Phylogeny of Triticeae (Poaceae) Based on Three Organelle Genes, Two Single-Copy Nuclear Genes, and Morphology

Triticeae are renowned for their complicated taxonomy, but their phylogeny is equally intricate and perplexing, and remains largely unresolved. Based on morphology and nucleotide sequences from two plastid genes (rbcL, rpoA), one mitochondrial gene (coxII), and two single-copy nuclear genes (DMC1, EF-G), the most comprehensive hypothesis (both with respect to taxa and data points) of the phylogeny of diploid Triticeae to date is presented. The incongruence length difference tests clearly indicate that the four logical data partitions (morphology and the three genome compartments) are mutually incongruent, except the mitochondrial and nuclear sequences. Nonetheless, a total evidence approach results in a highly resolved, strongly supported consensus tree, though partitioned Bremer support points to a high level of conflict among the individual data sets

How Many Loci Does it Take to DNA Barcode a Crocus?

BACKGROUND: DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species. METHODOLOGY AND PRINCIPAL FINDINGS: Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will--as is the case in crocus--undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached--even in a taxonomic context. CONCLUSIONS/SIGNIFICANCE: The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting

Genomes, Chromosomes, and Genes and the Concept of Homology

The traditional application of genome analysis in phylogenetic inference is questionable. Hypotheses about phylogeny are based upon the analysis of homologous characters, existing as a consequence of common descent. The concept of homology in morphology and molecular biology is well-defined: To count as an homology any character must pass the similarity, congruence, and conjunction tests. In genome analysis homology is related to the behaviour of chromosomes during meiosis: homologous chromosomes pair, nonhomologous chromosomes do not. Thus, in genome analysis homology becomes a purely operational concept. How well does this operational concept work? And what are the relationships, if any, between this operational concept of homology and the homology concept of morphology and molecular biology

N-acylphosphatidylethanolamine-hydrolysing phospholipase D lacks the ability to transphosphatidylate

AbstractThe N-acylphosphatidylethanolamine-hydrolysing phospholipase D (NAPE-PLD) generates N-acylethanolamines, including N-arachidonoyl-ethanolamine (anandamide), that may be neuroprotective and analgesic. The properties of NAPE-PLD from rat heart and brain microsomes are investigated and compared to those of other PLDs. NAPE-PLD is inhibited by the fatty acid aminohydrolase inhibitor MAFP in high concentrations (≥100 μM) while PMSF in high concentrations (10 mM) tends to stabilise NAPE-PLD activity. Oleate inhibits NAPE-PLD but the enzyme is not affected by PIP2, α-synuclein or mastoparan. Furthermore, it is for the first time reported that NAPE-PLD is not capable of catalysing a transphosphatidylation reaction like most other known PLDs

Plastome evolution in hemiparasitic mistletoes

Santalales is an order of plants consisting almost entirely of parasites. Some, such as Osyris, are facultative root parasites whereas others, such as Viscum, are obligate stem parasitic mistletoes. Here, we report the complete plastome sequences of one species of Osyris and three species of Viscum, and we investigate the evolutionary aspects of structural changes and changes in gene content in relation to parasitism. Compared with typical angiosperms plastomes, the four Santalales plastomes are all reduced in size (10–22% compared with Vitis), and they have experienced rearrangements, mostly but not exclusively in the border areas of the inverted repeats. Additionally, a number of protein-coding genes (matK, infA, ccsA, rpl33, and all 11 ndh genes) as well as two transfer RNA genes (trnG-UCC and trnV-UAC) have been pseudogenized or completely lost. Most of the remaining plastid genes have a significantly changed selection pattern compared with other dicots, and the relaxed selection of photosynthesis genes is noteworthy. Although gene loss obviously reduces plastome size, intergenic regions were also shortened. As plastome modifications are generally most prominent in Viscum, they are most likely correlated with the increased nutritional dependence on the host compared with Osyris