L. A. S. JOHNSON REVIEW No. 2 Use of nuclear genes for phylogeny reconstruction in plants
TL;DR: Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance.
Abstract: Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies.
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TL;DR: Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis, and it is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.
1,718 citations
TL;DR: Current Protocols in Molecular Biology Title NLM.
1,258 citations
TL;DR: The process of selecting and refining a plant barcode is reviewed; the factors which influence the discriminatory power of the approach are evaluated; some early applications of plant barcoding are described and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcode to advance.
Abstract: The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.
993 citations
TL;DR: The defining properties of serpentine soil and the pioneering work leading to three established physiological and evolutionary mechanisms hypothesized to be responsible for serpentine tolerance: tolerance of a low calcium-to-magnesium ratio, avoidance of Mg toxicity, or a high Mg requirement are reviewed.
Abstract: ▪ Abstract Plant adaptation to serpentine soil has been a topic of study for many decades, yet investigation of the genetic component of this adaptation has only recently begun. We review the defining properties of serpentine soil and the pioneering work leading to three established physiological and evolutionary mechanisms hypothesized to be responsible for serpentine tolerance: tolerance of a low calcium-to-magnesium ratio, avoidance of Mg toxicity, or a high Mg requirement. In addition, we review recent work in serpentine ecology documenting the high proportion of endemic species present, the adaptive morphologies of serpentine-tolerant plants, and the distinctive structure of serpentine communities. Studies of the physiological mechanisms proposed to confer serpentine tolerance have shown that uptake of particular ions and heavy metals varies between serpentine-tolerant and -intolerant species. Recent studies examining the genetic basis of serpentine adaptation have shown serpentine-adaptive quantitat...
615 citations
TL;DR: It is here argued that ITS sequences, despite drawbacks, can still produce insightful results in species-level phylogenetic studies or when non-anonymous nuclear markers are required, provided that a thoughtful use of them is made.
475 citations
Cites background from "L. A. S. JOHNSON REVIEW No. 2 Use o..."
...Even though several tests have been suggested (Small et al., 2004), the concern for identifying true orthologs remains until the phylogenetic analysis of the sequences is completed (Doyle and Doyle, 1999)....
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...However, this is not often the case possibly due to deep coalescence favored by large eVective population sizes, as compared to much smaller organellar genomes (Small et al., 2004)....
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...Surprisingly, this lucid caution was not echoed in the molecular systematist community until recently, when other voices have recommended routine utilization of low-copy nuclear genes given the potential pitfalls of the ITS region for inferring phylogenies (Álvarez and Wendel, 2003; Sang, 2002; Small et al., 2004)....
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...Just as primary disadvantages of LCNG come from their “complex genetic architecture and evolutionary dynamics” (Small et al., 2004), problems with ITS stem ultimately from complexity derived from the evolution of these markers at several levels, from the gene to the population....
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...…lucid caution was not echoed in the molecular systematist community until recently, when other voices have recommended routine utilization of low-copy nuclear genes given the potential pitfalls of the ITS region for inferring phylogenies (Álvarez and Wendel, 2003; Sang, 2002; Small et al., 2004)....
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15 Jan 2001
TL;DR: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years as mentioned in this paper and has been so popular, or so influential, that no other manual has been more widely used and influential.
Abstract: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential. Molecular Cloning, Fourth Edition, by the celebrated founding author Joe Sambrook and new co-author, the distinguished HHMI investigator Michael Green, preserves the highly praised detail and clarity of previous editions and includes specific chapters and protocols commissioned for the book from expert practitioners at Yale, U Mass, Rockefeller University, Texas Tech, Cold Spring Harbor Laboratory, Washington University, and other leading institutions. The theoretical and historical underpinnings of techniques are prominent features of the presentation throughout, information that does much to help trouble-shoot experimental problems. For the fourth edition of this classic work, the content has been entirely recast to include nucleic-acid based methods selected as the most widely used and valuable in molecular and cellular biology laboratories. Core chapters from the third edition have been revised to feature current strategies and approaches to the preparation and cloning of nucleic acids, gene transfer, and expression analysis. They are augmented by 12 new chapters which show how DNA, RNA, and proteins should be prepared, evaluated, and manipulated, and how data generation and analysis can be handled. The new content includes methods for studying interactions between cellular components, such as microarrays, next-generation sequencing technologies, RNA interference, and epigenetic analysis using DNA methylation techniques and chromatin immunoprecipitation. To make sense of the wealth of data produced by these techniques, a bioinformatics chapter describes the use of analytical tools for comparing sequences of genes and proteins and identifying common expression patterns among sets of genes. Building on thirty years of trust, reliability, and authority, the fourth edition of Mol
215,169 citations
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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...gov/BLAST/; (Altschul et al. 1990)] for similar sequences....
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18,553 citations
"L. A. S. JOHNSON REVIEW No. 2 Use o..." refers methods in this paper
...This value can be estimated by R. L. Small et a/. using a variety of genetic-distance algorithms available in most phylogenetic inference packages (e.g. PAUP* : Swofford 2002)....
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TL;DR: From the kinetic data, it becomes evident that the reductive amination reaction is highly adaptive to the ammonium environment.
14,480 citations
01 Jan 2001
13,011 citations