sequences (CDSs). Tetranucleotides (52.79%) were the most abundant microsatellite type in CDS, followed by trinucleotides (28.50%), dinucleotides (11.02%), pentanucleotides (4.42%), mononucleotides (1.77%), and hexanucleotides (1.50%). A total of 984 CDSs containing microsatellites were assigned 11152 Gene Ontology (GO) functional terms. Gene Ontology (GO) analysis demonstrated that cellular process, cell and binding were the most frequent GO terms in biological process, cellular component and molecular function, respectively. Thirty-two novel highly polymorphic (PIC > 0.5) SSR markers for Naja atra were developed from cross-species amplification based on the tetranucleotide microsatellite sequences in the king cobra genome. The number of alleles (NA) per locus had between 3 and 11 alleles with an average of 6.5, the polymorphism information content (PIC) value ranged from 0.521 to 0.858 (average = 0.707), the observed heterozygosity (Ho) of 32 microsatellite loci ranged from 0.292 to 0.875 (mean = 0.678), the expected heterozygosity (HE) ranged from 0.561 to 0.889 (average = 0.761), and 3 microsatellite loci exhibited statistically significant departure from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction (p < 0.003).

OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer.

Microsatellite mining is a common outcome of the in silico approach to genomic studies. The resulting short tandemly repeated DNA could be used as molecular markers for studying polymorphism, genotyping and forensics. The omni short tandem repeat finder and primer designer (OSTRFPD) is among the few versatile, platform-independent open-source tools written in Python that enables researchers to identify and analyse genome-wide short tandem repeats in both nucleic acids and protein sequences. OSTRFPD is designed to run either in a user-friendly fully featured graphical interface or in a command line interface mode for advanced users. OSTRFPD can detect both perfect and imperfect repeats of low complexity with customisable scores. Moreover, the software has built-in architecture to simultaneously filter selection of flanking regions in DNA and generate microsatellite-targeted primers implementing the Primer3 platform. The software has built-in motif-sequence generator engines and an additional option to use the dictionary mode for custom motif searches. The software generates search results including general statistics containing motif categorisation, repeat frequencies, densities, coverage, guanine–cytosine (GC) content, and simple text-based imperfect alignment visualisation. Thus, OSTRFPD presents users with a quick single-step solution package to assist development of microsatellite markers and categorise tandemly repeated amino acids in proteome databases. Practical implementation of OSTRFPD was demonstrated using publicly available whole-genome sequences of selected Plasmodium species. OSTRFPD is freely available and open-sourced for improvement and user-specific adaptation.

SSRome: an integrated database and pipelines for exploring microsatellites in all organisms.

Over the past decade, many databases focusing on microsatellite mining on a genomic scale were released online with at least one of the following major deficiencies: (i) lacking the classification of microsatellites as genic or non-genic, (ii) not comparing microsatellite motifs at both genic and non-genic levels in order to identify unique motifs for each class or (iii) missing SSR marker development. In this study, we have developed ‘SSRome’ as a web-based, user-friendly, comprehensive and dynamic database with pipelines for exploring microsatellites in 6533 organisms. In the SSRome database, 158 million microsatellite motifs are identified across all taxa, in addition to all the mitochondrial and chloroplast genomes and expressed sequence tags available from NCBI. Moreover, 45.1 million microsatellite markers were developed and classified as genic or non-genic. All the stored motif and marker datasets can be downloaded freely. In addition, SSRome provides three user-friendly tools to identify, classify and compare motifs on either a genome- or transcriptome-wide scale. With the implementation of PHP, HTML and JavaScript, users can upload their data for analysis via a user-friendly GUI. SSRome represents a powerful database and mega-tool that will assist researchers in developing and dissecting microsatellite markers on a high-throughput scale.

Microsatellite mining in the genus Colletotrichum

Genomic data available in the public database are valuable resources for mining microsatellite or simple sequence repeat (SSR) markers. Though microsatellite markers are available for a few Colletotrichum species but their meagre number and species specificity warrants additional search in the publicly available genome databases. Therefore, in the present investigation, eight Colletotrichum genomes belonging to six clades were mined for microsatellites and we developed 57,170 microsatellite markers. Di and tri microsatellite motifs accounted for >80% share while tetra to deca motifs were rare. Ninety-nine percent of the microsatellites produced a single amplicion when subjected to electronic PCR. In silico cross transferability of the microsatellites exhibited specificity to respective species, illustrating the conserved sequences flanking the microsatellite regions. We found maximum microsatellite cross transferability among C. acutatum, C. fioriniae, and C. nymphaeae genomes that belong to acutatum clade. Thus suggesting that the microsatellites developed for one species in a genome clade may amplify other species of same clade. PCR amplification of 150 microsatellite markers confirms the locus specific amplification. Among the 110 microsatellites used for genotyping the 14 diverse races of C. lindemuthianum, 100 markers were polymorphic. Genotyping of 14 diverse bean anthracnose races with 50 SSR markers grouped them as per their geographic location. We report microsatellite markers for eight Colletotrichum genomes that belong to six clades and this is the first study of genome wide microsatellite marker development in the genus. These genome wide SSR markers will provide a useful tool to discover the population structure in Colletotrichum species and evolutionary insights in future.

Hemocytes transcriptome profile of the Chinese mitten crab (Eriocheir sinensis)

The Chinese mitten crab (Eriocheir sinensis) possesses an open circulatory system, in which hemolymph moves through interconnected sinuses or spaces surrounding organs called hemocoels. The hemocytes are classified into hyalinocytes, semigranulocytes, and granulocytes; and limited transcriptomics research is available. In this study, the transcriptome of the crab E. sinensis hemocytes was characterized. A total of 14,380,229 clean reads representing a total of 4.31 Gb nucleotides dataset were produced. A total of 67,047 contigs were obtained and 12.49% (8375) and 9.74% (6533) of the contigs were matched to data publicly available from the GenBank nr nucleotide and Uniprot databases, respectively. Among these contigs, 4344 contigs belong to three categories of Gene Ontology, 126 contigs to 21 subcategories of KEGG, and 4962 contigs to 25 categories of the COG database. A total of 508,379 and 345 transcripts of the E. sinensis showed >40% sequence similarity with transcripts expressed in the vertebrate blood cells from tilapia (Oreochromis niloticus), Chinese softshell turtle (Trionyx sinensis) and chicken (Gallus gallus) respectively. A total of 53,077 single nucleotide polymorphisms were identified and 9912 SSRs for microsatellite mining were found. The most frequent repeat motifs detected were dinucleotide repeats, accounting for 37.52% of the total repeats. Our data provides an important gene resource for the exploitation of molecular marker-assisted breeding, immune mechanisms and conservation of germplasm in the crab E. sinensis.

Exploring single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes in the jellyfish (Rhopilema esculentum) by transcriptome sequencing

In this study, single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes (DEGs) in the oral parts, gonads, and umbrella parts of the jellyfish Rhopilema esculentum were analyzed by RNA-Seq technology. A total of 76.4 million raw reads and 72.1 million clean reads were generated from deep sequencing. Approximately 119,874 tentative unigenes and 149,239 transcripts were obtained. A total of 1,034,708 SNP markers were detected in the three tissues. For microsatellite mining, 5088 SSRs were identified from the unigene sequences. The most frequent repeat motifs were mononucleotide repeats, which accounted for 61.93%. Transcriptome comparison of the three tissues yielded a total of 8841 DEGs, of which 3560 were up-regulated and 5281 were down-regulated. This study represents the greatest sequencing effort carried out for a jellyfish and provides the first high-throughput transcriptomic resource for jellyfish.

In silico mining of microsatellites and analysis of genetic diversity among inter‐ and intra‐generic aphids of the subfamily Aphidinae

AbstractNearly 5 000 aphid species damage crops, either by sucking plant sap or as disease‐transmitting vectors. Microsatellites are used for understanding molecular diversity and eco‐geographical relationships among aphid species. Expressed sequence tag (EST)‐microsatellite motifs were identified through an in silico approach using inbuilt simple sequence repeat mining tools in aphid EST dataset. Microsatellite mining revealed one in every five aphid genes as containing a repeat motif, and out of 9 290 EST microsatellites mined from Aphis gossypii Glover and Acyrthosiphon pisum (Harris) (both Hemiptera: Aphididae), 80% were of A and/or T (AT, ATA, AAT, AATA, and ATTT) motifs, and the rest contained G and/or C motifs. All microsatellite sequences were annotated using BLAST. Primers for EST microsatellites were designed using the Primer 3.0 tool. 106 primer pairs of both dinucleotide repeats (DNRs) and trinucleotide repeats (TNRs), representing open reading frames (ORFs) and untranslated regions (UTRs), were synthesized to amplify 15 aphid species belonging to the subfamily Aphidinae, collected from diverse hosts. Four hundred forty‐five polymorphic alleles were amplified. Fifty TNR and 23 DNR microsatellites amplified across the species studied. Polymorphism information content values of microsatellites ranged from 0.23 to 0.91, amplifying 2–16 alleles. Genetic similarity indices were estimated using the ‘NTSYS‐pc’ software package. Unweighted pair group with arithmetic mean and principal component analysis resolved taxonomic relationships of the aphid species studied. The new aphid microsatellites developed will provide valuable information to researchers to study Indian aphid species diversity and genetic relationships.

Microsatellites mining in date palm (Phoenix dactylifera L.) and their cross transferability across Arecaceae family

Phoenix dactylifera L. (date palm) is the first publicly available nuclear genome sequence under Arecaceae family and indeed under the entire order Arecales. These genomic sequences were mined for microsatellites which could be used for marker assisted selection for important traits. We have developed an integrated, configurable and time effective microsatellite mining and annotation pipeline for this purpose. Microsatellite survey of date palm whole genome shotgun sequences using the developed pipeline detected a total of 166,760 perfect repeats with an average of one SSR per 2.2kb. Putative functions of these SSR-containing sequences within the proximity of genic regions were predicted. Primers targeting the functionally important SSR regions were designed and a set of eight SSR primers synthesized and were validated in vitro across five members of the Arecaceae family (coconut, arecanut, oilpalm, date palm and palmyrah palm). We have found that 28.6% of the SSRs are common among the members of arecaceae family. Those SSRs could be used in molecular marker analysis of less studied palm family members like arecanut and palmyrah palm.

LeishMicrosatDB: open source database of repeat sequences detected in six fully sequenced Leishmania genomes.

A Leishmania Microsatellite Database (LeishMicrosatDB) is reported for genome wise mining of microsatellites in six Leishmania species, using in silico techniques. This was created to provide parasitologists a platform to understand the genome characterization, mapping, phylogeny and evolutionary analysis. The present version of the database contains 1 738 669 simple sequence repeats of which 181 s756 repeats are present in compound form. The repeats can be sought in a chromosome using input parameters such as repeat type (mono- hexa), coding status, repeat unit length and repeat sequence motif. The genic repeats have been further hyperlinked with their corresponding locus id, and the database is appended with primer3 plus for primer designing of selected repeats with left and right flanking sequences up to 250 bp. Information on clustering and polymorphic repeats can also be retrieved. This database may also be adopted as a tool to study the relative occurrence and distribution of microsatellites across the parasitic genome. The database can enable a biologist to select markers at desired intervals over the chromosomes, and can be accessed as an open source repository at http://biomedinformri.com/leishmicrosat.Database URL: http://biomedinformri.com/leishmicrosat

Standalone EST microsatellite mining and analysis tool (SEMAT): for automated EST-SSR analysis in plants

Public databases contain large datasets of plant expressed sequence tags (ESTs) that can be used for mining microsatellite/simple sequence repeat markers. The identification and annotation of these markers take considerable time. Here, we describe an efficient, high-throughput microsatellite mining, and analysis pipeline, standalone EST microsatellite mining and analysis tool (SEMAT). The pipeline bundles sequence trimming, assembly, microsatellite identification, primer selection, and blast annotation, for which it consecutively uses SeqClean, CAP3, MISA, Primer3, and Blast. SEMAT is written using Perl scripts, and it runs under Ubuntu and Fedora Linux. SEMAT is an efficient and time-saving bioinformatics tool to accomplish the high throughput EST-SSR analysis. It is freely available from http://semat.cpcribioinformatics.in/.

In silico mining of microsatellites in coding sequences of the date palm (Arecaceae) genome, characterization, and transferability.

• Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene.• Methods and Results: Tandem repeat motifs of 3–6 bp were searched using a simple sequence repeat (SSR)–pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns.• Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.