Complete nucleotide sequence of the

Hupfer, H.; Świątek, M.; Hornung, Severin; Herrmann, Richard; Maier, Rainer M.; Chiu, W.; Sears, Barbara B.

doi:10.1007/s004380051204

Cited by 9 publications

(12 citation statements)

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“…The photosynthetic dicot cp genome size of angiosperms varies from 150,519 bp (Lotus; Kato et al, 2000) to 162,686 bp (Amborella; Goremykin et al, 2003), whereas the size of the Ampelopsis cp genome (161,090 bp) is also within this size range. The size of the IR region (26,394 bp) of the Ampelopsis is also well within the size range of other sequenced dicot genomes that range from 23,302 (Calycanthus; Goremykin et al, 2003) to 27,807 bp (Oenothera; Hupfer et al, 2000). However, the gene content and order of the Ampelopsis cp genome is exactly the same as that of Vitis , tobacco and many other unreorganized angiosperm cp genomes.…”

Section: Discussionsupporting

confidence: 57%

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

Raman

Park

2016

Front. Plant Sci.

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Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of the plant Ampelopsis.

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Section: Discussionsupporting

confidence: 57%

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

Raman

Park

2016

Front. Plant Sci.

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“…Total DNA was isolated from plants carrying plastomes I to V, respectively, using the DNeasy™ Plant Mini Kit (Qiagen, Hilden, Germany). Since a number of errors were noted in the original sequence of plastome I (30), especially in the IR as also noted by others (41), its DNA was re-sequenced completely. PCR-derived fragments or fragments subcloned from plastid chromosomes serving as sequencing templates, spanning both DNA strands and overlapping a minimum of 200 bp, were generated over the entire chromosome of these plastomes.…”

Section: Methodsmentioning

confidence: 99%

“…DNA from plastome I was prepared from intact chloroplasts essentially as described in (40). Molecular cloning, sequencing and sequence analysis were performed as given in (11,30). Total DNA was isolated from plants carrying plastomes I to V, respectively, using the DNeasy™ Plant Mini Kit (Qiagen, Hilden, Germany).…”

Section: Methodsmentioning

confidence: 99%

“…In preceding communications we have reported on the complete nucleotide sequence of the plastid chromosome of Oenothera elata subsp. hookeri strain johansen, representing the Oenothera plastome I (30), on an EST library derived from the Oenothera A genome (31), and on cell, tissue culture and transformation protocols of that material (32–34). In this study we present and compare the complete nucleotide sequences of representatives of the five basic Oenothera plastomes and deduce their evolutionary relationship and temporal appearance.…”

Section: Introductionmentioning

confidence: 99%

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The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera , subsection Oenothera : I. Sequence evaluation and plastome evolution †

Greiner

Wang

Rauwolf

et al. 2008

Nucleic Acids Research

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The flowering plant genus Oenothera is uniquely suited for studying molecular mechanisms of speciation. It assembles an intriguing combination of genetic features, including permanent translocation heterozygosity, biparental transmission of plastids, and a general interfertility of well-defined species. This allows an exchange of plastids and nuclei between species often resulting in plastome–genome incompatibility. For evaluation of its molecular determinants we present the complete nucleotide sequences of the five basic, genetically distinguishable plastid chromosomes of subsection Oenothera (=Euoenothera) of the genus, which are associated in distinct combinations with six basic genomes. Sizes of the chromosomes range from 163 365 bp (plastome IV) to 165 728 bp (plastome I), display between 96.3% and 98.6% sequence similarity and encode a total of 113 unique genes. Plastome diversification is caused by an abundance of nucleotide substitutions, small insertions, deletions and repetitions. The five plastomes deviate from the general ancestral design of plastid chromosomes of vascular plants by a subsection-specific 56 kb inversion within the large single-copy segment. This inversion disrupted operon structures and predates the divergence of the subsection presumably 1 My ago. Phylogenetic relationships suggest plastomes I–III in one clade, while plastome IV appears to be closest to the common ancestor.

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“…Gray) W. Dietr. & W. L. Wagner; NC_002693.1; Hupfer et al, 2000. Note: this sequence has been updated since this article was published.…”

Section: Appendixmentioning

confidence: 99%

Plastid primers for angiosperm phylogenetics and phylogeography

Prince

2015

Appl Plant Sci

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Premise of the study:PCR primers are available for virtually every region of the plastid genome. Selection of which primer pairs to use is second only to selection of the genic region. This is particularly true for research at the species/population interface.Methods:Primer pairs for 130 regions of the chloroplast genome were evaluated in 12 species distributed across the angiosperms. Likelihood of amplification success was inferred based upon number and location of mismatches to target sequence. Intraspecific sequence variability was evaluated under three different criteria in four species.Results:Many published primer pairs should work across all taxa sampled, with the exception of failure due to genomic reorganization events. Universal barcoding primers were the least likely to work (65% success). The list of most variable regions for use within species has little in common with the lists identified in prior studies.Discussion:Published primer sequences should amplify a diversity of flowering plant DNAs, even those designed for specific taxonomic groups. “Universal” primers may have extremely limited utility. There was little consistency in likelihood of amplification success for any given publication across lineages or within lineage across publications.

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Complete nucleotide sequence of the

Cited by 9 publications

References 0 publications

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera , subsection Oenothera : I. Sequence evaluation and plastome evolution †

Plastid primers for angiosperm phylogenetics and phylogeography

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