Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages

Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown. Transcriptome datasets were generated from four mycoheterotrophs in three families (Orchidaceae, Burmanniaceae, Triuridaceae) and related green plants and used for phylogenomic analyses to resolve relationships among the mycoheterotrophs, their relatives, and representatives across the monocots. Phylogenetic trees based on 602 genes were mostly congruent with plastome phylogenies, except for an Asparagales + Liliales clade inferred in the nuclear trees. Reduction and loss of chlorophyll synthesis and photosynthetic gene expression and relaxation of purifying selection on retained genes were progressive, with greater loss in older nonphotosynthetic lineages. One hundred seventy-four of 1375 plant benchmark universally conserved orthologous genes were undetected in any mycoheterotroph transcriptome or the genome of the mycoheterotrophic orchid Gastrodia but were expressed in green relatives, providing evidence for massively convergent gene loss in nonphotosynthetic lineages. We designate this set of deleted or undetected genes Missing in Mycoheterotrophs (MIM). MIM genes encode not only mainly photosynthetic or plastid membrane proteins but also a diverse set of plastid processes, genes of unknown function, mitochondrial, and cellular processes. Transcription of a photosystem II gene (psb29) in all lineages implies a nonphotosynthetic function for this and other genes retained in mycoheterotrophs. Nonphotosynthetic plants enable novel insights into gene function as well as gene expression shifts, gene loss, and convergence in nuclear genomes.

Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes

We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.

Sizing of ballistic arm protection for the VIRTUS body armour and load carriage system

INTRODUCTION

Severe haemorrhage from the arm that is unresponsive to direct pressure necessitates the application of a tourniquet. Detachable arm protection, referred to as brassards, are used by the UK Armed Forces to protect the upper arm from fragmentation threats. However, the coverage they originally provided was based on limited medical evidence. Medical consensus has determined that the dimensions of arm protection should in future be related to how far up the arm a tourniquet can be applied.

METHOD

CT scans of 120 male Armed Forces personnel were analysed to ascertain the vertical distances from acromion process to the point at which a tourniquet can applied, equating to the anterior axillary fold. These values were statistically compared with those derived from the 2007 UK Military anthropometric survey using a paired t-test. Additional distances were added to account for tourniquet width and slippage, with the total value compared with VIRTUS brassard length.

RESULTS

No significant difference (p<0.01) was found in mean acromion to axilla length (114 mm) compared with that found in the anthropometric survey confirming sample validity. The deltoid insertion lay 24 mm below the axillary fold for the 50th percentile value from CT. Essential arm coverage for the 99th percentile male in this study was calculated as 201 mm.

CONCLUSIONS

Based on this research, a single new brassard for the VIRTUS body armour and load carriage system was recommended and manufactured based on the 99th percentile. This is over 30% shorter than the existing VIRTUS brassard, reducing the overall weight burden for the soldier and improving heat dispersion, integration and interoperability. The new brassard has been issued to Armed Forces personnel since October 2018. The reduced mass of ballistic protective material in conjunction with requiring only a single size of brassard has already saved the Ministry of Defence £20 000 in procurement costs.

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots

PREMISE OF THE STUDY

We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification.

METHODS

We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth.

KEY RESULTS

Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches.

CONCLUSIONS

We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).

Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes

The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.

Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome

Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.

Drastic reduction of plastome size in the mycoheterotrophic Thismia tentaculata relative to that of its autotrophic relative Tacca chantrieri

PREMISE OF THE STUDY

Heterotrophic angiosperms tend to have reduced plastome sizes relative to those of their autotrophic relatives because genes that code for proteins involved in photosynthesis are lost. However, some plastid-encoded proteins may have vital nonphotosynthetic functions, and the plastome therefore may be retained after the loss of photosynthesis.

METHODS

We sequenced the plastome of the mycoheterotrophic species Thismia tentaculata and a representative of its sister genus, Tacca chantrieri, using next-generation technology, and we compared sequences and structures of genes and genomes of these species.

KEY RESULTS

The plastome of Tacca chantrieri is similar to those of other autotrophic taxa of Dioscoreaceae, except in a few local rearrangements and one gene loss. The plastome of Thismia tentaculata is ca. 16 kbp long with a quadripartite structure and is among the smallest known plastomes. Synteny is minimal between the plastomes of Tacca chantrieri and Thismia tentaculata. The latter includes only 12 candidate genes, with all except accD involved in protein synthesis. Of the 12 genes, trnE, trnfM, and accD are frequently among the few that remain in depauperate plastomes.

CONCLUSIONS

The plastome of Thismia tentaculata, like those of most other heterotrophic plants, includes a small number of genes previously suggested to be essential to plastome survival.

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales

Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification.

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots

Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses. Support was strong for 'deep' relationships among the commelinid orders, among the five palm subfamilies, and among tribes of the subfamily Coryphoideae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicated by model based analyses, with c. 22 rate shifts, and significant departure from a global clock. To date, this study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocot angiosperms, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade.

Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing

PREMISE OF THE STUDY

Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous-particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny.

METHODS

Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were used to enrich for chloroplast targets. Ten taxa were enriched using both methods for comparison. Chloroplast sequence data were generated for 31 representatives of the 14 Arecoideae tribes and five outgroup taxa. The phylogeny was reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses.

KEY RESULTS

Long range PCR and hybrid gene capture both enriched the plastid genome and provided similar sequencing coverage. Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae as the earliest-diverging lineage, implying that the development of flowers in triads defines a synapomorphy for the Arecoideae clade excluding Chamaedoreeae. Three major clades within this group were recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC), Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae + Euterpeae clade was resolved within the core arecoids. The POS clade was sister to a RRC + core arecoids clade, implying a shared ancestral area in South America for these three clades.

CONCLUSIONS

The plastome phylogeny recovered here provides robust resolution of previously ambiguous studies and new insights into palm evolution.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

BACKGROUND AND AIMS

Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life.

METHODS

Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support.

KEY RESULTS

Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies.

CONCLUSIONS

Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations.

The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation

PREMISE OF THE STUDY

Plastid genomes of nonphotosynthetic, mycoheterotrophic plants represent apt systems in which to study effects of relaxed evolutionary constraints. The few mycoheterotrophic angiosperm plastomes sequenced to date display drastic patterns of degradation/reduction relative to those of photosynthetic relatives. The goal of this study was to focus on a mycoheterotrophic orchid hypothesized to be in the "early" stages of plastome degradation, to provide perspective on this process.

METHODS

Short-read sequencing was used to generate a complete plastome sequence for Corallorhiza striata var. vreelandii, a mycoheterotrophic orchid, to investigate the extent of plastome degradation. Patterns of nonsynonymous/synonymous mutations were also assessed, and comparisons were made between Corallorhiza and other heterotrophic plant lineages.

KEY RESULTS

Corallorhiza yielded a plastome of 137505 bp, with several photosynthesis-related genes either lost or pseudogenized. Members of all major photosynthesis complexes, except ATP-synthase genes, were affected. "Housekeeping" genes were intact, despite the loss of a single tRNA. Intact photosynthesis genes (excluding atp genes) together displayed elevated nonsynonymous changes, while housekeeping genes did not.

CONCLUSIONS

The Corallorhiza plastome is not drastically reduced in overall size (∼6% reduction relative to that of photosynthetic Oncidium), but displays a pattern congruent with a loss of photosynthetic function. Comparing Corallorhiza with other heterotrophs allows some emergent evolutionary patterns to be inferred, but these remain as hypotheses to be tested, especially at lower taxonomic levels, and in lineages illustrating transitions from autotrophy to heterotrophy. The independent, unique processes of plastome modification among mycoheterotrophic lineages illustrate the urgency of their conservation.

ABC1K atypical kinases in plants: filling the organellar kinase void

Surprisingly few protein kinases have been demonstrated in chloroplasts or mitochondria. Here, we discuss the activity of bc(1) complex kinase (ABC1K) protein family, which we suggest locate in mitochondria and plastids, thus filling the kinase void. The ABC1Ks are atypical protein kinases and their ancestral function is the regulation of quinone synthesis. ABC1Ks have proliferated from one or two members in non-photosynthetic organisms to more than 16 members in algae and higher plants. In this review, we reconstruct the evolutionary history of the ABC1K family, provide a functional domain analysis for angiosperms and a nomenclature for ABC1Ks in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and maize (Zea mays). Finally, we hypothesize that targets of ABC1Ks include enzymes of prenyl-lipid metabolism as well as components of the organellar gene expression machineries.

Phylogeny of the Asparagales based on three plastid and two mitochondrial genes

PREMISE OF THE STUDY

The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial.

METHODS

Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated.

KEY RESULTS

The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent.

CONCLUSIONS

Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.

Comparative floral development in Lithospermum (Boraginaceae) and implications for the evolution and development of heterostyly

PREMISE OF THE STUDY

The evolution and development of floral developmental patterns were investigated in three heterostylous and three homostylous species of Lithospermum to determine whether species that independently acquired the same floral form follow the same pattern of development or different patterns.

METHODS

Using light and scanning electron microscopy, we observed developmental patterns in flowers at different stages of maturity. These patterns were compared within individual species, between heterostylous morphs, and among heterostylous and homostylous species.

KEY RESULTS

Although heterostyly has been determined by phylogenetic analysis to have originated independently in each of the heterostylous species, flowers of the long-style morph of each species follow similar patterns of gross development, as do those of the short-style morph. In addition, the flowers of each morph develop in a manner similar to those of their respective homostylous, herkogamous relatives. However, the developmental patterns of the stylar epidermal cells differ among these species and between heterostylous and homostylous species.

CONCLUSIONS

Floral developmental patterns in homostylous species provide evidence that modification of specific traits, such as patterns of stylar growth, can lead to the evolution of heterostyly. The developmental changes that affect the positions of the stigmas and anthers in each morph likely involve either temporal or spatial modifications of gene function. The floral developmental patterns described here and the occurrence of multiple types of herkogamy within some species of Lithospermum provide evidence that heterostylous species in the genus have originated via distinct evolutionary developmental pathways.

Subunit stoichiometry, evolution, and functional implications of an asymmetric plant plastid ClpP/R protease complex in Arabidopsis

The caseinolytic protease (Clp) protease system has been expanded in plant plastids compared with its prokaryotic progenitors. The plastid Clp core protease consists of five different proteolytic ClpP proteins and four different noncatalytic ClpR proteins, with each present in one or more copies and organized in two heptameric rings. We determined the exact subunit composition and stoichiometry for the intact core and each ring. The chloroplast ClpP/R protease was affinity purified from clpr4 and clpp3 Arabidopsis thaliana null mutants complemented with C-terminal StrepII-tagged versions of CLPR4 and CLPP3, respectively. The subunit stoichiometry was determined by mass spectrometry-based absolute quantification using stable isotope-labeled proteotypic peptides generated from a synthetic gene. One heptameric ring contained ClpP3,4,5,6 in a 1:2:3:1 ratio. The other ring contained ClpP1 and ClpR1,2,3,4 in a 3:1:1:1:1 ratio, resulting in only three catalytic sites. These ClpP1/R1-4 proteins are most closely related to the two subunits of the cyanobacterial P3/R complex and the identical P:R ratio suggests conserved adaptation. Furthermore, the plant-specific C-terminal extensions of the ClpP/R subunits were not proteolytically removed upon assembly, suggesting a regulatory role in Clp chaperone interaction. These results will now allow testing ClpP/R structure-function relationships using rationale design. The quantification workflow we have designed is applicable to other protein complexes.

Are substitution rates and RNA editing correlated?

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 non-edited 3^rd 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.

Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae)

Overlapping genes occur widely in microorganisms and in some plastid genomes, but unique properties are observed when such genes span the boundaries between single-copy and repeat regions. The termini of ndhH and ndhF, situated near opposite ends of the small single-copy region (SSC) in the plastid genomes of grasses (Poaceae), have migrated repeatedly into and out of the adjacent inverted-repeat regions (IR). The two genes are transcribed in the same direction, and the 5' terminus of ndhH extends into the IR in some species, while the 3' terminus of ndhF extends into the IR in others. When both genes extend into the IR, portions of the genes overlap and are encoded by the same nucleotide positions. Fine-scale mapping of the SSC-IR junctions across a sample of 92 grasses and outgroups, integrated into a phylogenetic analysis, indicates that the earliest grasses resembled the related taxa Joinvillea (Joinvilleaceae) and Ecdeiocolea (Ecdeiocoleaceae), with ca. 180 nucleotides of ndhH extending into the IR, and with ndhF confined to the SSC. This structure is maintained in early-diverging grass lineages and in most species of the BEP clade. In the PACMAD clade, ndhH lies completely or nearly completely within the SSC, and ca. 20 nucleotides of ndhF extend into the IR. The nucleotide substitution rate has increased in the PACMAD clade in the portion of ndhH that has migrated into the SSC.

Morphology of Hydatellaceae, an anomalous aquatic family recently recognized as an early-divergent angiosperm lineage

The family Hydatellaceae was recently reassigned to the early-divergent angiosperm order Nymphaeales rather than the monocot order Poales. This dramatic taxonomic adjustment allows comparison with other early-divergent angiosperms, both extant and extinct. Hydatellaceae possess some monocot-like features that could represent adaptations to an aquatic habit. Ecophysiological parallels can also be drawn from fossil taxa that are known from small achene-like diaspores, as in Hydatellaceae. Reproductive units of Hydatellaceae consist of perianthlike bracts enclosing several pistils and/or stamens. In species with bisexual reproductive units, a single unit resembles an "inside-out" flower, in which stamens are surrounded by carpels that are initiated centrifugally. Furthermore, involucre development in Trithuria submersa, with delayed growth of second whorl bracts, resembles similar delayed development of the second perianth whorl in Cabomba. Several hypotheses on the homologies of reproductive units in Hydatellaceae are explored. Currently, the most plausible interpretation is that each reproductive unit represents an aggregation of reduced unisexual apetalous flowers, which are thus very different from flowers of Nymphaeales. Each pistil in Hydatellaceae is morphologically and developmentally consistent with a solitary ascidiate carpel. However, ascidiate carpel development, consistent with placement in Nymphaeales, is closely similar to pseudomonomerous pistil development as in Poaes.

Phylogenetic relationships among Poaceae and related families as inferred from morphology, inversions in the plastid genome, and sequence data from the mitochondrial and plastid genomes

A phylogenetic analysis of the Poales was conducted to assess relationships among Poaceae and allied families. The analysis included 40 taxa, representing all families of the Poales as circumscribed by the Angiosperm Phylogeny Group (APG), plus five of the six unplaced Commelinid families in the APG system. The data matrix included 98 informative characters representing variation in morphology and chloroplast genome structure (including three inversions in the chloroplast genome), and 563 informative characters derived from rbcL and atpA nucleotide sequences. Ecdeiocolea has the 6-kilobase (kb) chloroplast genome inversion previously reported in Joinvillea and Poaceae, and like Joinvillea it lacks the trnT inversion that occurs in grasses. Analysis of the morphological data places Poaceae in an unresolved relationship relative to several other taxa, including Joinvillea and Ecdeiocolea, while analysis of the molecular and combined data resolves Ecdeiocolea as sister of Poaceae, with Joinvillea the sister of this group. Although the 6-kb and trnT inversions are non-homoplasious in the phylogenies obtained in this study, the 28-kb inversion is optimized as having originated twice (once in Restionaceae and another time in the most recent common ancestor of Ecdeiocolea, Joinvillea, and the grasses); an alternative interpretation is that it arose once and was later lost in Anarthria. Ecdeiocolea shares with Poaceae the presence of operculate, annulate pollen that lacks scrobiculi, and a dry, indehiscent fruit.

Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA, phytochrome B, rbcL, atpB, and morphology

Phylogenetic relationships within Celastraceae (spindle-tree family) were inferred from nucleotide sequence characters from the 5' end of 26S nuclear ribosomal DNA (including expansion segments D1-D3; 84 species sampled), phytochrome B (58 species), rbcL (31 species), atpB (23 species), and morphology (94 species). Among taxa of questionable affinity, Forsellesia is a member of Crossosomataceae, and Goupia is excluded from Celastraceae. However, Brexia, Canotia, Lepuropetalon, Parnassia, Siphonodon, and Stackhousiaceae are supported as members of Celastraceae. Gymnosporia and Tricerma are distinct from Maytenus, Cassine is supported as distinct from Elaeodendron, and Dicarpellum is distinct from Salacia. Catha, Maytenus, and Pristimera are not resolved as natural genera. Hippocrateaceae (including Plagiopteron and Lophopetalum) are a clade nested within a paraphyletic Celastraceae. These data also suggest that the Loesener's classification of Celastraceae sensu stricto and Hallé's classification of Hippocrateaceae are artificial. The diversification of the fruit and aril within Celastraceae appears to be complex, with multiple origins of most fruit and aril forms.

Mutations in MCT1 cDNA in patients with symptomatic deficiency in lactate transport

We identified 5 patients with subnormal erythrocyte lactate transport plus symptoms and signs of muscle injury on exercise and heat exposure. All had transport rates below the 95% envelope for normals. Three cases had rates 40-50% of mean normal. One was found to have a missense mutation in monocarboxylate transporter 1 (MCT1), the gene for the red cell lactate transporter (also expressed in skeletal muscle), at a conserved site, which was not mutated in a cohort of 90 normal humans. The other 2 cases had a different missense mutation (at a nonconserved site), which was also not mutated in the normal cohort. All 3 patients were heterozygotes. We presume that these mutations are responsible for their subnormal lactate transport, and hence their muscle injury under environmental stress; homozygous patients should be more seriously compromised. The other 2 cases had lactate transport rates 60-65% of mean normal, and their MCT1 revealed a third mutation, which proved to be a common polymorphism in the normal cohort. These 2 patients may be physiologic outliers in lactate transport, with their muscle damage arising from some other genetic defect.

Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences

We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.

A Competitive Allele-specific Oligomers Polymerase Chain Reaction Assay for the cis Double Mutation in AMPD1 That Is the Major Cause of Myo-adenylate Deaminase Deficiency

Background: Myo-adenylate deaminase deficiency (mADD) is the most common enzyme deficiency restricted to skeletal muscle, with a frequency of 1-2% in frozen muscle biopsies and complaints of easy fatigue and muscle cramping on exertion. A double C > T transition at coding bases 34 in exon 2 and 143 in exon 3 is the main cause of mADD. A 1-day assay using allele-specific oligomers and no isotope would be valuable for single cases. Methods and Results: Downstream primers with penultimate mismatch and 3' terminus matching the mutant or the normal base in exons 2 and 3 are used with a common upstream primer for each exon, to give amplimers of 150 bp for exon 2 and 200 bp for exon 3. A short common primer further downstream in exon 3 provides a competing 300-bp apmlimer whose product contribution is readily controlled by adjusting the annealing temperature. The entire procdure could be done in 1 day: DNA isolation, polymerase chain reaction (PCR), electrophoresis in agarose gel with ethidium bromide, and visualization by ultraviolet light. Deficient individuals have bands only with the mutant primers, normal persons have bands only with the normal primers, and heterozygotes (carriers) show bands with both primer sets. The empty slots show the 300-bp competing band, proving the PCR amplified the correct template. Allele-specific oligomers PCR results were verfied by dot blots and by restriction endonuclease analysis of exon 2. Conclusions: A simple and reliable allele-specific PCR assay using DNA from blood (or muscle) is now available for the diagnosis of individual cases of mADD caused by the common double-mtant AMPD1 gene, including the rare instances arising from homologous recombination between the two mutations.

Detection of very-rare-copy DNA in 0.2-ml dried human blood blots

A nested PCR assay for chromosome 7 inversions (as identified by the presence of T-cell receptor trans-rearrangements) can detect as rare a frequency as 1 copy in 300,000 leukocytes. To identify such rare occurrences from dried blood blots, the most conveniently obtained and stored samples for field population studies, demands a DNA extraction method that will provide both high quality and high yield. We have satisfied this requirement by extracting proteins and other components directly from the minced filter with phenol, before extracting the DNA with Chelex-water. This provides a near maximal yield of denatured DNA of sufficient quality to detect these translocations with a sensitivity equivalent to that of DNA purified from whole blood samples. Blots stored 6 months worked as well as fresh blots. In addition, we present a method for obtaining native DNA from the dried blots, although at a much lower yield. The successful use of blood blots to detect such rare events signals the feasibility of large-scale field studies involving diagnostic molecular epidemiology.

Comparative enzymology of AMP deaminase, adenylate kinase, and creatine kinase in vertebrate heart and skeletal muscle: the characteristic AMP deaminase levels of skeletal versus cardiac muscle are reversed in the North American toad

The specific activity of three characteristic enzymes, adenylate deaminase, adenylate kinase, and creatine kinase, in the skeletal muscles and heart of a variety of vertebrate land animals, including the human, are surveyed. Data from this study and available studies in the literature suggest that adenosine monophosphate deaminase in land vertebrates is quite high in white skeletal muscle, usually somewhat lower in red muscle, and 15- to 500-fold lower in cardiac muscle. Adenosine monophosphate deaminase is active primarily under ischemic or hypoxic conditions which occur frequently in white muscle, only occasionally in red muscle, and ought never occur in heart muscle, and this may therefore account for observed enzyme levels. The common North American toad, Bufo americanus, provides a striking exception to the rule with cardiac adenosine monophosphate deaminase as high as in mammalian skeletal muscle, whereas its skeletal muscle level of adenosine monophosphate deaminase is several times lower. The exceptional levels in the toad are not due to a change in substrate binding and are not accompanied by comparable change in the level of adenylate or creatine kinase. Nor do they signal any major change in isozyme composition, since a human muscle adenosine monophosphate deaminase-specific antiserum reacts with toad muscle adenosine monophosphate deaminase, but not with toad heart adenosine monophosphate deaminase. They do not represent any general anuran evolutionary strategy, since the bullfrog (Rana catesbeiana) and the giant tropic toad (Bufo marinus) have the usual vertebrate pattern of adenosine monophosphate deaminase distribution.(ABSTRACT TRUNCATED AT 250 WORDS)

Chloroplast DNA inversions and the origin of the grass family (Poaceae)

The phylogenetic affinities of the grass family (Poaceae) have long been debated. The chloroplast genomes of at least some grasses have been known to possess three inversions relative to the typical gene arrangement found in most flowering plants. We have surveyed for the presence of these inversions in grasses and other monocots by polymerase chain reaction amplification with primers constructed from sequences flanking the inversion end points. Amplification phenotypes diagnostic for the largest inversion (28 kilobase pairs) were found in genera representing all grass subfamilies, and in the nongrass families Restionaceae, Ecdeiocoleaceae, and Joinvilleaceae, but not in any other monocots--notably, Flagellariaceae, Anarthriaceae, Cyperaceae, or Juncaceae. This finding is consistent with one of the two principal views of grass phylogeny in suggesting that Poaceae and Cyperaceae (sedges) are not closest relatives. A second (approximately 6 kilobases) inversion appears to occur in a subset of the families possessing the 28-kilobase inversion and links Joinvilleaceae and Poaceae, while the smallest inversion appears unique to grasses. These inversions thus provide a nested set of phylogenetic characters, indicating a hierarchy of relationships in the grasses and allies, with Joinvilleaceae identified as the likely sister group to the Poaceae.

Medical implications of the lactate and ammonia relationship in anaerobic exercise

The genesis of the modern ischemic forearm exercise test (IFET) employing the measurement of lactate and ammonia as countervailing metabolites is briefly reviewed, along with the application of the lactate ammonia exercise ratio in the diagnosis of myoadenylate deaminase deficiency and disorders of glycolysis and glycogenolysis. Two cases are presented to illustrate the response patterns elicited, their reproducibility, the types of parameters that can be quantified, and the role the IFET may play in the differential diagnosis of fitness failures. The role of the ammonia measurement is emphasized here because the lactate response is more familiar. The roles of hypoxanthine responses and of muscle ammonia measurements in the evaluation of cases are examined, and some pertinent and recently introduced analytic methods are cited. The applications of newer approaches, such as aspiration biopsy and N-14 NMR spectroscopy, are discussed, along with an example of the new clinical defects in enzymes and membrane carriers that should be anticipated during the utilization of the IFET.

Clinical assay of the human erythrocyte lactate transporter. I. Principles, procedure, and validation

A clinically applicable method for the assay of lactate efflux from human red cells has been developed and described in detail. It requires only small volumes of blood and routine chemicals, and evaluates the process under physiological conditions and direction of lactate loading and transport. The decline of red cell lactate level fit a first order decay curve reasonably well, and better than the fit to zero order or second order plots. Bias is controlled by the use of least-squares curve fitting for all assays, and constraints on the elimination of outlier points. The assay shows a variety of inhibitor effects that may be considered typical for this transporter: potent inhibition by p-hydroxymercuribenzoate, but not by other types of sulfhydryl reagents; marked inhibition by phloretin, quercitin, and 1-fluoro-2,4-dinitrobenzene; lack of inhibition by the amine-reactive agents that block the chloride/carbonate exchanger, DIDS and SITS; and reversible competitive inhibition by alpha-cyano-4-OH-cinnamic acid. Harmaline and N-I-succinimide also produced effective inhibition. The assay also demonstrated transacceleration of L-lactate efflux in the presence of external additions of D-lactate, glycollate, iodoacetate, fluoropyruvate, and bromopyruvate, which are substituted monocarboxylates like lactate, but not by iodoacetamide or L-alanine. Such activation is a manifestation of a macromolecular carrier in operation, and cannot be explained by a pore or channel. These findings satisfy all reasonable criteria for a satisfactory and sensitive lactate transporter assay, which should be adequate to evaluate volunteers and patients for the normal range of this carrier, and to seek possible deficient states.

Clinical assay of the human erythrocyte lactate transporter. II. Analysis and display of normal human data

We have applied a lactate efflux assay to human red cells at two temperatures and with initial lactic acid loads up to 8 mM, metabolically generated. Efflux was about 1.5 times faster at external pH of 8.5 than at 7.5; the latter was the standard pH used thereafter. Multiple lactate loads in a single blood specimen demonstrated clear evidence of saturation kinetics at both pH levels, since the efflux rate did not increase proportionally with the lactate load. Best-fitting rectangular hyperboles were determined for 129-131 assays from 43 volunteers at 20 degrees and 30 degrees. In most cases high and low lactate loads permitted a two-point evaluation of saturation kinetics, and a positive indication was obtained in 88 of 89 tests. The apparent efflux Km and Vm values may be influenced by pH as well as by lactate levels and cannot be taken as rigorous, although they agree reasonably well with literature data on influx and exchange velocities. The data displayed a Hill constant of 1, a 30 degrees/20 degrees velocity ratio of 2.7, and no significant clustering by sex or age. A single assay with initial lactate level above 5 mM at 30 degrees should be sufficient to identify cases with a defective transporter, using the 95% tolerance limits developed in this report.

Levels of adenylate deaminase, adenylate kinase, and creatine kinase in frozen human muscle biopsy specimens relative to type 1/type 2 fiber distribution: evidence for a carrier state of myoadenylate deaminase deficiency

Myoadenylate deaminase deficiency is believed to reflect a genetic deficiency of skeletal muscle, but its pattern of inheritance has not been established. We examined, histochemically and by quantitative biochemical assay, muscle biopsy specimens from 3 putative carriers of this disorder. Adenylate kinase and creatine kinase were assayed in parallel with adenylate deaminase in order to establish enzyme activity ratios and the variation of each enzyme with fiber-type distribution. Control tissue consisted of 34 biopsy specimens without notable abnormalities from 30 patients, and included 4 specimen pairs with disparate fiber-type contributions. By linear regression analysis, adenylate deaminase level averaged 2.8-fold higher, and adenylate kinase 4.5-fold higher, in type 2 than in type 1 fibers, whereas creatine kinase level did not differ. The slopes of the regression lines resulting from analysis of the four specimen pairs from individual patients agreed well with the overall regression line in each plot. The 3 putative carriers had adenylate deaminase levels 2.5 to 5.7 times lower than the mean control value for their fiber-type distribution, but at least 20 times higher than their enzyme-deficient kinfolk. This finding indicates that a carrier state does exist, and that the deficiency state reflects an autosomal recessive inheritance pattern. Three additional biopsy specimens were excluded from evaluation when preliminary analysis showed elevated adenylate kinase/adenylate deaminase ratios that were outliers at the 1% level. This result suggests a carrier incidence of 10% in the muscle biopsy specimen population, which would markedly bias population estimates if undetected.

Consideration of atmospheric turbulence in laser systems design

The physical basis for various effects of atmospheric turbulence on laser systems is briefly discussed, and certain limitations of the theoretical results given by Tatarski are summarized. The most important conclusion is that Tatarski's results for amplitude and phase fluctuations, while they are not applicable for a laser beam of arbitrary diameter, do provide an adequate approximation when the beam diameter is at least a factor of 2 greater than the lateral correlation length for amplitude fluctuations, which is true in many applications. The effects analyzed in some detail are beam steering, beam spreading, image dancing, image blurring, scintillation, and phase fluctuations, certain of which are intimately related. As to specific applications, the signal-to-noise ratio for an AM signal passing through the turbulent atmosphere is derived in terms of the power fluctuation, and communication links are considered in terms of this ratio; the effect of power fluctuations on the probability of detection for the laser radar is discussed in general, and a special example is given; finally, the spot size on the moon's surface for a transmitter located on the earth's surface is calculated for different turbulence conditions.