Angiosperm Genes Research Articles

Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts.

Often during flowering plant evolution, ribosomal protein genes have been lost from the mitochondrion and transferred to the nucleus. Here, we show that substitution by a duplicated, divergent gene originally encoding the chloroplast or cytosolic ribosomal protein counterpart accounts for two missing mitochondrial genes in diverse angiosperms. The rps13 gene is missing from the mitochondrial genome of many rosids, and a transferred copy of this gene is not evident in the nucleus of Arabidopsis, soybean, or cotton. Instead, these rosids contain a divergent nuclear copy of an rps13 gene of chloroplast origin. The product of this gene from all three rosids was shown to be imported into isolated mitochondria but not into chloroplasts. The rps8 gene is missing from the mitochondrion and nucleus of all angiosperms examined. A divergent copy of the gene encoding its cytosolic counterpart (rps15A) was identified in the nucleus of four angiosperms and one gymnosperm. The product of this gene from Arabidopsis and tomato was imported successfully into mitochondria. We infer that rps13 was lost from the mitochondrial genome and substituted by a duplicated nuclear gene of chloroplast origin early in rosid evolution, whereas rps8 loss and substitution by a gene of nuclear/cytosolic origin occurred much earlier, in a common ancestor of angiosperms and gymnosperms.

Is clustering of plastid RNA editing sites a consequence of transitory loss of gene function? – Implications for past environmental and evolutionary events in plants

Abstract Editing changes individual nucleotides in RNA thereby distinguishing the mature transcript sequence from the corresponding genomic sequence. Most editing events in chloroplasts change cytosine to uracil bases at specific positions in transcripts. In hornwort and fern species uracil to cytosine conversions also take place. RNA editing in plastids probably emerged among the first land plants and affects different genes of different plants in different positions. A significant clustering of editing sites in certain genes is found within related taxa. The clustering is particularly evident in ndh genes in angiosperms, where editing sites account for about 50% of total (near 30) editing sites of plastids and are rather similar in a large number of species. In gymnosperms, ndh genes are edited to a much lower extent, and the few editing sites identified in bryophytes are different from those of angiosperms. On the basis of these data and the role of ndh genes in the protection against photooxidative stress, we make the following hypothesis for the origin and evolution of editing sites: (i) primary mutations accumulated in genes which became dispensable for plants in certain ecosystems; (ii) under changing environments, the functionality of these genes was recovered in some of the descendants by transcript editing; and (iii) secondary mutations led to a subsequent and gradual disappearance of editing sites. Evidence and further tests for this hypothesis are discussed.

Molecular Diversity and Physical Mapping of 5S rDNA in Wild and Cultivated Oat Grasses (Poaceae: Aveneae)

5S rDNA repeats studied in five genera of Aveneae have lengths between 285 and 329 bp (Avena sativa, Avena macrostachya, 26 species of Helictotrichon, Pseudarrhenatherum longifolium, Lagurus ovatus, and Trisetum spicatum). In only a single species (Helictotrichon aetolicum) an additional repeat of 456 bp occurs infrequently. Variation is largely due to insertions or deletions in the nontranscribed spacer as determined from sequences of 163 independent clones. The 5S gene of the Aveneae studied is conserved in length and sequence except for Helictotrichon bromoides and Helictotrichon marginatum in which duplications occur at two different sites. This new type of duplication and all duplications reported to date in 5S genes of angiosperms are shown to center on defined palindromic sequences. The “uncommon” 5S gene sequences detected in some Aveneae are not necessarily nonfunctional as pseudogenes because the essential features of the internal control region are maintained even after such duplication events. In each instance such gene sequences have spacers with unmodified structure, indicating that change in gene sequence is not necessarily coupled with change in adjacent spacers. The value of 5S spacer sequences for genomic identifications in Aveneae is exemplified in A. macrostachya (perennial), A. sativa (annual), and several diploid taxa of the genus Helictotrichon.

Two APETALA2-like genes of Picea abies are differentially expressed during development.

The EREBP/AP2 gene family codes for plant specific transcription factors. The first two gymnosperm genes of this family were isolated from Picea abies and shown to be structurally related, but not orthologous, to the angiosperm AP2-like genes. The two P. abies genes are differentially expressed in different organs and may be important developmental regulators.

Characterization of the mitochondrial nad7 gene in Physcomitrellapatens: Similarity with angiosperm nad7 genes

The nad7 gene, encoding the subunit 7 of NADH dehydrogenase complex I, is located in the mitochondrial genome in some species of green algae and seed plants, while it is nuclear-encoded in fungi and animals. In a liverwort, the presence of a mitochondrial nad7 pseudogene, and a nuclear nad7 gene has been reported. We have isolated the mitochondrial nad7 gene of the moss Physcomitrella patens. This gene is transcribed as a monocistronic mRNA and contains two group II introns that correspond to the first two of the four introns in the nad7 genes in angiosperms. Results of phylogenetic analysis supported monophyly of the nad7 genes of mosses and tracheophytes. Available data suggest that the nuclear transfer of the nad7 gene occurred only in the liverwort lineage, which diverged extensively from the mosses and tracheophytes with respect to the nad7 gene.

Genomics. Plant biology in 2010.

The completion of the Arabidopsis sequence will be followed by a new ten-year project that will determine the function of all angiosperm genes. Funding for the U.S. component of this multinational project will originate from a new initiative from the U.S. National Science Foundation called the 2010 Project. Progress toward completion of this ambitious project will necessitate significant changes in how the plant biology community selects and approaches research objectives. The plan envisions that the project will facilitate the development of a computational model of a virtual plant that will allow predictive queries about basic mechanisms underlying plant growth and development.

The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms.

A reexamination of the genome of the tomato (renamed Solanum lycopersicum L.) indicates that it contains five, or at most perhaps six, phytochrome genes (PHY), each encoding a different apoprotein (PHY). Five previously identified tomato PHY genes have been designated PHYA, PHYB1, PHYB2, PHYE, and PHYF. A molecular phylogenetic analysis is consistent with the hypothesis that the angiosperm PHY family is composed of four subfamilies (A, B, C/F, and E). Southern analyses indicate that the tomato genome does not contain both a PHYC and a PHYF. Molecular phylogenetic analyses presented here, which utilize for the first time full-length PHY sequences from two completely characterized angiosperm gene families, indicate that tomato PHYF is probably an ortholog of Arabidopsis PHYC. They also confirm that the angiosperm PHY family is undergoing relatively rapid differential evolution. Assuming PHYF is an ortholog of PHYC, PHY genes in eudicots are evolving (Ka/site) at 1.52-2.79 times the rate calculated as average for other plant nuclear genes. Again assuming PHYF is an ortholog of PHYC, the rate of evolution of the C and E subfamilies is at least 1.33 times the rate of the A and B subfamilies. PHYA and PHYB in eudicots are evolving at least 1.45 times as fast as their counterparts in the Poaceae. PHY functional domains also exhibit different evolutionary rates. The C-terminal region of angiosperm PHY (codons 800-1105) is evolving at least 2.11 times as fast as the photosensory domain (codons 200-500). The central region of a domain essential for phytochrome signal transduction (codons 652-712) is also evolving rapidly. Nonsynonymous substitutions occur in this region at 2.03-3.75 times the average rate for plant nuclear genes. It is not known if this rapid evolution results from selective pressure or from the absence of evolutionary constraint.

Evolution of Reproductive Organs in Land Plants

gene is the positive regulator of the MADS-box genes in flower primordia. The number of MADS-box genes presumably increased by gene duplications before the divergence of ferns and seed plants. Most MADS-box genes in ferns are expressed similarly in both vegetative and reproductive organs, while in gymnosperms, some MADS-box genes are specifically expressed in reproductive organs. This suggests that (1) the increase in the number of MADS-box genes and (2) the subsequent recruitment of some MADS-box genes as homeotic selector genes were important for the evolution of complex reproductive organs. The phylogenetic tree including both angiosperm and gymnosperm MADS-box genes indicates the loss of the A-function genes in the gymnosperm lineage, which is presumably related to the absence of perianths in extant gymnosperms. Comparison of expression patterns of orthologous MADS-box genes in angiosperms, Gnetales, and conifers supports the sister relationship of Gnetales and conifers over that of Gnetales and angiosperms predicted by phylogenetic trees based on amino acid and nucleotide sequences.

MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants.

The evolutionary origin of the angiosperms (flowering plants sensu stricto) is still enigmatic. Answers to the question of angiosperm origins are intimately connected to the identification of their sister group among extinct and extant taxa. Most phylogenetic analyses based on morphological data agree that among the groups of extant seed plants, the gnetophytes are the sister group of the angiosperms. According to this view, angiosperms and gnetophytes are the only extant members of a clade called "anthophytes" to emphasize their shared possession of flower-like reproductive structures. However, most phylogeny reconstructions based on molecular data so far did not support an anthophyte clade, but also could not clarify the case because support for alternative groupings has been weak or controversial. We have isolated 13 different homologs of MADS-type floral homeotic genes from the gnetophyte Gnetum gnemon. Five of these genes fall into monophyletic gene clades also comprising putatively orthologous genes from flowering plants and conifers, among them orthologs of floral homeotic B and C function genes. Within these clades the Gnetum genes always form distinct subclades together with the respective conifer genes, to the exclusion of the angiosperm genes. This provides strong molecular evidence for a sister-group relationship between gnetophytes and conifers, which is in contradiction to widely accepted interpretations of morphological data for almost a century. Our phylogeny reconstructions and the outcome of expression studies suggest that complex features such as flower-like reproductive structures and double-fertilization arose independently in gnetophytes and angiosperms.

Molecular control of early cone development inPinus radiata

A family of genes expressed during early stages of shoot development were isolated fromPinus radiata. A homologue of theLEAFY/FLORICAULA flower meristem-identity genes,NEEDLY (NLY), and three MADS-box genes,PrMADS1, PrMADS2 andPrMADS3 (Pinus radiata MADS-box genes), were expressed at early stages of initiation and differentiation of reproductive (male and female) cone buds, as well as vegetative buds. Expression ofNLY in transgenicArabidopsis thaliana promoted floral fate, demonstrating that it encodes a functional ortholog of theFLORICAUL A/LEAFY genes of angiosperms.

MADS-box genes active in developing pollen cones of Norway spruce (Picea abies) are homologous to the B-class floral homeotic genes in angiosperms.

The reproductive organs of conifers, the pollen cones and seed cones, differ in morphology from the angiosperm flower in several fundamental respects. In this report we present evidence to suggest that the two plant groups, in spite of these morphological differences and the long evolutionary distance between them, share important features in regulating the development of the reproductive organs. We present the cloning of three genes, DAL11, DAL12, and DAL13, from Norway spruce, all of which are related to the angiosperm B-class of homeotic genes. The B-class genes determine the identities of petals and stamens. They are members of a family of MADS-box genes, which also includes C-class genes that act to determine the identity of carpels and, in concert with B genes specify stamens in the angiosperm flower. Phylogenetic analyses and the presence of B-class specific C-terminal motifs in the DAL protein sequences imply homology to the B-class genes. Specific expression of all three genes in developing pollen cones suggests that the genes are involved in one aspect of B function, the regulation of development of the pollen-bearing organs. The different temporal and spatial expression patterns of the three DAL genes in the developing pollen cones indicate that the genes have attained at least in part distinct functions. The DAL11, DAL12, and 13 expression patterns in the pollen cone partly overlap with that of the previously identified DAL2 gene, which is structurally and functionally related to the angiosperm C-class genes. This result supports the hypothesis that an interaction between B- and C-type genes is required for male organ development in conifers like in the angiosperms. Taken together, our data suggests that central components in the regulatory mechanisms for reproductive organ development are conserved between conifers and angiosperms and, thus, among all seed plants.

A DEF/GLO-like MADS-box gene from a gymnosperm: Pinus radiata contains an ortholog of angiosperm B class floral homeotic genes.

The specification of floral organ identity during development depends on the function of a limited number of homeotic genes grouped into three classes: A, B, and C. Pairs of paralogous B class genes, such as DEF and GLO in Antirrhinum, and AP3 and PI in Arabidopsis, are required for establishing petal and stamen identity. To gain a better understanding of the evolutionary origin of petals and stamens, we have looked for orthologs of B class genes in conifers. Here we report cDNA cloning of PrDGL (Pinus radiata DEF/GLO-like gene) from radiata pine. We provide phylogenetic evidence that PrDGL is closely related to both DEF- and GLO-like genes of angiosperms, and is thus among the first putative orthologs of floral homeotic B function genes ever reported from a gymnosperm. Expression of PrDGL is restricted to the pollen strobili (male cones) and was not detected in female cones. PrDGL expression was first detected in emergent male cone primordia and persisted through the early stages of pollen cone bud differentiation. Based on the results of our phylogeny reconstructions and expression studies, we suggest that PrDGL could play a role in distinguishing between male (where expression is on) and female reproductive structures (where expression is off) in radiata pine. We speculate that this could be the general function of DEF/GLO-like genes in gymnosperms that may have been recruited for the distinction between stamens and carpels, the male and female reproductive organs of flowering plants, during the evolution of angiosperms out of gymnosperm-like ancestors.

A homeobox gene with potential developmental control function in the meristem of the conifer Picea abies.

Many homeobox genes control essential developmental processes in animals and plants. In this report, we describe the first cDNA corresponding to a homeobox gene isolated from a gymnosperm, the HBK1 gene from the conifer Picea abies (L.) Karst (Norway spruce). The sequence shows distinct similarities specifically to the KNOX (knotted-like homeobox) class of homeobox genes known from different angiosperm plants. The deduced amino acid sequence of HBK1 is strikingly similar within the homeodomain (84% identical) to the maize gene Knotted1 (Kn1), which acts to regulate cell differentiation in the shoot meristem. This similarity suggested that the phylogenetic association of HBK1 with the KNOX genes might be coupled to a conservation of gene function. In support of this suggestion, we have found HBK1 to be expressed in the apical meristem in the central population of nondifferentiated stem cells, but not in organ primordia developing at the flanks of the meristem. This pattern of expression is similar to that of Kn1 in the maize meristem. We show further that HBK1, when expressed ectopically in transgenic Arabidopsis plants, causes aberrations in leaf development that are similar to the effects of ectopic expression of angiosperm KNOX genes on Arabidopsis development. Taken together, these data suggest that HBK1 has a role, similar to the KNOX genes in angiosperms, in the control of cellular differentiation in the apical meristem of spruce. The data also indicate that KNOX-gene regulation of vegetative development is an ancient feature of seed plants that was present in the last common ancestor of conifers and angiosperms.

Loss of Introns in the Pollen-Specific Actin Gene Subfamily Members of Potato and Tomato

Most angiosperm actin genes, including the pollen-specific tobacco actin gene Tac25, contain three introns at conserved locations within their protein coding region. We have isolated one tomato and two potato actin genes that are related to this pollen-specific tobacco actin gene and which have lost one or two introns. The loss of these introns was likely the result of at least two gene conversion events with cDNAs derived from transcripts of pollen-specific genes.

Identification of NADPH:Protochlorophyllide Oxidoreductases A and B: A Branched Pathway for Light-Dependent Chlorophyll Biosynthesis in Arabidopsis thaliana

Illumination releases the arrest in chlorophyll (Chl) biosynthesis in etiolated angiosperm seedlings through the enzymatic photoreduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), the first light-dependent step in chloroplast biogenesis. NADPH: Pchlide oxidoreductase (POR, EC 1.3.1.33), a nuclear-encoded plastid-localized enzyme, mediates this unique photoreduction. Paradoxically, light also triggers a drastic decrease in the amounts of POR activity and protein before the Chl accumulation rate reaches its maximum during greening. While investigating this seeming contradiction, we identified two distinct Arabidopsis thaliana genes encoding POR, in contrast to previous reports of only one gene in angiosperms. The genes, designated PorA and PorB, by analogy to the principal members of the phytochrome photoreceptor gene family, display dramatically different patterns of light and developmental regulation. PorA mRNA disappears within the first 4 h of greening, whereas PorB mRNA persists even after 16 h of illumination, mirroring the behavior of two distinct POR protein species. Experiments designed to help define the functions of POR A and POR B demonstrate exclusive expression of PorA in young seedlings and of PorB both in seedlings and in adult plants. Accordingly, we propose the existence of a branched light-dependent Chl biosynthesis pathway in which POR A performs a specialized function restricted to the initial stages of greening and POR B maintains Chl levels throughout angiosperm development.

Clone bank and physical map of Lopezia miniata Lag. ex DC. ssp. miniata (Onagraceae) chloroplast DNA

A cpDNA clone bank from Lopezia miniata Lag. ex DC. ssp. miniata (Onagraceae) was constructed using the restriction enzymes HindIII and SacI. This clone bank represents 81.5% (78% of sequence complexity) of the 157.6 kb chloroplast genome. The genome is collinear with the “consensus” angiosperm gene arrangement and contains large single copy (85.8 kb), small single copy (19.6 kb), and inverted repeat (26.1 kb) regions of typical size for chlorophylous angiosperms. Approximately 130.2 kb of unique sequence are present. A restriction site map for Bcll, BglI, HindIII, KpnI, PstI, PvuII, SacI, SalI, SmaI, XbaI, and XhoI is presented.

Characterization and Evolutionary Relationships of Magnolia Legumin‐Encoding cDNAs Representing two Divergent Gene Subfamilies

We have cloned and sequenced three different cDNAs encoding legumins of Magnolia salicifolia. Analysis of the nucleotide and derived amino acid sequences shows that the cDNAs designated A2, A11, and B14 represent two divergent subfamilies with nucleotide similarities of only about 55%. The B14 cDNA codes for a relatively methionine‐rich legumin precursor, and the β‐chain of this protein is shown to be glycosylated; neither feature is common in legumins. In an evolutionary analysis, the B14 legumin cDNA is relatively similar to gymnospermous legumin sequences and paralogous to all angiosperm legumins hitherto known. The A legumin sequence clusters with those of monocot legumins in a low angiosperm branch. We conclude that the evolution of legumin genes in angiosperms involved an early gene duplication which resulted in the progenitor of the B14 legumin, on the one hand, and the progenitor of A2, A11 and modem angiosperm legumins, on the other hand.

Characterization and evolutionary relationships of Magnolia legumin-encoding cDNAs representing two divergent gene subfamilies.

We have cloned and sequenced three different cDNAs encoding legumins of Magnolia salicifolia. Analysis of the nucleotide and derived amino acid sequences shows that the cDNAs designated A2, A11, and B14 represent two divergent subfamilies with nucleotide similarities of only about 55%. The B14 cDNA codes for a relatively methionine-rich legumin precursor, and the beta-chain of this protein is shown to be glycosylated; neither feature is common in legumin. In an evolutionary analysis, the B14 legumin cDNA is relatively similar to gymnospermous legumin sequences and paralogous to all angiosperm legumins hitherto known. The A legumin sequence clusters with those of monocot legumins in a low angiosperm branch. We conclude that the evolution of legumin genes in angiosperms involved an early gene duplication which resulted in the progenitor of the B14 legumin, on the one hand, and the progenitor of A2, A11 and modern angiosperm legumins, on the other hand.

Analysis of gene regulation in growing pollen tubes of angiosperm and gymnosperm species using microprojectile bombardment

A microprojectile based transient expression assay was used to investigate the functional conservation of gene regulatory mechanisms in the male gametophytes of an angiosperm (Nicotiana tabacum) and two gymnospermous (Picea abies and Pinus pinaster) species. The activities of two angiosperm gene promoters, which have previously shown to be either preferentially expressed in the male gametophyte (lat52) or highly expressed in both the sporophyte and male gametophyte (ActI), were analysed. The results showed that in P. abies and P. pinaster, activity of the Act1 promoter was significantly higher than the activity of the lat52 promoter, while the converse was observed in N. tabacum. Detailed analysis of lat52 5’promoter deletions demonstrated that although the minimal ‐67 bp lat52 core promoter was active at low levels in all three species, upstream regulatory elements conserved among several pollen‐expressed genes, including the PBI element, were not functional in P. abies and P. pinaster. These results suggest that both taxa‐specific and conserved regulatory mechanisms operate to control gene expression during pollen germination and tube growth.

Analysis of gene regulation in growing pollen tubes of angiosperm and gymnosperm species using microprojectile bombardment

A microprojectile based transient expression assay was used to investigate the functional conservation of gene regulatory mechanisms in the male gametophytes of an angiosperm (Nicotiana tabacum) and two gymnospermous (Picea abies and Pinus pinaster) species. The activities of two angiosperm gene promoters, which have previously shown to be either preferentially expressed in the male gametophyte (lat52) or highly expressed in both the sporophyte and male gametophyte (Act1), were analysed. The results showed that in P. abies and P. pinaster, activity of the Act1 promoter was significantly higher than the activity of the lat52 promoter, while the converse was observed in N. tabacum. Detailed analysis of lat52 5' promoter deletions demonstrated that although the minimal −67 bp lat52 core promoter was active at low levels in all three species, upstream regulatory elements conserved among several pollen-expressed genes, including the PBI element, were not functional in P. abies and P. pinaster. These results suggest that both taxa-specific and conserved regulatory mechanisms operate to control gene expression during pollen germination and tube growth