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A phylogenetic hypothesis for the genus Dendrochilum s.l. (including Bracisepalum) is based on nucleotide sequences of the nuclear ribosomal ITS and two plastid regions (matK, ycf1). The trees based on parsimony analysis of the nrITS and plastid partitions, respectively, are largely congruent, the only strongly supported conflict being the exact position of D. arachnites. Maximum likelihood analysis of the combined molecular matrix resulted in a tree with very high topological congruence to the parsimony consensus tree and to a fossil‐calibrated Bayesian inference tree that was used for dating. Our results confirm that monophyly of Dendrochilum is only supported if Bracisepalum is included in the former. They also suggest that only two subgenera (Dendrochilum, Platyclinis) should be recognized, whereas all other subgenera and sections previously proposed on a morphological basis should be treated as synonyms of subg. Platyclinis. Indeed, mapping of five vegetative and nine floral characters of alleged systematic value, using DELTRAN and ACCTRAN optimization, demonstrates pronounced morphological homoplasy. Molecular time calibration dates the origin of the genus to the Miocene and contradicts the hypothesis that most extant Dendrochilum species did not evolve until the Holocene. Inferred phylogenetic relationships between extant species, in combination with previously identified hotspots of narrow endemism, suggest that species endemism in Dendrochilum is predominantly centric. [ABSTRACT FROM AUTHOR]

A phylogenetic hypothesis for tribe Podochileae with emphasis on subtribe Eriinae s.s. is based on nucleotide sequences of the nuclear ITS and four plastid regions (matK, trnL-F spacer, trnL intron and ycf1). The strict consensus tree based on parsimony is largely congruent with the maximum likelihood tree with a few major differences; most importantly, monophyly of Podochileae as recently circumscribed is strongly supported by the maximum likelihood tree but not recovered in the parsimony analysis. Monophyly of Thelasiinae s.s. (without Ridleyella) and Eriinae s.l. (including Podochilinae) is supported, whereas Eria s.l. appears polyphyletic. The generic circumscription of Eriinae s.s. (excluding Podochilinae) is revised, and 21 genera are accepted, including two not previously recognized. Nomenclatural changes and a key to genera in Eriinae are provided. [ABSTRACT FROM AUTHOR]

Biodiversity biobank A subset of biodiversity repositories and collections that store DNA, RNA or tissue samples of biodiversity, (in general excluding human material). DNA degradation Chemical breakdown of the DNA molecule. Endonucleases cut the DNA or RNA molecules inside the molecule, exonucleases from either end. [Extracted from the article]

In order to study the evolution of mitochondrial genomes in the early branching lineages of the monocotyledons, i.e., the Acorales and Alismatales, we are sequencing complete genomes from a suite of key taxa. As a starting point the present paper describes the mitochondrial genome of Butomus umbellatus (Butomaceae) based on next-generation sequencing data. The genome was assembled into a circular molecule, 450,826 bp in length. Coding sequences cover only 8.2% of the genome and include 28 protein coding genes, four rRNA genes, and 12 tRNA genes. Some of the tRNA genes and a 16S rRNA gene are transferred from the plastid genome. However, the total amount of recognized plastid sequences in the mitochondrial genome is only 1.5% and the amount of DNA transferred from the nucleus is also low. RNA editing is abundant and a total of 557 edited sites are predicted in the protein coding genes. Compared to the 40 angiosperm mitochondrial genomes sequenced to date, the GC content of the Butomus genome is uniquely high (49.1%). The overall similarity between the mitochondrial genomes of Butomus and Spirodela (Araceae), the closest relative yet sequenced, is low (less than 20%), and the two genomes differ in size by a factor 2. Gene order is also largely unconserved. However, based on its phylogenetic position within the core alismatids Butomus will serve as a good reference point for subsequent studies in the early branching lineages of the monocotyledons. [ABSTRACT FROM AUTHOR]

A phylogenetic analysis of the genus Colchicum (including Bulbocodium and Merendera) is presented. The phylogeny includes all but four of the 100 species and all subspecies currently recognized in the genus, two insufficiently known species (C. mirzoevae, C. stenopetalum), and one cultivated specimen (C. laetum hort.) probably of hybrid origin. The analysis is based on 292 parsimony-informative characters derived from nucleotide sequences from six plastid regions (trnL intron, trnL-irnF IGS, trnY-trnD IGS, trnH-psbA IGS, atpB-rbcL IGS, rps16 intron) and 33 morphological, life history, and chromosomal characters. The genus Coichicum is strongly supported as monophyletic. The morphological data are considerably more homoplasious than the molecular characters, but provide added resolution to the trees derived from a combined analysis. The phylogenetic hypothesis is largely in conflict with the subgenera and sections recognized by Stefanov, and agrees better with some of the informal species groups defined by Persson in earlier publications. Additional data will be needed to resolve all relationships. [ABSTRACT FROM AUTHOR]

Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single-copy, protein coding genes located on six of the seven chromosome pairs in the diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitionsshowed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses,patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re-classification. [ABSTRACT FROM AUTHOR]

Background: RNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are found in some groups. The underlying processes responsible for the distribution of edited sites are largely unknown, but gene function, substitution rate, and gene conversion have been proposed to influence editing frequencies. Results: We studied five mitochondrial genes in the monocot order Alismatales, all showing marked differences in editing frequencies among taxa. A general tendency to lose edited sites was observed in all taxa, but this tendency was particularly strong in two clades, with most of the edited sites lost in parallel in two different areas of the phylogeny. This pattern is observed in at least four of the five genes analyzed. Except in the groups that show an unusually low editing frequency, the rate of C-to-T changes in edited sites was not significantly higher that in nonedited 3rd codon positions. This may indicate that selection is not actively removing edited sites in nine of the 12 families of the core Alismatales. In all genes but ccmB, a significant correlation was found between frequency of change in edited sites and synonymous substitution rate. In general, taxa with higher substitution rates tend to have fewer edited sites, as indicated by the phylogenetically independent correlation analyses. The elimination of edited sites in groups that lack or have reduced levels of editing could be a result of gene conversion involving a cDNA copy (retroprocessing). If so, this phenomenon could be relatively common in the Alismatales, and may have affected some groups recurrently. Indirect evidence of retroprocessing without a necessary correlation with substitution rate was found mostly in families Alismataceae and Hydrocharitaceae (e.g., groups that suffered a rapid elimination of all their edited sites, without a change in substitution rate). Conclusions: The effects of substitution rate, selection, and/or gene conversion on the dynamics of edited sites in plant mitochondria remain poorly understood. Although we found an inverse correlation between substitution rate and editing frequency, this correlation is partially obscured by gene retroprocessing in lineages that have lost most of their edited sites. The presence of processed paralogs in plant mitochondria deserves further study, since most evidence of their occurrence is circumstantial. [ABSTRACT FROM AUTHOR]

In the most comprehensive study to date we explored the phylogeny and evolution of the genus Asparagus , with emphasis on the southern African species. We included 211 accessions, representing 77 (92%) of the southern African, 6 (17%) of the tropical African, 10 (56%) of the strictly European and 6 (9%) of the Eurasian species. We analyzed DNA sequences from three plastid regions ( trn H- psb A, trn D-T, ndh F) and from the nuclear region phytochrome C (PHYC) with parsimony and maximum likelihood methods, and recovered a monophyletic Asparagus . The phylogeny conflicts with all previous infra-generic classifications. It has many strongly supported clades, corroborated by morphological characters, which may provide a basis for a revised taxonomy. Additionally, the phylogeny indicates that many of the current species delimitations are problematic. Using biogeographic analyses that account for phylogenetic uncertainty (S-DIVA) and take into account relative branch lengths (Lagrange) we confirm the origin of Asparagus in southern Africa, and find no evidence that the dispersal of Asparagus follow the Rand flora pattern. We find that all truly dioecious species of Asparagus share a common origin, but that sexual dimorphism has arisen independently several times. [ABSTRACT FROM AUTHOR]

Analyzes a phylogeny of the monocots on the basis of nucleotide sequence variation in genes, atpA, encoded in the mitochondrial genome and rbcl, encoded in the plastic genome. Resolution of a clade comprising magnoliid lineages as sister of the monocots; Comparison between jackknife and bootstrap values; Differences between the frequency-within-replicates and strict-consensus approaches.