A method for evolutionary studies on RFLP of chloroplast DNA, applicable to a range of plant species

Sandbrink, J.M.; Vellekoop, P.; Ham, Rianne van den; Brederode, J. van

doi:10.1016/0305-1978(89)90041-0

Cited by 40 publications

(21 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The organelle-enriched DNAs of R. glutinosa were isolated using Percoll gradient centrifugation method [18] and CTAB extraction method. The DNA concentration was quantified using a NanoDrop spectrophotometer (Thermo Scientific, Carlsbad, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

The Complete Chloroplast Genome Sequences of Six Rehmannia Species

Zeng

Zhou

Han

et al. 2017

Genes

View full text Add to dashboard Cite

Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order. The complete genomes ranged from 153,622 bp to 154,055 bp in length, including 133 genes encoding 88 proteins, 37 tRNAs, and 8 rRNAs. Three genes (rpoA, rpoC2, accD) have potentially experienced positive selection. Plastome size variation of Rehmannia was mainly ascribed to the expansion and contraction of the border regions between the inverted repeat (IR) region and the single-copy (SC) regions. Despite of the conserved structure in Rehmannia plastomes, sequence variations provide useful phylogenetic information. Phylogenetic trees of 23 Lamiales species reconstructed with the complete plastomes suggested that Rehmannia was monophyletic and sister to the clade of Lindenbergia and the parasitic taxa in Orobanchaceae. The interspecific relationships within Rehmannia were completely different with the previous studies. In future, population phylogenomic works based on plastomes are urgently needed to clarify the evolutionary history of Rehmannia.

show abstract

Section: Methodsmentioning

confidence: 99%

The Complete Chloroplast Genome Sequences of Six Rehmannia Species

Zeng

Zhou

Han

et al. 2017

Genes

View full text Add to dashboard Cite

show abstract

“…A modified Sandbrink high-salt isolation [76] with DNase I treatment was used to prepare the purified mitochondrial DNA for sequencing. A total of 200 grams of fresh young leaves were harvested from a single Liriodendron tulipifera tree (AR501) from the campus of Indiana University in Bloomington, Indiana.…”

Section: Methodsmentioning

confidence: 99%

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

et al. 2013

View full text Add to dashboard Cite

BackgroundThe mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing. However, the narrow phylogenetic breadth of available genomic data has limited our ability to reconstruct these traits in the ancestral flowering plant and, therefore, to infer subsequent patterns of evolution across angiosperms.ResultsWe sequenced the mitochondrial genome of Liriodendron tulipifera, the first from outside the monocots or eudicots. This 553,721 bp mitochondrial genome has evolved remarkably slowly in virtually all respects, with an extraordinarily low genome-wide silent substitution rate, retention of genes frequently lost in other angiosperm lineages, and conservation of ancestral gene clusters. The mitochondrial protein genes in Liriodendron are the most heavily edited of any angiosperm characterized to date. Most of these sites are also edited in various other lineages, which allowed us to polarize losses of editing sites in other parts of the angiosperm phylogeny. Finally, we added comprehensive gene sequence data for two other magnoliids, Magnolia stellata and the more distantly related Calycanthus floridus, to measure rates of sequence evolution in Liriodendron with greater accuracy. The Magnolia genome has evolved at an even lower rate, revealing a roughly 5,000-fold range of synonymous-site divergence among angiosperms whose mitochondrial gene space has been comprehensively sequenced.ConclusionsUsing Liriodendron as a guide, we estimate that the ancestral flowering plant mitochondrial genome contained 41 protein genes, 14 tRNA genes of mitochondrial origin, as many as 7 tRNA genes of chloroplast origin, >700 sites of RNA editing, and some 14 colinear gene clusters. Many of these gene clusters, genes and RNA editing sites have been variously lost in different lineages over the course of the ensuing ∽200 million years of angiosperm evolution.

show abstract

“…CpDNA was isolated according to the method of Sandbrink et al (1989) with modifications described by van Ham et al (1992). DNA was further purified according to the protocol of Doyle and Doyle (1987) and digested with eight restriction endonucleases: AvaI, BamHI, BclI, BglII, ClaI, DraI, HindIII, and SacI.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic relationships in the Crassulaceae inferred from chloroplast DNA restriction‐site variation

Ham

Hart

1998

American J of Botany

View full text Add to dashboard Cite

A restriction-site analysis of chloroplast DNA from 44 species, representing 19 genera and all six subfamilies of the Crassulaceae was conducted using 12 restriction endonucleases. A total of 969 variable sites was detected, 608 of which were phylogenetically informative and used in parsimony analysis. Estimated values of nucleotide sequence divergence were used to construct a distance tree by the neighbor-joining method. Maximum sequence divergence in the family was ϳ7%. Different tree inference methods yielded only moderately different topologies. The amount of support for the monophyletic groups obtained in the Wagner parsimony analysis was evaluated by bootstrap and decay analysis. There is very strong support for a basal division of the family, which separates the monophyletic subfamily Crassuloideae from all other taxa. Four of the six traditionally recognized subfamilies are indicated to be polyphyletic. These include the Cotyledonoideae, Sempervivoideae, Sedoideae, and Echeverioideae. The Kalanchoideae and the genera Cotyledon and Adromischus exhibit low levels of cpDNA sequence divergence relative to one another, suggesting a relatively recent radiation. The genera Sedum and Rosularia are indicated to be polyphyletic. Sedum comprises sister taxa of most of the other genera of the family.

show abstract

A method for evolutionary studies on RFLP of chloroplast DNA, applicable to a range of plant species

Cited by 40 publications

References 10 publications

The Complete Chloroplast Genome Sequences of Six Rehmannia Species

The Complete Chloroplast Genome Sequences of Six Rehmannia Species

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

Phylogenetic relationships in the Crassulaceae inferred from chloroplast DNA restriction‐site variation

Contact Info

Product

Resources

About