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(CP) Gene of Papaya Ri

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(CP) Gene of Papaya Ri Results and Discussion 4. RESULTS AND DISCUSSION 4.1 Genetic diversity analysis of coat protein (CP) gene of Papaya ringspot virus-P (PRSV-P) isolates from multiple locations of Western India Results – 4.1.1 Sequence analysis In this study, fourteen CP gene sequences of PRSV-P originating from multiple locations of Western Indian States, Gujarat and Maharashtra (Fig. 3.1), have been analyzed and compared with 46 other CP sequences from different geographic locations of America (8), Australia (1), Asia (13) and India (24) (Table 4.1; Fig. 4.1). The CP length of the present isolates varies from 855 to 861 nucleotides encoding 285 to 287 amino acids. Fig. 4.1: Amplification of PRSV-P coat protein (CP) gene from 14 isolates of Western India. From left to right lanes:1: Ladder (1Kb), 2: IN-GU-JN, 3: IN-GU-SU, 4: IN-GU-DS, 5: IN-GU-RM, 6: IN-GU-VL, 7: IN-MH-PN, 8: IN-MH-KO, 9: IN-MH-PL, 10: IN-MH-SN, 11: IN-MH-JL, 12: IN-MH-AM, 13: IN-MH-AM, 14: IN-MH-AK, 15: IN-MH-NS,16: Negative control. Red arrow indicates amplicon of Coat protein (CP) gene. Table 4.1: Sources of coat protein (CP) gene sequences of PRSV-P isolates from India and other countries used in this study. Country Name of Length GenBank Origin¥ Reference isolates* (nts) Acc No IN-GU-JN GU-Jamnagar 861 MG977140 This study IN-GU-SU GU-Surat 855 MG977142 This study IN-GU-DS GU-Desalpur 855 MG977139 This study India IN-GU-RM GU-Ratlam 858 MG977141 This study IN-GU-VL GU-Valsad 855 MG977143 This study IN-MH-PU MH-Pune 861 MH311882 This study Page | 36 Results and Discussion IN-MH-PN MH-Pune 861 MG977150 This study IN-MH-KO MH-Kolhapur 858 MG977147 This study IN-MH-PL MH-Palghar 858 MG977149 This study IN-MH-SN MH-Sangli 861 MG977151 This study IN-MH-JL MH-Jalgaon 858 MG977146 This study IN-MH-AM MH-Amravati 858 MG977145 This study IN-MH-AK MH-Akola 855 MG977144 This study IN-MH-NS MH-Nashik 858 MG977148 This study IN-PU-S MH-Pune 855 AY238881 Jain et al., 2004a IN-PU-M MH-Pune 855 AF063220 Jain et al., 2004a IN-HP HP 852 AY458617 Jain et al., 2004a IN-BH BH 852 EF210196 IN-RJ RJ 855 KF989499 IN-MP MP 858 KC149501 IN-AS AS 852 KC149500 IN-SIK SIK 852 DQ354072 Jain et al., 2004a IN-MG MG 861 MF356497 Mishra and Patil, 2018 IN-CG1 CG 861 DQ354071 IN-CG2 CG 852 AY491011 Jain et al., 2004a IN-HY HR 852 DQ088670 IN-JK JH-Ranchi 852 AY458619 Jain et al., 2004a IN-UP1 UP 855 AY238882 Jain et al., 2004a IN-UP2 UP 852 AY458620 Jain et al.,2004a IN-DL DL 846 AY238883 Jain et al., 2004a IN-WB WB 852 JN979406 Srinivasulu and IN-AP1 AP 918 DQ666638 SaiGopal, 2012 Srinivasulu and IN-AP2 AP 918 AY839864 SaiGopal, 2012 IN-TN1 TN 918 DQ666641 Srinivasulu and Page | 37 Results and Discussion SaiGopal, 2012 IN-TN2 TN 858 EF104919 Srinivasulu and IN-KE KE 918 DQ666640 SaiGopal, 2012 Srinivasulu and IN-KA1 KA 918 DQ666639 SaiGopal, 2012 IN-KA2 KA 918 AY238884 Jain et al.,2004a BD Bangladesh 861 AY423557 Jain et al., 2004a CH1-HN China 867 KT895257 CH2-LM China 858 KT633943 Shen et al.,2014 ID-1 Indonesia 831 AF374864 JP-S Japan 858 D50591 MY-M185P Malaysia 861 AB044342 MN-P Myanmar 851 AB822931 Asia NP-Ne2 Nepal 852 AB823733 (other PH Philippines 834 AF374863 than SL Sri Lanka 837 U14741 Bateson et al.,1994 India) TW-YK Taiwan 861 X97251 Wang et al.,1997 Charoensilp et TH Thailand 858 AY162218 al.,2003 VN-P24 Viet Nam 834 AF506867 BR-PA1 Brazil 861 KC748221 Martinez et al.,2014 CO Colombia 861 KT275938 Ortiz-Rojas et al.,2017 CU-MT1 Cuba 861 KC748227 Martinez et al.,2014 America US-FL US (Florida) 855 AF196839 Davis et al.,1999 US-HA US (Hawaii) 861 S46722 Yeh et al.,1992 JM-FS Jamaica 834 DQ104817 Chin et al.,2007 MX-VrAl Mexico 855 AF319496 VE-T Venezuela 837 DQ339578 Chin et al.,2007 Australia AU-BD Australia 837 U14736 Bateson et al.,1994 Page | 38 Results and Discussion *Name of the isolates are abbreviated or modified in this study. References mentioned only to published sequences. Blank cells/ Columns indicates only NCBI submitted sequences which are not published. ¥Indian States Name Abbreviated as: AP: Andhra Pradesh, AS: Assam, BH:Bihar, CG: Chhattisgarh, DL: Delhi, GU: Gujarat, HP: Himachal Pradesh, HR: Haryana, JK/JH: Jharkhand, KA: Karnataka, KE: Kerala, MG: Meghalaya, MH: Maharashtra, MP: Madhya Pradesh, SIK: Sikkim,RJ: Rajasthan, TN: Tamil Nadu, UP: Uttar Pradesh, WB: West Bengal. Previously reported KE (lysine and glutamic acid) repeats in the N-terminus of the PRSV CP (Silva-Rosales et al., 2000) were observed in all isolates of PRSV-P sequence analyzed. The conserved regions commonly found in Potyviruses CP sequences such as WCIEN, PQQID, DAG and QMKAAA (Shukla et al., 1994) were present in all the PRSV-P isolates from Maharashtra and Gujarat. The 14 CP sequences obtained from this study along with 46 other reported sequences of PRSV-P were compared at amino acid and nucleotide levels (Table 4.2). A general summary of sequence diversity among 60 isolates of PRSV-P, including present isolates of Gujarat and Maharashtra, from different countries and continents have been presented (Table 4.3). The isolates from Maharashtra and Gujarat when compared with other Asian countries and other Indian isolates, showed significantly diverse heterogeneity with the sequence identity of 82-98 % at amino acid (aa) level and 81-100 % at nucleotide (nt) level amongst each other (Table 4.3). Similarly, isolates from neighboring countries showed presence of diverse PRSV population (at aa level) 87-91 % sequence identity with Bangladesh, 85-93 % with Nepal, 85-89 % with Myanmar, 87-90 % with Sri Lanka and 88-93 % with China. However, the PRSV-P isolates from Gujarat and Maharashtra were found more closely related with the PRSV-P isolate from Japan (92-94 %) and USA (91-95 %) at aa level (Table 4.2). All Indian isolates showed identity of aa to Asian isolates by 81–96 %, Australian isolates by 83-93 %, whereas showed 81- 97% with American isolates. Considerably heterogeneous population of PRSV-P was observed within Gujarat which showed the amino acid sequence identity of 91-100 %. A similar situation was also observed within Maharashtra where the shared aa sequence identities among the PRSV-P population were between 91-99 % (Table 4.3). Page | 39 Results and Discussion Table 4.2: PRSV coat protein (CP) gene (amino acid) percent identity between PRSV-P isolates from this study and other reported isolates from different countries. Gujarat State Maharashtra State JL PL SN NS PN PU JN AK SU DS KO VL AM - PRSV-P isolates RM - - - - - - - - - - - - - GU GU GU GU MH MH MH MH MH MH GU MH MH MH - - - - - - - - - - - - - - IN IN IN IN IN IN IN IN IN IN IN IN IN IN IN-HP 86 91 87 90 91 89 90 90 89 88 91 90 90 93 IN-MG 86 92 88 90 91 89 91 90 89 88 92 91 90 92 IN-BH 86 91 87 90 91 89 91 90 89 89 90 90 91 89 IN-RJ 94 94 98 96 94 92 92 94 91 93 94 94 94 90 IN-MP 90 94 90 92 94 96 95 94 95 92 92 92 93 92 IN-AS 85 90 86 89 90 88 89 89 88 87 91 91 89 92 IN-SIK 85 90 86 89 90 88 89 89 88 87 91 91 89 93 IN-CG2 87 91 87 91 91 90 92 91 90 89 91 91 91 90 IN-CG1 91 94 92 94 94 94 93 94 93 94 93 93 95 93 IN-HY 86 92 88 90 92 90 92 91 90 90 91 91 92 93 IN-JK 86 92 88 91 92 90 91 91 90 90 92 91 92 93 India IN-UP2 87 91 87 91 91 90 92 91 90 89 91 91 91 94 (other IN-UP1 90 95 92 93 95 93 93 97 92 94 93 94 95 84 states) IN-DL 87 92 89 91 92 91 92 91 90 90 92 92 92 82 IN-WB 86 92 87 91 92 91 91 90 90 90 91 91 91 85 IN-AP1 84 89 85 86 89 90 90 88 90 87 86 86 88 90 IN-AP2 82 86 83 85 86 87 87 86 87 84 83 83 86 84 IN-TN1 85 89 85 87 89 90 90 88 89 86 86 86 88 83 IN-TN2 90 94 90 92 94 95 96 94 95 92 92 92 94 90 IN-KE 83 89 85 86 89 89 89 87 89 85 85 85 87 90 IN-KA1 84 88 84 86 88 88 89 88 89 85 85 85 87 90 IN-KA2 91 95 91 93 95 97 97 95 98 93 92 92 95 92 IN-PU-S 91 96 93 94 95 94 94 98 93 95 94 95 96 90 IN-PU-M 91 96 93 94 95 94 94 98 93 95 94 95 96 90 VN-P24 87 92 90 90 92 90 90 90 89 90 90 90 91 90 Asia ID-1 87 91 89 89 91 91 90 91 91 90 90 89 90 88 ( other PH 84 89 87 87 89 87 87 88 87 87 87 87 87 85 than TW-YK 89 94 91 92 93 92 94 93 92 91 92 93 93 90 India) CH1-HN 90 92 91 91 92 92 92 92 91 91 90 91 92 88 CH2-LM 90 93 91 91 93 92 93 93 92 91 91 92 93 90 TH 89 93 92 91 93 92 92 92 91 91 91 92 92 89 Page | 40 Results and Discussion JP-S 90 94 92 93 94 93 93 94 92 93 92 93 94 90 MN-P 86 89 87 87 89 87 87 87 87 85 87 87 87 85 NP-Ne2 85 90 86 89 90 88 90 89 88 88 90 90 90 93 BD 87 91 89 90 91 91 90 91 91 89 90 90 91 89 SL 87 90 88 89 90 89 90 90 89 88 87 88 90 86 MY-M185P 89 93 91 91 93 92 92 93 91 91 91 92 92 89 Australia AU-BD 89 92 90 91 92 91 91 91 91 91 90 91 91 89 Cu-MT1 89 93 91 93 92 92 92 92 91 91 91 91 92 89 BR-PA1 89 93 91 92 93 92 92 93 92 91 92 92 93 90 US-HA 91 95 93 94 95 94 94 94 93 94 94 94 95 92 US-FL 91 95 93 93 95 93 93 94 93 93 93 93 94 91 America CO 88 92 90 91 92 91 91 92 91 90 91 91 92 89 MX-VrAl 89 93 91 92 92 92 92 93 91 92 91 91 93 90 VE-T 87 91 89 90 90 89 89 90 89 89 89 89 90 87 JM-FS 84 88 86 87 87 87 87 87 86 85 86 86 87 86 Table 4.3: Summary of coat protein (CP) gene identity (percent minimum – maximum) at amino acid (diagonally lower values in blue) and nucleotide (diagonally upper values in yellow) levels between PRSV-P isolates from India and other countries.
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