Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East India
The genetic variability of ‘Candidatus Liberibacter asiaticus’ (CLas) population associated with huanglongbing (HLB) disease of citrus in North Eastern (NE) region of India, a geographically locked region, and home for the diversity of many citrus species was analyzed on the basis of tandem repeat n...
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| Format: | Article |
| Language: | English |
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Hanrimwon Publishing Company
2019-12-01
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| Series: | The Plant Pathology Journal |
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| Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901247 |
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| author | Yanglem Herojit Singh Susheel Kumar Sharma Bireswar Sinha Virendra Kumar Baranwal N. Bidyananda Singh Ngathem Taibangnganbi Chanu Subhra S. Roy Meraj A. Ansari Arati Ningombam Ph. Sobita Devi Ashis Kumar Das Salvinder Singh K. Mamocha Singh Narendra Prakash |
| author_facet | Yanglem Herojit Singh Susheel Kumar Sharma Bireswar Sinha Virendra Kumar Baranwal N. Bidyananda Singh Ngathem Taibangnganbi Chanu Subhra S. Roy Meraj A. Ansari Arati Ningombam Ph. Sobita Devi Ashis Kumar Das Salvinder Singh K. Mamocha Singh Narendra Prakash |
| author_sort | Yanglem Herojit Singh |
| collection | DOAJ |
| description | The genetic variability of ‘Candidatus Liberibacter asiaticus’ (CLas) population associated with huanglongbing (HLB) disease of citrus in North Eastern (NE) region of India, a geographically locked region, and home for the diversity of many citrus species was analyzed on the basis of tandem repeat numbers (TRN) in variable CLIBASIA_01645 genomic loci. Fifty-five CLas strains sampled from different groves of NE Hill (NEH) region of India were in single amplicon group, but there was remarkable genetic variability in TRNs. The TRN in HLB-associated CLas strains varied from 0-21 and two novel repeat motifs were also identified. Among the NE population of CLas, TRN5 and TRN9 were most frequent (total frequency of 36.36%) followed by TRN4 (14.55%) and TRN6, TNR7 with a frequency of 12.73% each. Class II type CLas genotypes (5 < TRN ≤ 10) had highest prevalence (frequency of 60.00%) in the samples characterized in present study. Class I (TRN ≤ 5) genotypes were second highest prevalent (29.09%) in the NEH region. Further analysis of genetic diversity parameters using Nei's measure (H value) indicated wide genetic diversity in the CLas strains of NE India (H value of 0.58-0.86). Manipur CLas strains had highest genetic variability (0.86) as compared to Eastern, Southern and Central India. The R10 values (TRN ≤ 10/TRN > 10) of NE CLas population was 10.43 (73/7), higher from other regions of India. Present study conclusively reported the occurrence of high genetic variability in TRN of CLas population in North East Indian citrus groves which have evolved to adapt to the specific ecological niche. |
| first_indexed | 2024-12-11T01:59:16Z |
| format | Article |
| id | doaj.art-2d82c045e65544e3a5b084e88c303b0f |
| institution | Directory Open Access Journal |
| issn | 1598-2254 |
| language | English |
| last_indexed | 2024-12-11T01:59:16Z |
| publishDate | 2019-12-01 |
| publisher | Hanrimwon Publishing Company |
| record_format | Article |
| series | The Plant Pathology Journal |
| spelling | doaj.art-2d82c045e65544e3a5b084e88c303b0f2022-12-22T01:24:32ZengHanrimwon Publishing CompanyThe Plant Pathology Journal1598-22542019-12-0135664465310.5423/PPJ.OA.03.2019.006110.5423PPJ.OA.03.2019.0061Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East IndiaYanglem Herojit Singh0Susheel Kumar Sharma1Bireswar Sinha2Virendra Kumar Baranwal3N. Bidyananda Singh4Ngathem Taibangnganbi Chanu5Subhra S. Roy6Meraj A. Ansari7Arati Ningombam8Ph. Sobita Devi9Ashis Kumar Das10Salvinder Singh11K. Mamocha Singh12Narendra Prakash13Department of Plant Pathology, College of Agriculture, Central Agricultural University, Imphal 795004, IndiaICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004, IndiaDepartment of Plant Pathology, College of Agriculture, Central Agricultural University, Imphal 795004, IndiaAdvanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004, IndiaICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004, IndiaICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004, IndiaICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004, IndiaICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004, IndiaDepartment of Plant Pathology, College of Agriculture, Central Agricultural University, Imphal 795004, IndiaICAR-Central Citrus Research Institute, Nagpur 440010, IndiaDepartment of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, IndiaDepartment of Entomology, College of Agriculture, Central Agricultural University, Imphal 795004, IndiaICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004, IndiaThe genetic variability of ‘Candidatus Liberibacter asiaticus’ (CLas) population associated with huanglongbing (HLB) disease of citrus in North Eastern (NE) region of India, a geographically locked region, and home for the diversity of many citrus species was analyzed on the basis of tandem repeat numbers (TRN) in variable CLIBASIA_01645 genomic loci. Fifty-five CLas strains sampled from different groves of NE Hill (NEH) region of India were in single amplicon group, but there was remarkable genetic variability in TRNs. The TRN in HLB-associated CLas strains varied from 0-21 and two novel repeat motifs were also identified. Among the NE population of CLas, TRN5 and TRN9 were most frequent (total frequency of 36.36%) followed by TRN4 (14.55%) and TRN6, TNR7 with a frequency of 12.73% each. Class II type CLas genotypes (5 < TRN ≤ 10) had highest prevalence (frequency of 60.00%) in the samples characterized in present study. Class I (TRN ≤ 5) genotypes were second highest prevalent (29.09%) in the NEH region. Further analysis of genetic diversity parameters using Nei's measure (H value) indicated wide genetic diversity in the CLas strains of NE India (H value of 0.58-0.86). Manipur CLas strains had highest genetic variability (0.86) as compared to Eastern, Southern and Central India. The R10 values (TRN ≤ 10/TRN > 10) of NE CLas population was 10.43 (73/7), higher from other regions of India. Present study conclusively reported the occurrence of high genetic variability in TRN of CLas population in North East Indian citrus groves which have evolved to adapt to the specific ecological niche.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901247‘candidatus liberibacter asiaticus’clibasia_01645 locushuanglongbingnorth east indiatandem repeat number |
| spellingShingle | Yanglem Herojit Singh Susheel Kumar Sharma Bireswar Sinha Virendra Kumar Baranwal N. Bidyananda Singh Ngathem Taibangnganbi Chanu Subhra S. Roy Meraj A. Ansari Arati Ningombam Ph. Sobita Devi Ashis Kumar Das Salvinder Singh K. Mamocha Singh Narendra Prakash Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East India The Plant Pathology Journal ‘candidatus liberibacter asiaticus’ clibasia_01645 locus huanglongbing north east india tandem repeat number |
| title | Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East India |
| title_full | Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East India |
| title_fullStr | Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East India |
| title_full_unstemmed | Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East India |
| title_short | Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ‘Candidatus Liberibacter asiaticus’ Prevalent in North East India |
| title_sort | genetic variability based on tandem repeat numbers in a genomic locus of candidatus liberibacter asiaticus prevalent in north east india |
| topic | ‘candidatus liberibacter asiaticus’ clibasia_01645 locus huanglongbing north east india tandem repeat number |
| url | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901247 |
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