Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species.
BACKGROUND: The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2010-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2965122?pdf=render |
| _version_ | 1817967990455402496 |
|---|---|
| author | Sribash Roy Antariksh Tyagi Virendra Shukla Anil Kumar Uma M Singh Lal Babu Chaudhary Bhaskar Datt Sumit K Bag Pradhyumna K Singh Narayanan K Nair Tariq Husain Rakesh Tuli |
| author_facet | Sribash Roy Antariksh Tyagi Virendra Shukla Anil Kumar Uma M Singh Lal Babu Chaudhary Bhaskar Datt Sumit K Bag Pradhyumna K Singh Narayanan K Nair Tariq Husain Rakesh Tuli |
| author_sort | Sribash Roy |
| collection | DOAJ |
| description | BACKGROUND: The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task. METHODOLOGY AND PRINCIPAL FINDINGS: We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome--ITS, and three from plastid genome--trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation. CONCLUSIONS/SIGNIFICANCE: We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case. |
| first_indexed | 2024-04-13T20:02:08Z |
| format | Article |
| id | doaj.art-89dfd01517aa4d2981ff643cc535b870 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T20:02:08Z |
| publishDate | 2010-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-89dfd01517aa4d2981ff643cc535b8702022-12-22T02:32:10ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-01-01510e1367410.1371/journal.pone.0013674Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species.Sribash RoyAntariksh TyagiVirendra ShuklaAnil KumarUma M SinghLal Babu ChaudharyBhaskar DattSumit K BagPradhyumna K SinghNarayanan K NairTariq HusainRakesh TuliBACKGROUND: The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task. METHODOLOGY AND PRINCIPAL FINDINGS: We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome--ITS, and three from plastid genome--trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation. CONCLUSIONS/SIGNIFICANCE: We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case.http://europepmc.org/articles/PMC2965122?pdf=render |
| spellingShingle | Sribash Roy Antariksh Tyagi Virendra Shukla Anil Kumar Uma M Singh Lal Babu Chaudhary Bhaskar Datt Sumit K Bag Pradhyumna K Singh Narayanan K Nair Tariq Husain Rakesh Tuli Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species. PLoS ONE |
| title | Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species. |
| title_full | Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species. |
| title_fullStr | Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species. |
| title_full_unstemmed | Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species. |
| title_short | Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species. |
| title_sort | universal plant dna barcode loci may not work in complex groups a case study with indian berberis species |
| url | http://europepmc.org/articles/PMC2965122?pdf=render |
| work_keys_str_mv | AT sribashroy universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT antarikshtyagi universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT virendrashukla universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT anilkumar universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT umamsingh universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT lalbabuchaudhary universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT bhaskardatt universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT sumitkbag universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT pradhyumnaksingh universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT narayananknair universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT tariqhusain universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies AT rakeshtuli universalplantdnabarcodelocimaynotworkincomplexgroupsacasestudywithindianberberisspecies |