Molecular Markers and Concepts of Plant Evolutionary Relationships: Progress, Promise, and Future Prospects

Soltis, Douglas E.; Moore, Michael J.; Burleigh, Gordon; Soltis, Pamela S.

doi:10.1080/07352680802665297

Cited by 24 publications

(13 citation statements)

References 152 publications

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“…These datasets have mainly involved concatenated sequences of proteincoding genes that are shared among green algal chloroplast genomes. To date, 26 complete green algal plastid genomes have been sequenced and assembled (Wakasugi et al, 1997;Turmel et al, 1999b;Lemieux et al, 2000;Maul et al, 2002;Turmel et al, 2002b;Pombert et al, 2005;Turmel et al, 2005;Bélanger et al, 2006;de Cambiaire et al, 2006;Pombert et al, 2006;Turmel et al, 2006a;de Cambiaire et al, 2007;Lemieux et al, 2007;Robbens et al, 2007a;Brouard et al, 2008;Turmel et al, 2008;Turmel et al, 2009a;Turmel et al, 2009b;Zuccarello et al, 2009;Brouard et al, 2010;Brouard et al, 2011), in addition to more than 30 angiosperm plastid genomes (Soltis et al, 2009). Chloroplast genomes are particularly useful for phylogenetic reconstruction because of their relatively high and condensed gene content, in comparison to nuclear genomes.…”

Section: Green Lineage Relationshipsmentioning

confidence: 99%

Phylogeny and Molecular Evolution of the Green Algae

Leliaert

Smith

Moreau

et al. 2012

Critical Reviews in Plant Sciences

749

655

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Section: Green Lineage Relationshipsmentioning

confidence: 99%

Phylogeny and Molecular Evolution of the Green Algae

Leliaert

Smith

Moreau

et al. 2012

Critical Reviews in Plant Sciences

749

655

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“…Many types of multi-locus methods are well known and include random amplified polymorphic DNA (RAPD, [14,15]), amplified fragment length polymorphism (AFLP, [16]), inter-sample sequence repeats (ISSR, [17]) and a few alternative techniques involving some modifications of these [18-23]. They are still used and have many applications [24-26]. Collectively they have been referred to as arbitrarily amplified DNA markers (AADs; excluding single-locus techniques such as microsatellites, or SSRs).…”

Section: Arbitrarily Amplified Dna Markers (Aads)mentioning

confidence: 99%

Advances in plant gene-targeted and functional markers: a review

et al. 2013

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Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.

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“…Another advantage of cpDNA is that it has a moderate evolutionary rate, resulting in relatively high-resolution phylogeny among species. Therefore, many phylogenetic studies of plant species have employed cpDNA variation (Soltis, Moore, Burleigh, & Soltis, 2009).…”

Section: Introductionmentioning

confidence: 99%

Frequent chloroplast capture among Isodon (Lamiaceae) species in Japan revealed by phylogenies based on variation in chloroplast and nuclear DNA

Ogishima

Horie

Kimura

et al. 2019

Plant Species Biology

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A recent phylogenetic study based only on chloroplast DNA (cpDNA) variation revealed that populations of an Isodon species are frequently embedded paraphyletically among other Isodon species. This phylogenetic discrepancy between species taxonomy and molecular phylogeny was considered to have resulted from chloroplast DNA captures and/or incomplete lineage sorting. To elucidate which of these factors was mainly responsible for the observed phylogenetic pattern, we performed phylogenetic analyses of multiple populations of Isodon species in Japan using cpDNA variation, three single‐copy nuclear genes, and double‐digest restriction‐site‐associated DNA sequencing (ddRAD‐seq). Although a species often shared chlorotypes with other species, our phylogenetical analyses based on variation in the three single‐copy nuclear genes and the ddRAD‐seq data showed that most populations belonging to the same species were monophyletic at the species level, suggesting that chloroplast capture may have frequently occurred between Isodon species. Some populations of an intraspecific taxon were embedded paraphyletically within the species, regardless of the large amount of phylogenetic information in nuclear DNA; this incongruity may have resulted from incomplete lineage sorting.

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Molecular Markers and Concepts of Plant Evolutionary Relationships: Progress, Promise, and Future Prospects

Cited by 24 publications

References 152 publications

Phylogeny and Molecular Evolution of the Green Algae

Phylogeny and Molecular Evolution of the Green Algae

Advances in plant gene-targeted and functional markers: a review

Frequent chloroplast capture among Isodon (Lamiaceae) species in Japan revealed by phylogenies based on variation in chloroplast and nuclear DNA

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