Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species

被引:142
作者
Roy, Sribash [1 ]
Tyagi, Antariksh [1 ]
Shukla, Virendra [1 ]
Kumar, Anil [1 ]
Singh, Uma M. [1 ]
Chaudhary, Lal Babu [2 ]
Datt, Bhaskar [2 ]
Bag, Sumit K. [1 ]
Singh, Pradhyumna K. [1 ]
Nair, Narayanan K. [2 ]
Husain, Tariq [2 ]
Tuli, Rakesh [1 ]
机构
[1] CSIR, Natl Bot Res Inst, Dept Plant Mol Biol & Genet Engn, Lucknow, Uttar Pradesh, India
[2] CSIR, Natl Bot Res Inst, Dept Plant Biodivers & Conservat Biol, Lucknow, Uttar Pradesh, India
关键词
LAND PLANTS; PHYLOGENETIC-RELATIONSHIPS; DIVERSITY; SEQUENCES; TAXONOMY; GENUS; AFLP; POPULATIONS; RBCL;
D O I
10.1371/journal.pone.0013674
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页数:14
相关论文
共 69 条
[1]   Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP [J].
Abdalla, AM ;
Reddy, OUK ;
El-Zik, KM ;
Pepper, AE .
THEORETICAL AND APPLIED GENETICS, 2001, 102 (2-3) :222-229
[2]  
AHRENDT LESLIE WALTER ALLAM, 1961, JOUR LINNEAN SOC LONDON BOT, V57, P1
[3]   Ribosomal ITS sequences and plant phylogenetic inference [J].
Alvarez, I ;
Wendel, JF .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2003, 29 (03) :417-434
[4]  
Awano T, 2009, P NATL ACAD SCI USA, V106, P2794, DOI [10.1073/pnas.0812297106, 10.1073/pnas.0905845106]
[5]   Molecular systematics - Counting angels with DNA [J].
Blaxter, M .
NATURE, 2003, 421 (6919) :122-124
[6]   Relationships in Patagonian species of Berberis (Berberidaceae) based on the characterization of rDNA internal transcribed spacer sequences [J].
Bottini, M. C. J. ;
De Bustos, A. ;
Sanso, A. M. ;
Jouve, N. ;
Poggio, L. .
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, 2007, 153 (03) :321-328
[7]  
BOTTINI MCJ, 1999, 16 INT BOT C ST LOUI
[8]   Intraspecific and interspecific genetic and phylogenetic relationships in the genus Populus based on AFLP markers [J].
Cervera, MT ;
Storme, V ;
Soto, A ;
Ivens, B ;
Van Montagu, M ;
Rajora, OP ;
Boerjan, W .
THEORETICAL AND APPLIED GENETICS, 2005, 111 (07) :1440-1456
[9]   A proposal for a standardised protocol to barcode all land plants [J].
Chase, Mark W. ;
Cowan, Robyn S. ;
Hollingsworth, Peter M. ;
van den Berg, Cassio ;
Madrinan, Santiago ;
Petersen, Gitte ;
Seberg, Ole ;
Jorgsensen, Tina ;
Cameron, Kenneth M. ;
Carine, Mark ;
Pedersen, Niklas ;
Hedderson, Terry A. J. ;
Conrad, Ferozah ;
Salazar, Gerardo A. ;
Richardson, James E. ;
Hollingsworth, Michelle L. ;
Barraclough, Timothy G. ;
Kelly, Laura ;
Wilkinson, Mike .
TAXON, 2007, 56 (02) :295-299
[10]   Land plants and DNA barcodes: short-term and long-term goals [J].
Chase, MW ;
Salamin, N ;
Wilkinson, M ;
Dunwell, JM ;
Kesanakurthi, RP ;
Haider, N ;
Savolainen, V .
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2005, 360 (1462) :1889-1895