Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes

Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attraction artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported relationships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147147/1/tax25065680.pd

Virus Movements on the Plasma Membrane Support Infection and Transmission between Cells

How viruses are transmitted across the mucosal epithelia of the respiratory, digestive, or excretory tracts, and how they spread from cell to cell and cause systemic infections, is incompletely understood. Recent advances from single virus tracking experiments have revealed conserved patterns of virus movements on the plasma membrane, including diffusive motions, drifting motions depending on retrograde flow of actin filaments or actin tail formation by polymerization, and confinement to submicrometer areas. Here, we discuss how viruses take advantage of cellular mechanisms that normally drive the movements of proteins and lipids on the cell surface. A concept emerges where short periods of fast diffusive motions allow viruses to rapidly move over several micrometers. Coupling to actin flow supports directional transport of virus particles during entry and cell-cell transmission, and local confinement coincides with either nonproductive stalling or infectious endocytic uptake. These conserved features of virus–host interactions upstream of infectious entry offer new perspectives for anti-viral interference

Dynamics and Adaptive Benefits of Protein Domain Emergence and Arrangements during Plant Genome Evolution

Plant genomes are generally very large, mostly paleopolyploid, and have numerous gene duplicates and complex genomic features such as repeats and transposable elements. Many of these features have been hypothesized to enable plants, which cannot easily escape environmental challenges, to rapidly adapt. Another mechanism, which has recently been well described as a major facilitator of rapid adaptation in bacteria, animals, and fungi but not yet for plants, is modular rearrangement of protein-coding genes. Due to the high precision of profile-based methods, rearrangements can be well captured at the protein level by characterizing the emergence, loss, and rearrangements of protein domains, their structural, functional, and evolutionary building blocks. Here, we study the dynamics of domain rearrangements and explore their adaptive benefit in 27 plant and 3 algal genomes. We use a phylogenomic approach by which we can explain the formation of 88% of all arrangements by single-step events, such as fusion, fission, and terminal loss of domains. We find many domains are lost along every lineage, but at least 500 domains are novel, that is, they are unique to green plants and emerged more or less recently. These novel domains duplicate and rearrange more readily within their genomes than ancient domains and are overproportionally involved in stress response and developmental innovations. Novel domains more often affect regulatory proteins and show a higher degree of structural disorder than ancient domains. Whereas a relatively large and well-conserved core set of single-domain proteins exists, long multi-domain arrangements tend to be species-specific. We find that duplicated genes are more often involved in rearrangements. Although fission events typically impact metabolic proteins, fusion events often create new signaling proteins essential for environmental sensing. Taken together, the high volatility of single domains and complex arrangements in plant genomes demonstrate the importance of modularity for environmental adaptability of plants

Experimental and Molecular Approaches to Plant Bio-systematics, P. C. Hoch and

Posttranscriptional gene silencing (PTGS) is a nucleotide sequence-specific defense mechanism that can target both cellular and viral mRNAs. Here, three types of transgene-induced PTGS and one example of virus-induced PTGS were analyzed in plants. In each case, antisense RNA complementary to the targeted mRNA was detected. These RNA molecules were of a uniform length, estimated at 25 nucleotides, and their accumulation required either transgene sense transcription or RNA virus replication. Thus, the 25-nucleotide antisense RNA is likely synthesized from an RNA template and may represent the specificity determinant of PTGS. Posttranscriptional gene silencing occurs in plants and fungi transformed with foreign or endogenous DNA and results in the reduced accumulation of RNA molecules with sequence similarity to the introduced nucleic acid (1, 2). Double-stranded RNA induces a similar effect in nematodes (3), insects (4 ), and protozoa (5). PTGS can be suppressed by several virus-encoded proteins (6 ) and is closely related to RNA-mediated virus resistance and cross-protection in plants To account for the sequence specificity and posttranscriptional nature of PTGS, it has been proposed that antisense RNA forms a duplex with the target RNA, thereby promoting its degradation or interfering with its translation (12). If these hypothetical antisense RNA molecules are of a similar size to typical mRNAs, they would have been readily detected by routine RNA analyses. However, there have been no reports of such antisense RNA that is detected exclusively in plants or animals exhibiting PTGS. Nevertheless, PTGS-specific antisense RNA may exist, but may be too short for easy detection. We carried out analyses specifically to detect low molecular weight antisense RNA in four classes of PTGS in plants (13). The first class tested was transgene-induced PTGS of an endogenous gene ("cosuppression"). We used five tomato lines (T1.1, T1.2, T5.1, T5.2, and T5.3), each transformed with a tomato 1-aminocyclopropane-1-carboxylate oxidase (ACO) cDNA sequence placed downstream of the cauliflower mosaic virus 35S promoter (35S). Two lines (T5.2 and T5.3) exhibited PTGS of the endogenous ACO mRNA PTGS induced by transgenes can also occur when a transgene does not have homology to an endogenous gene (1). Therefore, we tested whether this type of PTGS was also associated with small antisense RNA. We analyzed three tobacco lines carrying 35S-␤-glucuronidase (GUS) transgenes. Two of these lines, T4 (15) and 6b5 (16), exhibited PTGS of GUS. The third line (6b5ϫ271) tested was produced by crossing 6b5 with line 271 (17 ), in which there is a transgene suppressor of the 35S promoter in 6b5. There was no PTGS of GUS in 6b5ϫ271 because of the transcriptional suppression of the 35S GUS transgene (18). Hybridization with a GUS-specific probe revealed that low molecular weight GUS antisense RNA was present in T4 and 6b5 Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK. *To whom correspondence should be addressed. Email: [email protected]

Genetic control of floral zygomorphy in pea (Pisum sativum L.)

Floral zygomorphy (flowers with bilateral symmetry) has multiple origins and typically manifests two kinds of asymmetries, dorsoventral (DV) and organ internal (IN) asymmetries in floral and organ planes, respectively, revealing the underlying key regulators in plant genomes that generate and superimpose various mechanisms to build up complexity and different floral forms during plant development. In this study, we investigate the loci affecting these asymmetries during the development of floral zygomorphy in pea (Pisum sativum L.). Two genes, LOBED STANDARD 1 (LST1) and KEELED WINGS (K), were cloned that encode TCP transcription factors and have divergent functions to constitute the DV asymmetry. A previously undescribed regulator, SYMMETRIC PETALS 1 (SYP1), has been isolated as controlling IN asymmetry. Genetic analysis demonstrates that DV and IN asymmetries could be controlled independently by the two kinds of regulators in pea, and their interactions help to specify the type of zygomorphy. Based on the genetic analysis in pea, we suggest that variation in both the functions and interactions of these regulators could give rise to the wide spectrum of floral symmetries among legume species and other flowering plants