RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids

Oxelman, Bengt; Yoshikawa, Nori; McConaughy, Betty L.; Luo, Jie; Denton, Amy L.; Hall, Benjamin D.

doi:10.1016/j.ympev.2004.01.014

Cited by 57 publications

(30 citation statements)

References 40 publications

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“…Paralog sequences of rpb2 have been reported from other plant families of core eudicots, Malvaceae (Pfeil et al 2004) and others (Oxelman et al 2004;Luo et al 2007). Even though several copy sequences of rpb2 were found from each species sample, no paralog of rpb2 was found in our results, since all copy sequences originating from one sample always formed a monophyletic group and never made a clade with sequences originating from different species samples (Fig.…”

Section: Discussioncontrasting

confidence: 41%

“…Several paralogs of rpb2 have been found in some members of the core eudicots but, even in such cases, copy numbers were low and identification of homologs was easy (Oxelman and Bremer 2000). Therefore, rpb2 is still phylogenetically informative even when duplication of the gene has occurred (Oxelman and Bremer 2000;Oxelman et al 2004;Luo et al 2007). Moreover, recent studies reported that the rpb2 gene was useful for exploring low-level phylogenetic relationships in the palm family (Loo et al 2006;Roncal et al 2005;Thomas et al 2006), in the genus Silene of the Caryophyllaceae family (Popp and Oxelman 2001), and in the genus Elymus of the Poaceae family (Sun et al 2007).…”

Section: Introductionmentioning

confidence: 99%

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Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences

Fijridiyanto

Murakami

2009

J Plant Res

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The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.

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Section: Discussioncontrasting

confidence: 41%

Section: Introductionmentioning

confidence: 99%

Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences

Fijridiyanto

Murakami

2009

J Plant Res

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“…rpoB is a universal gene found in all domains of life, as well as in many viruses. It has been adopted as a phylogenetic marker for studies of the Bacteria [57], the Archaea [58], and the Eukaryota [59], as well as for metagenomic studies of phylogenetic diversity in the Sargasso Sea [19]. Homologs of RpoB were identified in Genbank, genomes and the GOS metagenomic data using the same approach as for RecA with one significant difference.…”

Section: Resultsmentioning

confidence: 99%

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

Halpern

et al. 2011

PLoS ONE

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BackgroundMost of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species.Methodology/Principal FindingsWe designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences.Conclusions/SignificanceOf the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.

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“…The use of RPB2 gene, on the other hand, was first explored in a broad angiosperm study (Denton et al, 1998) and later used for several seed plants (Popp & Oxelman, 2001;Nickerson & Drouin, 2004;Oxelman et al, 2004;Pfeil et al, 2004). These studies found RPB2 to be phylogenetically informative but also found evidence of two or even more paralogues.…”

Section: West Indian Palm Phylogenies Based On Low-copy Nuclear Genesmentioning

confidence: 99%

Molecular Phylogenetic Studies of Caribbean Palms (Arecaceae) and Their Relationships to Biogeography and Conservation

2008

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The Caribbean Islands are one of the world's 34 biodiversity hotspots, remarkable for its biological richness and the high level of threat to its flora and fauna. The palms (family Arecaceae) are well represented in the West Indies, with 21 genera (three endemic) and 135 species (121 endemic). We provide an overview of phylogenetic knowledge of West Indian Palms, including their relationships within a plastid DNA-based phylogeny of the Arecaceae. We present new data used to reconstruct the phylogeny of tribe Cryosophileae, including four genera found in the West Indies, based on partial sequences of the low-copy nuclear genes encoding phosphoribulokinase (PRK) and subunit 2 of RNA polymerase II (RPB2). Recently published phylogenetic studies of tribe Cocoseae, based on PRK sequences, and tribes Cyclospatheae and Geonomateae, based on PRK and RPB2 sequences, also provide information on the phylogenetic relationships of West Indian palms. Results of these analyses show many independent origins of the West Indian Palm flora. These phylogenetic studies reflect the complex envolutionary history of the West Indies and no single biogeographical pattern emerges for these palms. The present day distributions of West Indian palms suggest complicated evolutionary interchange among islands, as well as between the West Indies and surrounding continents. We identified six palm lineages that deserve conservation priority. Species-level phylogenies are needed for Copernicia, Sabal, and Roystonea before we can build a more complete understanding of the origin and diversification of West Indian palms.Resumen Las Islas del Caribe constituyen uno de los 34 "hotspots" de biodiversidad del mundo, notables por su riqueza biológica y el alto grado de amenaza de su flora y fauna. La familia Arecaceae esta bien representada en Las Antillas con 21 géneros (tres endémicos) y 135 especies (121 endémicas). Presentamos una síntesis del conocimiento filogénetico de las palmas de Las Antillas incluyendo su posición dentro de la filogenia de la familia Arecaceae basada en ADN cloroplástico. Construímos una nueva filogenia para la tribu Cryosophileae, Bot. Rev. (2008) 74:78-102

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RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids

Cited by 57 publications

References 40 publications

Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences

Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

Molecular Phylogenetic Studies of Caribbean Palms (Arecaceae) and Their Relationships to Biogeography and Conservation

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