Evolution of flower shape in <Emphasis Type="Italic">Plantago lanceolata</Emphasis>

Plantago lanceolata produces small actinomorphic (radially symmetric), wind-pollinated flowers that have evolved from a zygomorphic, biotically pollinated ancestral state. To understand the developmental mechanisms that might underlie this change in flower shape, and associated change in pollination syndrome, we analyzed the role of CYC-like genes in P. lanceolata. Related zygomorphic species have two CYC-like genes that are expressed asymmetrically in the dorsal region of young floral meristems and in developing flowers, where they affect the rate of development of dorsal petals and stamens. Plantago has a single CYC-like gene (PlCYC) that is not expressed in early floral meristems and there is no apparent asymmetry in the pattern of PlCYC expression during later flower development. Thus, the evolution of actinomorphy in Plantago correlates with loss of dorsal-specific CYC-like gene function. PlCYC is expressed in the inflorescence stem, in pedicels, and relatively late in stamen development, suggesting a novel role for PlCYC in compacting the inflorescence and retarding stamen elongation in this wind pollinated species.     

CYCLOIDEA 2 Clade Genes: Key Players in the Control of Floral Symmetry,Inflorescence Architecture,and Reproductive Organ Development

Undoubted lines of evidence point out that members of CYCLOIDEA (CYC) 2 clade are essential players to control flower symmetry and, amusingly, also are determinants of capitula architecture (pseudanthium). In several species, CYC-like genes influence the androecium patterning, but to date, the function of these genes in the development of gynoecium organs is less clear. In this review, we first reported details about floral symmetry and an overview of genes and molecular mechanisms regulating the development of zygomorphism in different angiosperm lineages (e.g., basal and core eudicots and monocots). Then, we paid emphasis on the role of CYC-like genes in the development of heterogamous inflorescence of sunflower as well as other Asteraceae and some species within the Dipsacaceae family. Helianthus annuus is particularly attractive because it represents a useful model to study the role of CYC-like genes on shaping floral corolla as well as the differentiation of reproductive organs in different flowers of pseudanthia. A special attention was reserved to inflorescence morphology mutants of sunflower (i.e., Chrysanthemoids2 and tubular ray flower) because they provide useful information on the role of CYC-like genes in the radiate capitulum evolution. Finally, we discuss data from literature to suggest that CYC-like genes are also co-opted to regulate stamen and carpel differentiation likely throughout their interaction with the cell cycle and flower organ identity genes. The recruitment of reproductive organs in ray flowers also supports the phylogenetic origin of a radiate inflorescence of sunflower from a discoid capitulum and suggests that in sterile zygomorphic ray flower primordia the latent identity to differentiate both microsporangium and macrosporangium was conserved.     

Why are orchid flowers so diverse? Reduction of evolutionary constraints by paralogues of class B floral homeotic genes

Background

The nearly 30 000 species of orchids produce flowers of unprecedented diversity. However, whether specific genetic mechanisms contributed to this diversity is a neglected topic and remains speculative. We recently published a theory, the ‘orchid code’, maintaining that the identity of the different perianth organs is specified by the combinatorial interaction of four DEF-like MADS-box genes with other floral homeotic genes.

Scope

Here the developmental and evolutionary implications of our theory are explored. Specifically, it is shown that all frequent floral terata, including all peloric types, can be explained by monogenic gain- or-loss-of-function mutants, changing either expression of a DEF-like or CYC-like gene. Supposed dominance or recessiveness of mutant alleles is correlated with the frequency of terata in both cultivation and nature. Our findings suggest that changes in DEF- and CYC-like genes not only underlie terata but also the natural diversity of orchid species. We argue, however, that true changes in organ identity are rare events in the evolution of orchid flowers, even though we review some likely cases.

Conclusions

The four DEF paralogues shaped floral diversity in orchids in a dramatic way by modularizing the floral perianth based on a complex series of sub- and neo-functionalization events. These genes may have eliminated constraints, so that different kinds of perianth organs could then evolve individually and thus often in dramatically different ways in response to selection by pollinators or by genetic drift. We therefore argue that floral diversity in orchids may be the result of an unprecedented developmental genetic predisposition that originated early in orchid evolution.Key words: Orchidaceae, orchid evolution, evo-devo; perianth, class B genes, DEFICIENS, subfunctionalization, neofunctionalization, gene duplication, peloria, modularization     

Significance of consensus CYC‐binding sites found in the promoters of both ChCYC and ChRAD genes in Chirita heterotricha (Gesneriaceae)

Abstract CYC‐like genes are widely conserved in controlling floral dorsoventral asymmetry (zygomorphy) through persistent expression in corresponding domains in core eudicots. To understand how CYC‐like gene expression is maintained during flower development, we selected Chirita heterotricha as a material and isolated the promoter sequences of the ChCYC1C and ChCYC1D genes, homologs of CYC, by inverse polymerase chain reaction. Further promoter analyses led to the identification of a putative cis‐regulatory element in each promoter matching the consensus DNA binding site for Antirrhinum CYC protein: GGCCCCTC at ?165 for ChCYC1C, and GGCCCCCC at ?163 for ChCYC1D. This indicates that both the ChCYC1C and ChCYC1D genes have probably evolved autoregulatory loops to sustain their expression in developing flowers. We also isolated the coding and promoter sequences of the ChRAD gene, a homolog of Antirrhinum RAD. Promoter analysis showed that the ChRAD gene promoter also contained a putative CYC‐binding site (GGCCCAC at ?134). Therefore, ChRAD is likely a direct target of the ChCYC1 genes, which is similar to Antirrhinum RAD. These results imply that the establishment of floral zygomorphy in Chirita may have been achieved by the evolution of an autoregulatory loop for CYC‐like genes, which was probably accompanied by simultaneous co‐option of the RAD‐like gene into their regulatory network.     

Geographic distribution,evolution, and disease importance of species within the Neotropical Anopheles albitarsis Group (Diptera,Culicidae)

The Anopheles albitarsis group of mosquitoes comprises eight recognized species and one mitochondrial lineage. Our knowledge of malaria vectorial importance and the distribution and evolution of these taxa is incomplete. We constructed ecological niche models (ENMs) for these taxa and used hypothesized phylogenetic relationships and ENMs to investigate environmental and ecological divergence associated with speciation events. Two major clades were identified, one north (Clade 1) and one south (Clade 2) of the Amazon River that likely is or was a barrier to mosquito movement. Clade 1 species occur more often in higher average temperature locations than Clade 2 species, and taxon splits within Clade 1 corresponded with a greater divergence of variables related to precipitation than was the case within Clade 2. Comparison of the ecological profiles of sympatric species and sister species support the idea that phylogenetic proximity is related to ecological similarity. Anopheles albitarsis I, An. janconnae, and An. marajoara ENMs had the highest percentage of their predicted suitable habitat overlapping distribution models of Plasmodium falciparum and P. vivax, and warrant additional studies of the transmission potential of these species. Phylogenetic proximity may be related to malaria vectorial importance within the Albitarsis Group.     

Early evolution of the MFT-like gene family in plants

Angiosperm genes sharing a conserved phosphatidylethanolamine-binding (PEPB) domain have been shown to be involved in the control of shoot meristem identity and flowering time. The family is divided into three subfamilies, FT-like, TFL1-like and MFT-like. This study is focused on the evolution of the MFT-like clade, suggested to be ancestral to the two other clades. We report that the bryophyte Physcomitrella patens and the lycopod Selaginella moellendorfii contain four and two MFT-like genes respectively. Neither species have any FT or TFL1-like genes. Furthermore, we have identified a new subclade of MFT-like genes in Angiosperms. Quantitative expression analysis of MFT-like genes in Physcomitrella patens reveals that the expression patterns are circadian and reaches maximum in gametangia and sporophytes. Our data suggest that the occurrence FT and TFL1-like genes, is associated with the evolution of seed plants. Expression data for Physcomitrella MFT-like genes implicates an involvement in the development of reproductive tissues in the moss.     

Survey of resistance gene analogs in <Emphasis Type="Italic">Solanum caripense</Emphasis>, a relative of potato and tomato,and update on <Emphasis Type="Italic">R</Emphasis> gene genealogy

The resistance (R) proteins of the TIR- and non-TIR (or CC-) superfamilies possess a nucleotide binding site (NBS) domain. Within an R gene, the NBS is the region of highest conservation, suggesting an essential role in triggering R protein activity. We compared the NBS domain of functional R genes and resistance gene analogs (RGA) amplified from S. caripense genomic DNA via PCR using specific and degenerate primers with its counterpart from other plants. An overall high degree of sequence conservation was apparent throughout the P-loop, kinase-2 and kinase-3a motifs of NBS fragments from all plants. Within the non-TIR class of R genes a prominent sub-class similar to the potato R1 gene conferring resistance to late blight, was detected. All non-TIR-R1-like R gene fragments that were sequenced possessed an intact open reading frame, whereas 22% of all non-TIR-non-R1-like fragments and 59% of all TIR-NBS RGA fragments had an interrupted reading frame or contained transposon-specific sequence. The non-TIR-R1-like fragments had high similarity to Solanaceae R genes and low similarity to RGAs of other plant species including A. thaliana and the cereals. It is concluded that appearance of the non-TIR-R1-like NBS domain represents a relatively recent evolutionary development. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

AZFY-like sequence in fish,with comments on the evolution of theZFY family of genes in vertebrates

ZFY-like genes have been observed in a variety of vertebrate species. Although originally implicated as the primary testis-determining gene in humans and other placental mammals, more recent evidence indicates a role(s) outside that of testis determination. In this study, DNA from five species of fish,Carasius auratus, Rivulus marmoratus, Xiphophorus maculatus, X. milleri, andX. nigrensis was subjected to Southern blot analysis using a PCR-amplified fragment of mouseZFY-like sequence as a probe. Restriction fragment patterns were not polymorphic between sexes in any one species but showed a different pattern for each species. With one exception,Rivulus, a 3.1-kb band from theEcoRI digestion was common to all. Sequence and open reading frame analysis of this fragment showed a strong homology to other known vertebrateZFY-like genes. Of particular interest in this gene is a novel third finger domain similar to one human and one alligatorZFY-like gene. Our studies and others provide evidence for a family of vertebrateZFY genes, with those having this novel third finger being representative of the ancestral condition.     

Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae)

The evolutionary pattern of the myc-like anthocyanin regulatory gene antR-Cor was examined in the dwarf dogwood species complex (Cornus Subgenus Arctocrania) that contains two diploid species (C. canadensis and C. suecica), their putative hybrids with intermediate phenotypes, and a tetraploid derivative (C. unalaschkensis). Full-length sequences of this gene (∼4 kb) were sequenced and characterized for 47 dwarf dogwood samples representing all taxa categories from 43 sites in the Pacific Northwest. Analysis of nucleotide diversity indicated departures from neutral evolution, due most likely to local population structure. Neighbor-joining and haplotype network analyses show that sequences from the tetraploid and diploid intermediates are much more strongly diverged from C. suecica than from C. canadensis, and that the intermediate phenotypes may represent an ancestral group to C. canadensis rather than interspecific hybrids. Seven amino acid mutations that are potentially linked to myc-like anthocyanin regulatory gene function correlate with petal colors differences that characterize the divergence between two diploid species and the tetraploid species in this complex. The evidence provides a working hypothesis for testing the role of the gene in speciation and its link to the petal coloration. Sequencing and analysis of additional nuclear genes will be necessary to resolve questions about the evolution of the dwarf dogwood complex.     

Resurrection of an ancestral gene: functional and evolutionary analyses of the Ng<Emphasis Type="Italic">rol</Emphasis> genes transferred from<Emphasis Type="Italic"> Agrobacterium</Emphasis> to<Emphasis Type="Italic"> Nicotiana</Emphasis>

The Ngrol genes, which have high similarity in sequence to the rol genes of Agrobacterium rhizogenes, are present in the genome of untransformed plants of Nicotiana glauca. It is thought that bacterial infection resulted in the transfer of the Ngrol genes to plants early in the evolution of the genus Nicotiana, since several species in this genus contain rol-like sequences but others do not. Plants transformed with the bacterial rol genes exhibit various developmental and morphological changes. The presence of rol-like sequences in plant genomes is therefore thought to have contributed to the evolution of Nicotiana species. This paper focuses on studies of the Ngrol genes in present-day plants and during the evolution of the genus Nicotiana. The functional sequences of several Ngrol genes may have been conserved after their ancient introduction from a bacterium to the plant. Resurrection of an ancestral function of one of the Ngrol genes, as examined by physiological and evolutionary analyses, is also described. The origin of the Ngrol genes is then considered, based on results of molecular phylogenetic analyses. The effects of the horizontal transfer of the Ngrol genes and mutations in the genes are discussed on the plants of the genus Nicotiana during evolution.Seishiro Aoki is the recipient of the Botanical Society Award for Young Scientist, 2002.     

Characterization of candidate class A,B and E floral homeotic genes from the perianthless basal angiosperm <Emphasis Type="Italic">Chloranthus spicatus</Emphasis> (Chloranthaceae)

The classic ABC model explains the activities of each class of floral homeotic genes in specifying the identity of floral organs. Thus, changes in these genes may underlay the origin of floral diversity during evolution. In this study, three MADS-box genes were isolated from the perianthless basal angiosperm Chloranthus spicatus. Sequence and phylogenetic analyses revealed that they are AP1-like, AP3-like and SEP3-like genes, and hence these genes were termed CsAP1, CsAP3 and CsSEP3, respectively. Due to these assignments, they represent candidate class A, class B and class E genes, respectively. Expression patterns suggest that the CsAP1, CsAP3 and CsSEP3 genes function during flower development of C. spicatus. CsAP1 is expressed broadly in the flower, which may reflect the ancestral function of SQUA-like genes in the specification of inflorescence and floral meristems rather than in patterning of the flower. CsAP3 is exclusively expressed in male floral organs, providing the evidence that AP3-like genes have ancestral function in differentiation between male and female reproductive organs. CsSEP3 expression is not detectable in spike meristems, but its mRNA accumulates throughout the flower, supporting the view that SEP-like genes have conserved expression pattern and function throughout angiosperm. Studies of synonymous vs nonsynonymous nucleotide substitutions indicate that these genes have not evolved under changes in evolutionary forces. All the data above suggest that the genes may have maintained at least some ancestral functions despite the lack of perianth in the flowers of C. spicatus. Nucleotide sequences data from this article have been deposited with the EMBL/GenBank Data Libraries under accession numbers AY316311, AY397762 and AY379963.     

The rice R gene family: two distinct subfamilies containing several miniature inverted-repeat transposable elements

The R and B genes of maize regulate the anthocyanin biosynthetic pathway and constitute a small gene family whose evolution has been shaped by polyploidization and transposable element activity. To compare the evolution of regulatory genes in the distinct but related genomes of rice and maize, we previously isolated two R homologues from rice (Oryza sativa). The Ra1 gene on chromosome 4 can activate the anthocyanin pathway, whereas the Rb gene, of undetermined function, maps to chromosome 1. In this study, rice R genes have been further characterized. First, we found that an Rb cDNA can induce pigmentation in maize suspension cells. Second, another rice R homologue (Ra2) was identified that is more closely related to Ra1 than to Rb. Domesticated rice and its wild relatives harbor multiple Ra-like and Rb-like genes despite the fact that rice is a true diploid with the smallest genome of all the grass species analyzed to date. Finally, several miniature inverted-repeat transposable elements (MITEs) were found in R family members. Their possible role in hastening the divergence of R genes is discussed.     

Molecules and the Body Plan: TheHoxGenes of Cirripedes (Crustacea)

Among arthropods, Cirripedia (barnacles) are remarkable in that they completely lack abdominal segments. This feature prompted us to study theHoxgenes of three cirripede species, representing a wide array of the diversity of these organisms, a segmented sessile barnacle,Elminius modestus(Thoracica), the parasite of a crab,Sacculina carcini(Rhizocephala), and the burrowing barnacleTrypetesa lampas(Acrothoracica). Using PCR amplification of genomic DNA and cDNA and library probing, we have found seven clear cirripedian homologues of the eight homeoticHoxgenes known in insects, includinglabialandproboscipediahomologues, that were not previously reported in crustaceans. In addition we have isolated a divergentAntp-like gene, namedDiva, that we homologize to theftzgene of insects. The homeotic geneabdominalA(abdA) was not retrieved from any of these three cirripede species. By contrast, we have found all eight homeotic homologue genes, includingabdA, inUlophysema oeresundense, a crustacean possessing a well-developed abdomen, belonging to the Ascothoracica, generally thought to be the sister group of Cirripedia. Since we have found in barnacles homeobox-containing genes that are more divergent from theAntennapediatype than the typicalabdA, we believe that abona fide abdAgene would not have escaped our search. Hence, theabdAgene has been lost or is profoundly derived in sequence during the evolution leading to the cirripedian lineage. If confirmed, the lack ofabdAwould represent the first case in which the loss of a homeotic gene is correlated with a change in body plan during the evolution of metazoans.     

Analysis of the sequence variations in the Mhc DRB1-like gene of the endangered Humboldt penguin (Spheniscus humboldti)

The Major Histocompatibility Complex (Mhc) genomic region of many vertebrates is known to contain at least one highly polymorphic class II gene that is homologous in sequence to one or other of the human Mhc DRB1 class II genes. The diversity of the avian Mhc class II gene sequences have been extensively studied in chickens, quails, and some songbirds, but have been largely ignored in the oceanic birds, including the flightless penguins. We have previously reported that several penguin species have a high degree of polymorphism on exon 2 of the Mhc class II DRB1-like gene. In this study, we present for the first time the complete nucleotide sequences of exon 2, intron 2, and exon 3 of the DRB1-like gene of 20 Humboldt penguins, a species that is presently vulnerable to the dangers of extinction. The Humboldt DRB1-like nucleotide and amino acid sequences reveal at least eight unique alleles. Phylogenetic analysis of all the available avian DRB-like sequences showed that, of five penguin species and nine other bird species, the sequences of the Humboldt penguins grouped most closely to the Little penguin and the mallard, respectively. The present analysis confirms that the sequence variations of the Mhc class II gene, DRB1, are useful for discriminating among individuals within the same penguin population as well those within different penguin population groups and species.The nucleotide sequence and amino acid sequence data reported in this paper have been submitted to the DDBJ database and have been assigned the accession numbers AB088371–AB088374, AB089199, AB154393–AB154399, and AB162144.     

Taxonomic characterization of Shiraia-like fungi isolated from bamboos in Japan

The molecular phylogeny of nuclear LSU rDNA sequences (D1/D2 domain), ITS regions, and beta-tubulin gene (tub2) showed that the seven strains of Shiraia-like fungi obtained from fresh bamboo tissues as endophytes were closely related to Shiraia bambusicola and had three distinctive lineages (groups A-C). The closest group (group A) to S. bambusicola produced distinctive prawn-shaped conidioma-like structures that differed from conidiomata in the anamorph of S. bambusicola. Currently, none of the morphological structures and molecular database records were compatible with our Shiraia-like fungi. These results reveal that Shiraia-like fungi group A is supposed to be a new species that should be assigned into a novel genus/species related to S. bambusicola.     

TheAdh genomic region ofDrosophila ambigua: Evolutionary trends in different species

Summary The study of individual genes is essential to a comprehensive understanding of genome evolution. The wealth of information on alcohol dehydrogenase (Adh) inDrosophila makes this gene particularly suitable for such analysis. We have characterized more than 4 kb of the genomicAdh region inDrosophila ambigua and compared this region toDrosophila mauritiana andDrosophila pseudoobscura. The presence of two genes,Adh and 3ORF (open reading frame), has been confirmed and some of their essential features have been inferred from primary structural analysis. Inter- and intraspecific comparisons have led us to support that both genes may have diverged from an ancient precursor. They appear to be evolving independently, and show a species-specific pattern. TheAdh in theobscura group species lacks amino acids three and four when compared to the species of themelanogaster group and has accumulated most of its amino acid replacements in the third exon. Neither characteristic is observed when any other group species are compared, which suggests that these may be particular features of the evolution of theobscura group. The 3ORF is highly conserved among the three species analyzed, although variability in the length of the third exon and the nucleotide substitution rate, which is much higher than inAdh, are worth noting. According to our data, both mutation/fixation rates and the distribution of mutations vary over time, which makes it difficult to predict the evolutionary dynamics of specific genome regions.