A comparative analysis of distribution and conservation of microsatellites in the transcripts of sequenced Fusarium species and development of genic-SSR markers for polymorphism analysis.
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.
National Bureau of Agriculturally Important Microorganisms, Mau-275101, Uttar Pradesh, India sahil77786@gmail.com.
Sahil
S
Mahfooz
National Bureau of Agriculturally Important Microorganisms, Mau-275101, Uttar Pradesh, India.
Arpita
A
Srivastava
National Bureau of Agriculturally Important Microorganisms, Mau-275101, Uttar Pradesh, India.
Alok K
AK
Srivastava
National Bureau of Agriculturally Important Microorganisms, Mau-275101, Uttar Pradesh, India.
Dilip K
DK
Arora
D003198:Computer Simulation; D020224:Expressed Sequence Tags; D005670:Fusarium / Q000235:genetics*; D005819:Genetic Markers; D014644:Genetic Variation; D018895:Microsatellite Repeats; D010802:Phylogeny; D011110:Polymorphism, Genetic
D005819:Genetic Markers
Fusarium species; comparative genomics; genetic diversity; polymorphic markers