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Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants.

Haq SU, Jain R, Sharma M, Kachhwaha S, Kothari SL - Int J Genomics (2014)

Bottom Line: Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75.The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%.Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, University of Rajasthan, Jaipur 302004, India.

ABSTRACT
Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%. Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.

No MeSH data available.


Related in: MedlinePlus

Details of predicted amino acids encoded by trinucleotide motifs.
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Related In: Results  -  Collection


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fig5: Details of predicted amino acids encoded by trinucleotide motifs.

Mentions: Among 263 microsatellites, trinucleotide repeat motifs were the most abundant, with a frequency of 47.52% followed by tetra- (19.77%), di- (19.01%), penta- (9.12%), and hexanucleotide (4.56%) repeats. Varshney et al. [42] reported that trinucleotide repeats (TNRs) are the most common, followed by either dinucleotide repeats (DNRs) or tetranucleotide (TTNRs) repeats. Our result of trinucleotide repeat frequency is in close agreement with previous studies reporting 48.5% in sugarcane [49] and 48% in Setaria italic [32]. Some other studies also reported high TNRs, namely, cereals [50], Ricinus communis [51], Eucalyptus globulus [52], sugarcane [12], and Setaria italica [31]. The reason for the abundance of trinucleotide repeats in plants might be attributed to absence of frameshift mutations [53]. Among all types of trinucleotide motifs, AAG/CTT, CCG/CGG, and AGC/CTG were in high proportion. Motifs GGA/TTC, CCT/AGG, GAA/TTC, and CCG/GGC were also detected. These motifs can form hairpin-like structures, which stabilize and allow them to escape from repair mechanisms [15, 54]. Each trinucleotide motif encodes a particular amino acid including stop codon which participates within protein in various metabolic activities [20, 55]. Predictable, twenty different types of amino acids were detected in trinucleotide motifs including one stop codon (Figure 5). Amino acids (leucine, serine, alanine, and arginine) encoded by trinucleotide motifs are in agreement with earlier studies [20, 30, 55, 56].


Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants.

Haq SU, Jain R, Sharma M, Kachhwaha S, Kothari SL - Int J Genomics (2014)

Details of predicted amino acids encoded by trinucleotide motifs.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4217358&req=5

fig5: Details of predicted amino acids encoded by trinucleotide motifs.
Mentions: Among 263 microsatellites, trinucleotide repeat motifs were the most abundant, with a frequency of 47.52% followed by tetra- (19.77%), di- (19.01%), penta- (9.12%), and hexanucleotide (4.56%) repeats. Varshney et al. [42] reported that trinucleotide repeats (TNRs) are the most common, followed by either dinucleotide repeats (DNRs) or tetranucleotide (TTNRs) repeats. Our result of trinucleotide repeat frequency is in close agreement with previous studies reporting 48.5% in sugarcane [49] and 48% in Setaria italic [32]. Some other studies also reported high TNRs, namely, cereals [50], Ricinus communis [51], Eucalyptus globulus [52], sugarcane [12], and Setaria italica [31]. The reason for the abundance of trinucleotide repeats in plants might be attributed to absence of frameshift mutations [53]. Among all types of trinucleotide motifs, AAG/CTT, CCG/CGG, and AGC/CTG were in high proportion. Motifs GGA/TTC, CCT/AGG, GAA/TTC, and CCG/GGC were also detected. These motifs can form hairpin-like structures, which stabilize and allow them to escape from repair mechanisms [15, 54]. Each trinucleotide motif encodes a particular amino acid including stop codon which participates within protein in various metabolic activities [20, 55]. Predictable, twenty different types of amino acids were detected in trinucleotide motifs including one stop codon (Figure 5). Amino acids (leucine, serine, alanine, and arginine) encoded by trinucleotide motifs are in agreement with earlier studies [20, 30, 55, 56].

Bottom Line: Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75.The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%.Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, University of Rajasthan, Jaipur 302004, India.

ABSTRACT
Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%. Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.

No MeSH data available.


Related in: MedlinePlus