Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs

Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.

Expression of HtKNOT1, a class I KNOX gene, overlaps cell layers and development compartments of differentiating cells in stems and flowers of Helianthus tuberosus

In plant, post-embryonic development relies on the activities of indeterminate cell populations termed meristems, spatially clustered cell lineages, wherein a subset divides indeterminately. For correct growth, the plant must maintain a constant flow of cells through the meristem, where the input of dividing pluripotent cells offsets the output of differentiating cells. KNOTTED1-like homeobox (KNOX) genes are expressed in specific patterns in the plant meristems and play important roles in maintaining meristematic cell identity. We have analyzed the expression pattern of HtKNOT1, a class I KNOX gene of Helianthus tuberosus, in stems, inflorescence meristems, floral meristems and floral organs. HtKNOT1 is expressed in cambial cells, phloem cells and xylematic parenchyma within apical stem internodes, while in basal internodes HtKNOT1 expression was restricted to the presumptive initials and recently derived phloem cells. In the reproductive phase, HtKNOT1 mRNAs were detected in both the inflorescence and floral meristems as well within lateral organ primordia (i.e. floral bracts, petals, stamens and carpels). In more differentiated flowers, the expression of HtKNOT1 was restricted to developing ovules and pollen mother cells. HtKNOT1 may play a dual role being required to maintain the meristem initials as well as initiating differentiation and/or conferring new cell identity. In particular, it is possible that HtKNOT1 cooperates at floral level with additional factors that more specifically control floral organs and pollen development in H. tuberosus.

Genome plasticity during the acquisition of embryogenic competence

Hypocotyl explants from carrot and other species experience concomitant segregation events and differentiation of homeotic structures during the first 20 days of culture on 2,4-dichlorophenoxyacetic acid (2,4-D). In addition to these cyto-morphological changes, significant amounts of nuclear DNA are lost, the molecular details of which we investigate in this paper. We have developed a slot-blot analysis assay to study the DNA content of a series of carrot samples; besides the leaves, this survey ranged over different culture timepoints: hypocotyls, cell lines, and somatic embryo stages. We carried on to study the relationship between this DNA loss and sequence complexity modulation. Results from probing sequences that correspond to different degrees of complexity, such as medium repetitive and unique sequences as well as sequences belonging to both classes (ribosomal cistrons, ubiquitin, actin, and chalcone synthase), consistently manifested a reduction in DNA levels during the acquisition of embryogenic competence. In some cases, the cultured cells would contain only 10% of the gene copies observed in the reference tissues. Modulation trends also showed that DNA levels of most sequences recover at the torpedo-plantlet stage, which again correlates DNA modulation and the acquisition of embryogenic competence. These results suggest that similar DNA variations may occur in plants in vivo during meiosis, possibly so that meiotic division may be properly completed.

Altered patterns of gene expression in Arabidopsis elicited by cauliflower mosaic virus (CaMV) infection and by a CaMV gene VI transgene

Cauliflower mosaic virus (CaMV) gene VI protein (P6) is an important determinant of symptom expression. Differential display polymerase chain reaction (PCR) was used to identify changes in gene expression in Arabidopsis elicited by a P6 transgene that causes a symptomatic phenotype. We used slot blot hybridization to measure the abundance of mRNAs complementary to 66 candidate PCR products in transgenic, CaMV-infected, and uninfected Arabidopsis plants. CaMV-infected and P6 transgenic plants showed broadly similar changes in abundance of mRNA species. In P6 transgenic plants we detected 18 PCR products that showed unambiguous changes in abundance plus another 15 that showed more limited changes (approximately twofold). CaMV-infected plants showed 17 unambiguous and 13 limited changes. Down-regulated species include those encoding a novel, phenol-like sulfotransferase, and a glycine-rich, RNA-binding protein. Up-regulated species included ones encoding an myb protein, glycine-rich and stress-inducible proteins, and a member of a previously unreported gene family. CaMV infection causes alterations in expression of many Arabidopsis genes. Transgene-mediated expression of P6 mimics virus infection in its effect on host gene expression, providing a potential mechanism for this process.

Transgenic Arabidopsis lines expressing gene VI from cauliflower mosaic virus variants exhibit a range of symptom-like phenotypes and accumulate inclusion bodies

Gene VI of cauliflower mosaic virus (CaMV) is an important determinant of symptom expression during infection. We have constructed a series of transgenic Arabidopsis lines that express gene VI protein (P6) from two CaMV isolates (Bari-1 and Cabb B-JI) that cause mild and severe symptoms, respectively, in Arabidopsis, and from a recombinant virus (Baji-31) with a hybrid gene VI that causes very severe symptoms. From 41 transgenic lines analyzed, 17 showed symptom-like phenotypes that ranged from mild vein chlorosis to severe chlorosis and stunting. P6 levels in transgenic lines varied from undetectable in the lowest expressors to levels greater than those in CaMV-infected plants. There was a strong correlation between phenotype severity and the level of P6, and with the gene VI origin in the order, Baji-31 > B-JI > Bari-1. This was similar to symptom severity in Arabidopsis infected with the respective CaMV variant. We also found that transgenic P6 accumulated in inclusion bodies that were similar to those found in infected plants but lacking virions. We conclude that expression of P6, in the absence of virus replication, elicits a subset of the host symptom responses normally observed during infection and that the level, sequence, and possibly the form of P6 are important in potentiating the process.

Identification of genes up-regulated in dedifferentiating Nicotania glauca pith tissue, using an improved method for constructing a subtractive cDNA library

Pith explants of Nicotiana glauca grown in vitro in synthetic medium supplemented with 2,4 dichlorophenoxyacetic acid (2, 4 D), are induced to dedifferentiate. Treatment with actinomycin D within the first 4-8 h of culture (but not later) is lethal and the explants die, implying a requirement for de novo transcription. The genes expressed during the initial period of culture are presumably critical for subsequent cell survival and proliferation, but so far their identity is unknown. We have constructed a subtractive cDNA library, enriched in sequences more abundant in dedifferentiating tissue than in pith. The subtractive library contains approximately seven major species, two of which, NGSUB7 and NGSUB8, are highly abundant. In Northern blots, these two hybridized to mRNA species whose abundance increased significantly but transiently during the first 4 to 8 h of culture. The sequence of NGSUB7 showed no significant homology at a nucleotide or derived amino acid level with any previously reported sequence. NGSUB8 however, showed significant homology over part of the derived amino acid sequence to several yeast and bacterial proteins with DNA binding function. We propose that the two recombinants represent transcripts from two novel genes edeA and edeB, which are expressed early in dedifferentiation.

Non-random alkylation of DNA sequences induced in vivo by chemical mutagens

Previous studies of the interaction of alkylating agents on the eukaryotic genome support the idea that induction of DNA adducts is at specific genomic sites. Here we show molecular and cytological evidence that alkylation is rather specific. Mammalian cell cultures were exposed to different doses of mutagens and the DNA was analyzed by density gradient ultracentrifugation, hydroxylapatite fractionation, and by restriction enzyme analysis. Studies with the labelled mutagens N-ethyl-N-nitrosourea and N-methyl-N'-nitro-N-nitrosoguanidine show that there is a non-random distribution of the adducts. The adducts are found more frequently in A-T, G-C rich satellite DNA and highly repetitive sequences. Analysis with restriction enzymes shows that both methyl and ethyl groups influence the restriction patterns of the enzymes HpaII and MspI that recognize specific endogenous DNA methylation. These data suggest, as a subsequent mechanism, a modification in the pattern of the normal endogenous methylation of 5-methylcytosine.

5-azacytidine-induced tumorous transformation and DNA hypomethylation in Nicotiana tissue cultures

The phenomenon of habituation is considered in plant tissue cultures to be a real process of chemical tumorogenesis; the cultures acquire the capacity of autonomous growth in a hormone-free medium under the influence of a variety of chemical and physical agents. Treatments with 5-azacytidine (AzaC) of in vitro cultured cells of the Nicotiana glauca x N. langsdorffii nontumorous hybrid (NNT) during the culture cycle led to the induction of a habituated phenotype. The repetitive DNA sequences showed a significant lower level of endogenous methylation in the treated cells in comparison with the normal ones. It is worth noting that it was impossible until now to habituate this strain by conventional methods and that the treatments were effective only in the first 5 days of subculturing; various evidence (cytological and biochemical) pointed out a phenomenon of DNA amplification, occurring in the same period. Moreover, analysis of DNA from control and treated cells shows the induction of variations in the endogenous methylation pattern by AzaC in a critical period of cell culture. These results suggest that demethylation can act as a switch from hormone-dependent to autonomous proliferation by activation of genes coding for or regulating the synthesis of growth factors.