DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India Article Swipe
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· 2022
· Open Access
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· DOI: https://doi.org/10.3390/genes13122294
Taro (Colocasia esculenta L. Schott, Araceae), an ancient root and tuber crop, is highly polygenic, polyphyletic, and polygeographic in nature, which leads to its rapid genetic erosion. To prevent the perceived loss of taro diversity, species discrimination and genetic conservation of promising taro genotypes need special attention. Reports on genetic discrimination of taro at its center of origin are still untapped. We performed DNA barcoding of twenty promising genotypes of taro indigenous to the northeastern hill region of India, deploying two chloroplast-plastid genes, matK and rbcL, and the ribosomal nuclear gene ITS2. The secondary structure of ITS2 was determined and molecular phylogeny was performed to assess genetic discrimination among the taro genotypes. The matK and rbcL genes were highly efficient (>90%) in amplification and sequencing. However, the ITS2 barcode region achieved significant discrimination among the tested taro genotypes. All the taro genotypes displayed most similar sequences at the conserved matK and rbcL loci. However, distinct sequence lengths were observed in the ITS2 barcode region, revealing accurate discriminations among the genotypes. Multiple barcode markers are unrelated to one another and change independently, providing different estimations of heritable traits and genetic lineages; thus, they are advantageous over a single locus in genetic discrimination studies. A dynamic programming algorithm that used base-pairing interactions within a single nucleic acid polymer or between two polymers transformed the secondary structures into the symbol code data to predict seven different minimum free energy secondary structures. Our analysis strengthens the potential of the ITS2 gene as a potent DNA barcode candidate in the prediction of a valuable secondary structure that would help in genetic discrimination between the genotypes while augmenting future breeding strategies in taro.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/genes13122294
- https://www.mdpi.com/2073-4425/13/12/2294/pdf?version=1670260993
- OA Status
- gold
- Cited By
- 6
- References
- 37
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4311705871
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4311705871Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.3390/genes13122294Digital Object Identifier
- Title
-
DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of IndiaWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-12-05Full publication date if available
- Authors
-
Mayengbam Premi Devi, Madhumita Dasgupta, Sansuta Mohanty, Susheel Kumar Sharma, Vivek Hegde, Subhra Saikat Roy, Rennya Renadevan, Kinathi Bipin Kumar, Hitendra Kumar Patel, Manas Ranjan SahooList of authors in order
- Landing page
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https://doi.org/10.3390/genes13122294Publisher landing page
- PDF URL
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https://www.mdpi.com/2073-4425/13/12/2294/pdf?version=1670260993Direct link to full text PDF
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.mdpi.com/2073-4425/13/12/2294/pdf?version=1670260993Direct OA link when available
- Concepts
-
Colocasia esculenta, Biology, DNA barcoding, Genetics, Genetic diversity, Locus (genetics), Gene pool, Genetic structure, Genotype, Barcode, Gene, Genetic variation, Botany, Evolutionary biology, Population, Demography, Operating system, Computer science, SociologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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6Total citation count in OpenAlex
- Citations by year (recent)
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2025: 2, 2024: 2, 2023: 2Per-year citation counts (last 5 years)
- References (count)
-
37Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.the | 29, 73, 87, 109, 126, 134, 139, 147, 160, 168, 221, 225, 241, 244, 254, 268 |
| abstract_inverted_index.two | 80, 218 |
| abstract_inverted_index.was | 97, 102 |
| abstract_inverted_index.ITS2 | 96, 127, 161, 245 |
| abstract_inverted_index.Taro | 0 |
| abstract_inverted_index.acid | 214 |
| abstract_inverted_index.code | 227 |
| abstract_inverted_index.data | 228 |
| abstract_inverted_index.free | 234 |
| abstract_inverted_index.gene | 90, 246 |
| abstract_inverted_index.help | 263 |
| abstract_inverted_index.hill | 75 |
| abstract_inverted_index.into | 224 |
| abstract_inverted_index.loss | 31 |
| abstract_inverted_index.matK | 83, 113, 149 |
| abstract_inverted_index.most | 143 |
| abstract_inverted_index.need | 44 |
| abstract_inverted_index.over | 194 |
| abstract_inverted_index.rbcL | 115, 151 |
| abstract_inverted_index.root | 8 |
| abstract_inverted_index.taro | 33, 42, 52, 70, 110, 136, 140 |
| abstract_inverted_index.that | 206, 261 |
| abstract_inverted_index.they | 191 |
| abstract_inverted_index.used | 207 |
| abstract_inverted_index.were | 117, 157 |
| abstract_inverted_index.ITS2. | 91 |
| abstract_inverted_index.among | 108, 133, 167 |
| abstract_inverted_index.crop, | 11 |
| abstract_inverted_index.genes | 116 |
| abstract_inverted_index.leads | 21 |
| abstract_inverted_index.loci. | 152 |
| abstract_inverted_index.locus | 197 |
| abstract_inverted_index.rapid | 24 |
| abstract_inverted_index.rbcL, | 85 |
| abstract_inverted_index.seven | 231 |
| abstract_inverted_index.still | 59 |
| abstract_inverted_index.taro. | 276 |
| abstract_inverted_index.thus, | 190 |
| abstract_inverted_index.tuber | 10 |
| abstract_inverted_index.which | 20 |
| abstract_inverted_index.while | 270 |
| abstract_inverted_index.would | 262 |
| abstract_inverted_index.India, | 78 |
| abstract_inverted_index.assess | 105 |
| abstract_inverted_index.center | 55 |
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| abstract_inverted_index.energy | 235 |
| abstract_inverted_index.future | 272 |
| abstract_inverted_index.genes, | 82 |
| abstract_inverted_index.highly | 13, 118 |
| abstract_inverted_index.origin | 57 |
| abstract_inverted_index.potent | 249 |
| abstract_inverted_index.region | 76, 129 |
| abstract_inverted_index.single | 196, 212 |
| abstract_inverted_index.symbol | 226 |
| abstract_inverted_index.tested | 135 |
| abstract_inverted_index.traits | 186 |
| abstract_inverted_index.twenty | 66 |
| abstract_inverted_index.within | 210 |
| abstract_inverted_index.Reports | 47 |
| abstract_inverted_index.Schott, | 4 |
| abstract_inverted_index.ancient | 7 |
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| abstract_inverted_index.barcode | 128, 162, 171, 251 |
| abstract_inverted_index.between | 217, 267 |
| abstract_inverted_index.dynamic | 203 |
| abstract_inverted_index.genetic | 25, 38, 49, 106, 188, 199, 265 |
| abstract_inverted_index.lengths | 156 |
| abstract_inverted_index.markers | 172 |
| abstract_inverted_index.minimum | 233 |
| abstract_inverted_index.nature, | 19 |
| abstract_inverted_index.nuclear | 89 |
| abstract_inverted_index.nucleic | 213 |
| abstract_inverted_index.polymer | 215 |
| abstract_inverted_index.predict | 230 |
| abstract_inverted_index.prevent | 28 |
| abstract_inverted_index.region, | 163 |
| abstract_inverted_index.similar | 144 |
| abstract_inverted_index.special | 45 |
| abstract_inverted_index.species | 35 |
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| abstract_inverted_index.Multiple | 170 |
| abstract_inverted_index.accurate | 165 |
| abstract_inverted_index.achieved | 130 |
| abstract_inverted_index.analysis | 239 |
| abstract_inverted_index.breeding | 273 |
| abstract_inverted_index.distinct | 154 |
| abstract_inverted_index.erosion. | 26 |
| abstract_inverted_index.observed | 158 |
| abstract_inverted_index.polymers | 219 |
| abstract_inverted_index.sequence | 155 |
| abstract_inverted_index.studies. | 201 |
| abstract_inverted_index.valuable | 258 |
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| abstract_inverted_index.deploying | 79 |
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| abstract_inverted_index.esculenta | 2 |
| abstract_inverted_index.genotypes | 43, 68, 141, 269 |
| abstract_inverted_index.heritable | 185 |
| abstract_inverted_index.lineages; | 189 |
| abstract_inverted_index.molecular | 100 |
| abstract_inverted_index.perceived | 30 |
| abstract_inverted_index.performed | 62, 103 |
| abstract_inverted_index.phylogeny | 101 |
| abstract_inverted_index.potential | 242 |
| abstract_inverted_index.promising | 41, 67 |
| abstract_inverted_index.providing | 181 |
| abstract_inverted_index.revealing | 164 |
| abstract_inverted_index.ribosomal | 88 |
| abstract_inverted_index.secondary | 93, 222, 236, 259 |
| abstract_inverted_index.sequences | 145 |
| abstract_inverted_index.structure | 94, 260 |
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| abstract_inverted_index.untapped. | 60 |
| abstract_inverted_index.(Colocasia | 1 |
| abstract_inverted_index.attention. | 46 |
| abstract_inverted_index.augmenting | 271 |
| abstract_inverted_index.determined | 98 |
| abstract_inverted_index.diversity, | 34 |
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| abstract_inverted_index.indigenous | 71 |
| abstract_inverted_index.polygenic, | 14 |
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| abstract_inverted_index.strategies | 274 |
| abstract_inverted_index.structures | 223 |
| abstract_inverted_index.estimations | 183 |
| abstract_inverted_index.programming | 204 |
| abstract_inverted_index.sequencing. | 124 |
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| abstract_inverted_index.structures. | 237 |
| abstract_inverted_index.transformed | 220 |
| abstract_inverted_index.advantageous | 193 |
| abstract_inverted_index.base-pairing | 208 |
| abstract_inverted_index.conservation | 39 |
| abstract_inverted_index.interactions | 209 |
| abstract_inverted_index.northeastern | 74 |
| abstract_inverted_index.amplification | 122 |
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| abstract_inverted_index.polygeographic | 17 |
| abstract_inverted_index.discriminations | 166 |
| abstract_inverted_index.chloroplast-plastid | 81 |
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| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5064274070, https://openalex.org/A5009467221 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 10 |
| corresponding_institution_ids | https://openalex.org/I1332470094, https://openalex.org/I179420787, https://openalex.org/I185638415, https://openalex.org/I4210111975 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/16 |
| sustainable_development_goals[0].score | 0.6200000047683716 |
| sustainable_development_goals[0].display_name | Peace, Justice and strong institutions |
| citation_normalized_percentile.value | 0.94818932 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |