Polynucleotide sequences of candida dubliniensis and probes for detection

Abstract

The present invention relates to identification of centromeric sequences of Candida dubliniensis and localization of CdCse4p centromeric histone to the identified region. Also the present invention relates to distinguishing Candida dubliniensis from other members of genus Candida.

1 . A polynucleotide sequence consisting of SEQ ID NO 1, 2, 3, 4, 5, 6, 7 or 8. 
     
     
         2 .- 25 . (canceled) 
     
     
         26 . A set of polynucleotide primers comprising forward and reverse primers that hybridize to a centromeric region of  Candida dubliniensis  selected from the group consisting of Chromosome 1, Chromosome 2, Chromosome 3, Chromosome 4, Chromosome 5, Chromosome 6, Chromosome 7 and Chromosome R. 
     
     
         27 . A set of 20 primers as claimed in  claim 26 , wherein the forward and the reverse primers are used for amplification of centromeric region of chromosome 1 of  Candida dubliniensis.    
     
     
         28 . A set of 20 primers according to  claim 27  consisting of SEQ ID NOS. 9, 11, 13, 15, 17, 19, 21, 23, 25 and 27 as forward primers and SEQ ID NOS. 10, 12, 14, 16, 18, 20, 22, 24, 26 and 28 as corresponding reverse primers respectively. 
     
     
         29 . A set of 14 primers as claimed in  claim 26 , wherein the forward and the reverse primers are used for amplification of centromeric region of chromosome 2 of  Candida dubliniensis.    
     
     
         30 . A set of 14 primers according to  claim 29  consisting of SEQ ID NOS. 29, 31, 33, 35, 37, 39 and 41 as forward primers and SEQ ID NOS. 30, 32, 34, 36, 38, 40 and 42 as corresponding reverse primers respectively. 
     
     
         31 . A set of 10 primers as claimed in  claim 26 , wherein the forward and the reverse primers are used for amplification of centromeric regions of chromosome 3 of  Candida dubliniensis.    
     
     
         32 . A set of 10 primers according to  claim 31  consisting of SEQ ID NOS. 43, 45, 47, 49 and 51 as forward primers and SEQ ID NOS. 44, 46, 48, 50 and 52 as corresponding reverse primers respectively. 
     
     
         33 . A set of 16 primers as claimed in  claim 26 , wherein the forward and the reverse primers are used for amplification of centromeric regions of chromosome 4 of  Candida dubliniensis.    
     
     
         34 . A set of 16 primers according to  claim 33  consisting of SEQ ID NOS. 53, 55, 57, 59, 61, 63, 65 and 67 as forward primers and SEQ ID NOS. 54, 56, 58, 60, 62, 64, 66 and 68 as corresponding reverse primers respectively. 
     
     
         35 . A set of 10 primers as claimed in  claim 26 , wherein the forward and the reverse primers are used for amplification of centromeric regions of chromosome 5 of  Candida dubliniensis.    
     
     
         36 . A set of 10 primers according to  claim 35  consisting of SEQ ID NOS. 69, 71, 73, 75 and 77 as forward primers and SEQ ID NOS. 70, 72, 74, 76 and 78 as corresponding reverse primers respectively. 
     
     
         37 . A set of 16 primers as claimed in  claim 26 , wherein the forward and the reverse primers are used for amplification of centromeric regions of chromosome 6 of  Candida dubliniensis.    
     
     
         38 . A set of 16 primers according to  claim 37  consisting of SEQ ID NOS. 79, 81, 83, 85, 87, 89, 91 and 93 as forward primers and SEQ ID NOS. 80, 82, 84, 86, 88, 90, 92 and 94 as corresponding reverse primers respectively. 
     
     
         39 . A set of 18 primers as claimed in  claim 26 , wherein the forward and the reverse primers are used for amplification of centromeric regions of chromosome 7 of  Candida dubliniensis.    
     
     
         40 . A set of 18 primers according to  claim 39  consisting of SEQ ID NOS. 95, 97, 99, 101, 103, 105, 107, 109 and 111 as forward primers and SEQ ID NOS. 96, 98, 100, 102, 104, 106, 108, 110 and 112 as corresponding reverse primers respectively. 
     
     
         41 . A set of 14 primers as claimed in  claim 26 , wherein the forward and the reverse primers are used for amplification of centromeric regions of chromosome R of  Candida dubliniensis.    
     
     
         42 . A set of 14 primers according to  claim 41  consisting of SEQ ID NOS. 114, 116, 118, 120, 122, 123 and 126 as forward primers and SEQ ID NOS. 113, 115, 117, 119, 121, 124 and 125 as corresponding reverse primers respectively. 
     
     
         43 . A process of identification of centromeric sequences of  Candida dubliniensis , said method comprising steps of:
 a) identifying putative Cse4p binding region; and   b) amplifying the putative Cse4p binding region to identify centromeric sequences of the  Candida dubliniensis.      
     
     
         44 . The process as claimed in  claim 43 , wherein the identification of putative Cse4p biding regions is carried out by sequence analysis and chromatin immunoprecipitation. 
     
     
         45 . The process as claimed in  claim 43 , wherein the amplification of the putative Cse4p binding regions is carried out using any set of a forward primer selected from the group consisting of SEQ ID NOS. 9, 11, 13, 15, 17, 19, 21, 23, 25 and 27 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, respectively, for chromosome 1 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 29, 31, 33, 35, 37, 39 and 41 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 30, 32, 34, 36, 38, 40 and 42, respectively, for chromosome 2 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 43, 45, 47, 49 and 51 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 44, 46, 48, 50 and 52, respectively, for chromosome 3 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 53, 55, 57, 59, 61, 63, 65 and 67 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 54, 56, 58, 60, 62, 64, 66 and 68, respectively, for chromosome 4 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 69, 71, 73, 75 and 77 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 70, 72, 74, 76 and 78, respectively, for chromosome 5 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 79, 81, 83, 85, 87, 89, 91 and 93 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 80, 82, 84, 86, 88, 90, 92 and 94, respectively, for chromosome 6 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 95, 97, 99, 101, 103, 105, 107, 109 and 111 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 96, 98, 100, 102, 104, 106, 108, 110 and 112, respectively, for chromosome 7 of  Candida dubliniensis  and a forward primer selected from the group consisting of SEQ ID NOS. 114, 116, 118, 120, 122, 123 and 126 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 113, 115, 117, 119, 121, 124 and 125, respectively, for chromosome R of  Candida dubliniensis ; or any combination of said primers thereof. 
     
     
         46 . A method of distinguishing  Candida dubliniensis  from  Candida albicans  in a sample, said method comprising steps of
 a) isolating DNA from the organism in the sample; and   b) amplifying the Cse4p binding regions with primers capable of amplifying said regions in the  Candida dubliniensis  to distinguish it from  Candida albicans.      
     
     
         47 . The method as claimed in  claim 46 , wherein the identification of putative Cse4p biding regions is carried out by sequence analysis and chromatin immunoprecipitation. 
     
     
         48 . The method as claimed in  claim 46 , wherein the amplification of the putative Cse4p binding regions is carried out using any set of a forward primer selected from the group consisting of SEQ ID NOS. 9, 11, 13, 15, 17, 19, 21, 23, 25 and 27 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, respectively, for chromosome 1 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 29, 31, 33, 35, 37, 39 and 41 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 30, 32, 34, 36, 38, 40 and 42, respectively, for chromosome 2 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 43, 45, 47, 49 and 51 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 44, 46, 48, 50 and 52, respectively, for chromosome 3 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 53, 55, 57, 59, 61, 63, 65 and 67 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 54, 56, 58, 60, 62, 64, 66 and 68, respectively, for chromosome 4 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 69, 71, 73, 75 and 77 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 70, 72, 74, 76 and 78, respectively, for chromosome 5 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 79, 81, 83, 85, 87, 89, 91 and 93 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 80, 82, 84, 86, 88, 90, 92 and 94, respectively, for chromosome 6 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 95, 97, 99, 101, 103, 105, 107, 109 and 111 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 96, 98, 100, 102, 104, 106, 108, 110 and 112, respectively, for chromosome 7 of  Candida dubliniensis  and a forward primer selected from the group consisting of SEQ ID NOS. 114, 116, 118, 120, 122, 123 and 126 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 113, 115, 117, 119, 121, 124 and 125, respectively, for chromosome R of  Candida dubliniensis ; or any combination of said primers thereof. 
     
     
         49 . A kit for identification of  Candida dubliniensis  comprising a set of primers having SEQ ID NOS. 9 to 126. 
     
     
         50 . The kit as claimed in  claim 49 , wherein the amplification of the putative Cse4p binding regions is carried out using any set of a forward primer selected from the group consisting of SEQ ID NOS. 9, 11, 13, 15, 17, 19, 21, 23, 25 and 27 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, respectively, for chromosome 1 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 29, 31, 33, 35, 37, 39 and 41 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 30, 32, 34, 36, 38, 40 and 42, respectively, for chromosome 2 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 43, 45, 47, 49 and 51 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 44, 46, 48, 50 and 52, respectively, for chromosome 3 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 53, 55, 57, 59, 61, 63, 65 and 67 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 54, 56, 58, 60, 62, 64, 66 and 68, respectively, for chromosome 4 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 69, 71, 73, 75 and 77 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 70, 72, 74, 76 and 78, respectively, for chromosome 5 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 79, 81, 83, 85, 87, 89, 91 and 93 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 80, 82, 84, 86, 88, 90, 92 and 94, respectively, for chromosome 6 of  Candida dubliniensis ; a forward primer selected from the group consisting of SEQ ID NOS. 95, 97, 99, 101, 103, 105, 107, 109 and 111 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 96, 98, 100, 102, 104, 106, 108, 110 and 112, respectively, for chromosome 7 of  Candida dubliniensis  and a forward primer selected from the group consisting of SEQ ID NOS. 114, 116, 118, 120, 122, 123 and 126 and its corresponding reverse primer selected from the group consisting of SEQ ID NOS. 113, 115, 117, 119, 121, 124 and 125, respectively, for chromosome R of  Candida dubliniensis ; or any combination of said primers thereof.