Evolutionary genomics of LysM genes in land plants

Background  

The ubiquitous LysM motif recognizes peptidoglycan, chitooligosaccharides (chitin) and, presumably, other structurally-related oligosaccharides. LysM-containing proteins were first shown to be involved in bacterial cell wall degradation and, more recently, were implicated in perceiving chitin (one of the established pathogen-associated molecular patterns) and lipo-chitin (nodulation factors) in flowering plants. However, the majority of LysM genes in plants remain functionally uncharacterized and the evolutionary history of complex LysM genes remains elusive.     

Stepwise origin and functional diversification of the AFL subfamily B3 genes during land plant evolution

The AFL genes (ABI3/VP1, FUS3 and LEC2) belong to the plant-specific B3 superfamily, playing important roles in regulating seed development and maturation. It is unclear, however, whether these genes appeared at the same time as the origin of seed plants and if all these genes are necessary and sufficient for seed development for all seed plants. By conducting a genome-wide comparative analysis of the putative AFL genes in various plant species, we found that the ABI3 homologous genes existed in all land plant genomes, but the FUS3 homologous were present only in seed plant genomes and the LEC2-like sequences only in dicot genomes. Phylogenetic analysis indicated that the AFL genes had undergone successive rounds of gene duplication and subsequent diversification during land plant evolution, resulting in the stepwise origin of the ABI3, FUS3 and LEC2 genes. Comparison of gene structure of the AFL genes revealed a trend of decreasing in the number of conserved domains from ABI3 to FUS3 and LEC2.     

Morphological evolution in land plants: new designs with old genes

The colonization and radiation of multicellular plants on land that started over 470 Ma was one of the defining events in the history of this planet. For the first time, large amounts of primary productivity occurred on the continental surface, paving the way for the evolution of complex terrestrial ecosystems and altering global biogeochemical cycles; increased weathering of continental silicates and organic carbon burial resulted in a 90 per cent reduction in atmospheric carbon dioxide levels. The evolution of plants on land was itself characterized by a series of radical transformations of their body plans that included the formation of three-dimensional tissues, de novo evolution of a multicellular diploid sporophyte generation, evolution of multicellular meristems, and the development of specialized tissues and organ systems such as vasculature, roots, leaves, seeds and flowers. In this review, we discuss the evolution of the genes and developmental mechanisms that drove the explosion of plant morphologies on land. Recent studies indicate that many of the gene families which control development in extant plants were already present in the earliest land plants. This suggests that the evolution of novel morphologies was to a large degree driven by the reassembly and reuse of pre-existing genetic mechanisms.     

Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants

Background  

The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases (GSKs) are non-receptor serine/threonine protein kinases that are involved in a variety of biological processes. In contrast to the two members of the GSK3 family in mammals, plants appear to have a much larger set of divergent GSK genes. Plant GSKs are encoded by a multigene family; analysis of the Arabidopsis genome revealed the existence of 10 GSK genes that fall into four major groups. Here we characterized the structure of Arabidopsis and rice GSK genes and conducted the first broad phylogenetic analysis of the plant GSK gene family, covering a taxonomically diverse array of algal and land plant sequences.     

Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes

Abstract Relationships among families of the lower Diptera (formerly suborder ‘Nematocera’) have been exceptionally difficult to resolve. Multiple hypotheses based on morphology have been proposed to identify the earliest lineages of flies and place the phylogenetic origin of the higher flies (Brachycera), but convincing support is limited. Here we resolve relationships among the major groups of lower Diptera using sequence data from four nuclear markers, including both ribosomal (28S rDNA) and protein‐coding (CAD, TPI and PGD) genes. Our results support both novel and traditional arrangements. Most unexpectedly, the small, highly‐specialized family Deuterophlebiidae appears to be sister to all remaining Diptera. Other results include the resolution of the traditional infra‐orders Culicomorpha (including a novel superfamily Simulioidea = Thaumaleidae + Simuliidae), Tipulomorpha (Tipulidae sensu lato + Trichoceridae) and Bibionomorpha sensu lato. We find support for a limited Psychodomorpha (Blephariceridae, Tanyderidae and Psychodidae) and Ptychopteromorpha (Ptychopteridae), whereas the placement of several enigmatic families (Nymphomyiidae, Axymyiidae and Perissommatidae) remains ambiguous. According to genetic data, the infra‐order Bibionomorpha is sister to the Brachycera. Much of the phylogenetic signal for major lineages was found in the 28S rDNA gene, whereas protein‐coding genes performed variably at different levels. In addition to elucidating relationships, we also estimate the age of major lower dipteran clades, based on molecular divergence time estimates using relaxed‐clock Bayesian methods and fossil calibration points.     

Phylogenetics and reticulate evolution in Pistacia (Anacardiaceae)

The systematic position and intrageneric relationships of the economically important Pistacia species (Anacardiaceae) are controversial. The phylogeny of Pistacia was assessed using five data sets: sequences of nuclear ribosomal ITS, the third intron of the nuclear nitrate reductase gene (NIA-i3), and the plastid ndhF, trnL-F and trnC-trnD. Significant discordance was detected among ITS, NIA-i3, and the combined plastid DNA data sets. ITS, NIA-i3, and the combined plastid data sets were analyzed separately using Bayesian and parsimony methods. Both the ITS and the NIA-i3 data sets resolved the relationships among Pistacia species well; however, these two data sets had significant discordance. The ITS phylogeny best reflects the evolutionary relationships among Pistacia species. Lineage sorting of the NIA-i3 alleles may explain the conflicts between the NIA-i3 and the ITS data sets. The combined analysis of three plastid DNA data sets resolved Pistacia species into three major clades, within which only a few subclades were supported. Pistacia was shown to be monophyletic in all three analyses. The previous intrageneric classification was largely inconsistent with the molecular data. Some Pistacia species appear not to be genealogical species, and evidence for reticulate evolution is presented. Pistacia saportae was shown to be a hybrid with P. lentiscus (maternal) and P. terebinthus (paternal) as the parental taxa.     

The evolution and diversification of Dicers in plants

Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants ( approximately 200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots.     

A synthetic combination of mutations, including fs(1)pyr? Su(b) , r? Su(b) and b , causes female sterility and reduces embryonic viability in Drosophila melanogaster

A Drosophila melanogaster mutant, fs(1)pyr ^Su(b) , carrying a mutation that maps to the tip of the X chromosome, has been isolated. The mutation, when present alone, does not confer a detectable phenotype. However, this mutation causes female sterility and reduces embryonic viability when combined with mutations which deregulate the pyrimidine and β-alanine pools. Embryos that are homozygous for the mutations fs(1)pyr ^Su(b) , r ^Su(b) [previously designated as Su(b)] and b, and originate from a female parent homozygous for the three mutations show severely reduced viability. Newly laid eggs begin development normally, but the majority of the embryos die just before the eggs are due to hatch. Received: 15 May 1998 / Accepted: 18 January 1999     

Phylogenetics and evolution of nematode-trapping fungi (Orbiliales) estimated from nuclear and protein coding genes

The systematic classification of nematode-trapping fungi is redefined based on phylogenies inferred from sequence analyses of 28S rDNA, 5.8S rDNA and beta-tubulin genes. Molecular data were analyzed with maximum parsimony, maximum likelihood and Bayesian analysis. An emended generic concept of nematode-trapping fungi is provided. Arthrobotrys is characterized by adhesive networks, Dactylellina by adhesive knobs, and Drechslerella by constricting-rings. Phylogenetic placement of taxa characterized by stalked adhesive knobs and non-constricting rings also is confirmed in Dactylellina. Species that produce unstalked adhesive knobs that grow out to form loops are transferred from Gamsylella to Dactylellina, and those that produce unstalked adhesive knobs that grow out to form networks are transferred from Gamsylella to Arthrobotrys. Gamsylella as currently circumscribed cannot be treated as a valid genus. A hypothesis for the evolution of trapping-devices is presented based on multiple gene data and morphological studies. Predatory and nonpredatory fungi appear to have been derived from nonpredatory members of Orbilia. The adhesive knob is considered to be the ancestral type of trapping device from which constricting rings and networks were derived via two pathways. In the first pathway adhesive knobs retained their adhesive material forming simple two-dimension networks, eventually forming complex three-dimension networks. In the second pathway adhesive knobs lost their adhesive materials, with their ends meeting to form nonconstricting rings and they in turn formed constricting rings with three inflated-cells.     

Mutations induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in the lacZ and cII genes of Muta™ Mouse

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) found in chewing tobacco, snuff, cigarettes, and cigars is a tobacco-specific nitrosamine and classified as a possible human carcinogen (Class 2B) by the International Agency for Research on Cancer (IARC). NNK given intraperitoneally was seen to induce lung and liver adenomas.To evaluate the genotoxicity of NNK in vivo, NNK was intraperitoneally administered to Muta™ Mouse at two concentrations (125 and 250 mg/kg, once a week for 4 weeks) followed by the measurement of mutant frequencies in the lacZ and cII genes from lung and liver in the same mice. Characterization of the types of the mutation was determined by sequencing the cII genes from mutant plaques. The mutant frequencies in both target genes from both organs dose-dependently increased up to 10 times compared to those of the control group. For the types of mutations, the ratio of the G:C to A:T mutation in the total number of mutants was less than the ratio of A:T to T:A and A:T to C:G transversion, contrary to a previous report [Cancer Res, 49 (1989) 5305]. The A:T to T:A transversion was the most highly induced mutation both in the lung and liver cII genes. The increasing rate of mutant frequencies in lung and liver over the vehicle control was 55 and 56 times, respectively, while the increasing rate of G:C to A:T transition was only 1.9 and 2.8 times, respectively.These observations show that NNK predominantly induces DNA adducts leading to A:T to T:A and/or A:T to C:G mutations in the transgene.     

荷叶铁线蕨孢子体解剖结构和组织化学特征研究

荷叶铁线蕨为岩生珍稀蕨类植物,分布在中国重庆市万州、涪陵等极少地区.为揭示荷叶铁线蕨生长特性,采集栽培在种质资源圃中的荷叶铁线蕨根样、根状茎、在阳光下生长和在阴暗环境下生长的叶片,固定于甲醛-酒精-乙酸溶液中,用双面刀片进行徒手切片,分别用三种0.1％苏丹红、0.1％硫酸氢黄连素-苯胺兰、0.05％甲苯胺蓝染色剂染色,...     

Phylogenetics of tribe Orchideae (Orchidaceae: Orchidoideae) based on combined DNA matrices: inferences regarding timing of diversification and evolution of pollination syndromes

Background and aims

Tribe Orchideae (Orchidaceae: Orchidoideae) comprises around 62 mostly terrestrial genera, which are well represented in the Northern Temperate Zone and less frequently in tropical areas of both the Old and New Worlds. Phylogenetic relationships within this tribe have been studied previously using only nuclear ribosomal DNA (nuclear ribosomal internal transcribed spacer, nrITS). However, different parts of the phylogenetic tree in these analyses were weakly supported, and integrating information from different plant genomes is clearly necessary in orchids, where reticulate evolution events are putatively common. The aims of this study were to: (1) obtain a well-supported and dated phylogenetic hypothesis for tribe Orchideae, (ii) assess appropriateness of recent nomenclatural changes in this tribe in the last decade, (3) detect possible examples of reticulate evolution and (4) analyse in a temporal context evolutionary trends for subtribe Orchidinae with special emphasis on pollination systems.

Methods

The analyses included 118 samples, belonging to 103 species and 25 genera, for three DNA regions (nrITS, mitochondrial cox1 intron and plastid rpl16 intron). Bayesian and maximum-parsimony methods were used to construct a well-supported and dated tree. Evolutionary trends in the subtribe were analysed using Bayesian and maximum-likelihood methods of character evolution.

Key Results

The dated phylogenetic tree strongly supported the recently recircumscribed generic concepts of Bateman and collaborators. Moreover, it was found that Orchidinae have diversified in the Mediterranean basin during the last 15 million years, and one potential example of reticulate evolution in the subtribe was identified. In Orchidinae, pollination systems have shifted on numerous occasions during the last 23 million years.

Conclusions

The results indicate that ancestral Orchidinae were hymenopteran-pollinated, food-deceptive plants and that these traits have been dominant throughout the evolutionary history of the subtribe in the Mediterranean. Evidence was also obtained that the onset of sexual deception might be linked to an increase in labellum size, and the possibility is discussed that diversification in Orchidinae developed in parallel with diversification of bees and wasps from the Miocene onwards.     

(Z)-3-nonenol, (Z,Z)-3,6-nonadienol and (S,S)-(-)-epianastrephin: male produced pheromones of the Mexican fruit fly

(Z)-3-nonenol, (Z,Z)-3,6-nonadienol and (S,S)-(-)-epianastrephin proved active as male-produced pheromones which elicited behavioral responses from virgin female Mexican fruit flies (Anastrepha ludens) (Diptera: Tephritidae) in laboratory bioassays. All three chemicals elicited attraction and/or locomotor arrest when tested individually. When tested together, (Z)-3-nonenol inhibited the behavioral effect of (Z,Z)-3,6-nonadienol but either of the alcohols synergized the effect of (S,S)-(-)-epianastrephin. Quantities of the pheromones per male abdomen were: (Z)-3-nonenol-100 ng; (Z,Z)-3,6-nonadienol-40 ng; and total epianastrephin (R,R and S,S enantiomers)-700 ng. Relative to the quantities in abdominal extract, males released these chemicals during sexual display in a blend containing a higher proportion of the alcohols.

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Résumé Le (Z)-3-nonènol, le (Z,Z)-3,6-nonadiènol et le (S,S)-(-)-épianastréphine produits par les mâles de la mouche mexicaine du fruit (Anastrepha ludens) (Diptera: Tephritidae) ont attirés les femelles lors de tests conduits en laboratoire. Le pouvoir attractif du (Z)-3-nonènol est faible comparé à celui des deux autres phéromones. Evalués ensemble, le (Z)-3-nonènol inhibe l'attractivité du (Z,Z)-3,6-nonadiènol mais chacun des deux alcools synergise l'effet attractif de la (S,S)-(-)-épianastréphine. Les quantités recouvrées par mâle dans un extrait abdominal étaient respectivement de 100, 40 et 700 ng pour le (Z)-3-nonènol, le (Z,Z)-3,6-nonadiènol, et l'épianastréphine totale (R,R et S,S) énantiomères. Comparées à ces valeurs, le mélange élange émis par les mâles lors de leur cour sexuelle est plus riche in alcools. Le rapport (Z)-3-nonènol (Z,Z)-3,6-nonadiènol est cependant identique dans l'extrait abdominal et dans le mélange émis par les mâles.

     

SET-domain proteins of the Su(var)3-9, E(z) and trithorax families

SET-domain (SET: Su(var)3-9, E(z) and Trithorax)-containing proteins were collected through sequence searches of the available databases. After removing redundancies, the proteins belonging to three families, SU(VAR)3-9, E(Z) and Trithorax, were selected. Analysis of the relationship between the different members is based on pairwise alignment, compilation, and comparison of their SET-domains. The level of homology of the SET-domains defined the distribution of the proteins into families and into clades within the families. The architecture of the entire protein supported the distribution pattern built upon SET-domain similarity. Parallel cladistic and protein-architecture analyses outlined two plausible criteria for predicting function.     

Conservation and diversification of HAIRY MERISTEM gene family in land plants

The shoot apical meristems (SAMs) of land plants are crucial for plant growth and organ formation. In several angiosperms, the HAIRY MERISTEM (HAM) genes function as key regulators that control meristem development and stem cell homeostasis. To date, the origin and evolutionary history of the HAM family in land plants remains unclear. Potentially shared and divergent functions of HAM family members from angiosperms and non-angiosperms are also not known. In constructing a comprehensive phylogeny of the HAM family, we show that HAM proteins are widely present in land plants and that HAM proteins originated prior to the divergence of bryophytes. The HAM family was duplicated in a common ancestor of angiosperms, leading to two distinct groups: type I and type II. Type-II HAM members are widely present in angiosperms, whereas type-I HAM members were independently lost in different orders of monocots. Furthermore, HAM members from angiosperms and non-angiosperms (including bryophytes, lycophytes, ferns and gymnosperms) are able to replace the role of the type-II HAM genes in Arabidopsis, maintaining established SAMs and promoting the initiation of new stem cell niches. Our results uncover the conserved functions of HAM family members and reveal the conserved regulatory mechanisms underlying HAM expression patterning in meristems, providing insight into the evolution of key stem cell regulators in land plants.