DNA barcoding in plants: Evolution and applications of in silico approaches and resources

被引：16

作者：

Bhargava, Mili ^{[1
]}

Sharma, Ashok ^{[1
]}

机构：

[1] CSIR, Div Biotechnol, Cent Inst Med & Aromat Plants, Lucknow 226015, Uttar Pradesh, India

来源：

MOLECULAR PHYLOGENETICS AND EVOLUTION | 2013年 / 67卷 / 03期

关键词：

DNA barcoding; Plants; Bioinformatics; Softwares; Databases; MULTIPLE SEQUENCE ALIGNMENT; MAXIMUM-LIKELIHOOD; SPECIES MEMBERSHIP; DATABASE; TOOL; RNA; PHYLOGENY; SOFTWARE; DISTANCE; SERVER;

D O I：

10.1016/j.ympev.2013.03.002

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Bioinformatics has played an important role in the analysis of DNA barcoding data. The process of DNA barcoding initially involves the available data collection from the existing databases. Many databases have been developed in recent years, e.g. MMDBD [Medicinal Materials DNA Barcode Database], BioBarcode, etc. In case of non-availability of sequences, sequencing has to be done in vitro for which a recently developed software ecoPrimers can be helpful. This is followed by multiple sequence alignment. Further, basic sequence statistics computation and phylogenetic analysis can be performed by MEGA and PHYLIP/PAUP tools respectively. Some of the recent tools for in silico and statistical analysis specifically designed for barcoding viz. CAOS (Character Based DNA Barcoding), BRONX (DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability), Spider (Analysis of species identity and evolution, particularly DNA barcoding), jMOTU and Taxonerator (Turning DNA Barcode Sequences into Annotated OTUs), OTUbase (Analysis of OTU data and taxonomic data), SAP (Statistical Assignment Package), etc. have been discussed and analysed in this review. The paper presents a comprehensive overview of the various in silico methods, tools, softwares and databases used for DNA barcoding of plants. (C) 2013 Elsevier Inc. All rights reserved.

引用

页码：631 / 641

页数：11

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