MOLECULAR CHARACTERIZATION OF PgiC IN A TETRAPLOID PLANT AND ITS DIPLOID RELATIVES

Functional Divergence between Subgenomes and Gene Pairs after Whole Genome Duplications

Gene loss following whole genome duplication (WGD) is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the originally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.

The legacy of diploid progenitors in allopolyploid gene expression patterns

Allopolyploidization (hybridization and whole-genome duplication) is a common phenomenon in plant evolution with immediate saltational effects on genome structure and gene expression. New technologies have allowed rapid progress over the past decade in our understanding of the consequences of allopolyploidy. A major question, raised by early pioneer of this field Leslie Gottlieb, concerned the extent to which gene expression differences among duplicate genes present in an allopolyploid are a legacy of expression differences that were already present in the progenitor diploid species. Addressing this question necessitates phylogenetically well-understood natural study systems, appropriate technology, availability of genomic resources and a suitable analytical framework, including a sufficiently detailed and generally accepted terminology. Here, we review these requirements and illustrate their application to a natural study system that Gottlieb worked on and recommended for this purpose: recent allopolyploids of Tragopogon (Asteraceae). We reanalyse recent data from this system within the conceptual framework of parental legacies on duplicate gene expression in allopolyploids. On a broader level, we highlight the intellectual connection between Gottlieb's phrasing of this issue and the more contemporary framework of cis- versus trans-regulation of duplicate gene expression in allopolyploid plants.

Ecological studies of polyploidy in the 100 years following its discovery

Polyploidy is a mutation with profound phenotypic consequences and thus hypothesized to have transformative effects in plant ecology. This is most often considered in the context of geographical and environmental distributions-as achieved from divergence of physiological and life-history traits-but may also include species interactions and biological invasion. This paper presents a historical overview of hypotheses and empirical data regarding the ecology of polyploids. Early researchers of polyploidy (1910 s-1930 s) were geneticists by training but nonetheless savvy to its phenotypic effects, and speculated on the importance of genome duplication to adaptation and crop improvement. Cytogenetic studies in the 1930 s-1950 s indicated that polyploids are larger (sturdier foliage, thicker stems and taller stature) than diploids while cytogeographic surveys suggested that polyploids and diploids have allopatric or parapatric distributions. Although autopolyploidy was initially regarded as common, influential writings by North American botanists in the 1940 s and 1950 s argued for the principle role of allopolyploidy; according to this view, genome duplication was significant for providing a broader canvas for hybridization rather than for its phenotypic effects per se. The emphasis on allopolyploidy had a chilling effect on nascent ecological work, in part due to taxonomic challenges posed by interspecific hybridization. Nonetheless, biosystematic efforts over the next few decades (1950s-1970s) laid the foundation for ecological research by documenting cytotype distributions and identifying phenotypic correlates of polyploidy. Rigorous investigation of polyploid ecology was achieved in the 1980s and 1990 s by population biologists who leveraged flow cytometry for comparative work in autopolyploid complexes. These efforts revealed multi-faceted ecological and phenotypic differences, some of which may be direct consequences of genome duplication. Several classical hypotheses about the ecology of polyploids remain untested, however, and allopolyploidy--regarded by most botanists as the primary mode of genome duplication--is largely unstudied in an ecological context.

Electrophoretic evidence for disomic inheritance and allopolyploid origin of the octoploid Cerastium alpinum (Caryophyllaceae)

The mode of inheritance of six enzyme markers in the octoploid alpine plant Cerastium alpinum was analyzed. Offspring from crosses between heterozygotes showed fixed heterozygosity at malate dehydrogenase-2, phosphoglucoisomerase-2, triosephosphate isomerase-2, and triosephosphate isomerase-3. Phosphoglucomutase-1 also showed fixed heterozygosity except in offspring from one cross. Fixed heterozygosity in five enzyme systems suggests that C. alpinum has originated through at least some allopolyploidization. Offspring from plants heterozygous for two alleles at the menadione reductase-1 (Mr-1) locus did not deviate significantly from a 1:2:1 ratio. The large proportion of homozygotes suggests disomic inheritance because any kind of polysomic inheritance would result in a substantially increased proportion of heterozygotes relative to disomic inheritance. Assuming a diploid model for Mr-1, this locus was used to analyze the population genetic structure within C. alpinum populations. Inbreeding was found in many alpine populations. This may help explain the large genetic distances found among alpine populations in a previous study. The analysis is only based on one segregating locus, and the results should therefore be treated with caution. However, by establishing the mode of inheritance through crosses, we have been able to use a codominant marker in population genetic analysis of an octoploid plant.

Reassessment of phylogenetic relationships in Clarkia sect. Sympherica

Clarkia (Onagraceae) is a genus of 42 annual species, mostly native to California, that has served as a model for many studies of plant evolutionary biology, particularly morphological, cytological, and genetic divergence; reproductive isolation; and speciation. Section Sympherica is the largest section with eight diploid and one allotetraploid species. Species in the section have provided important evidence about the evolution of reproductive isolation (C. lingulata derived from C. biloba) and large morphological change (C. dudleyana thought to be sister to the morphologically distinct C. heterandra, recently transferred into Clarkia from the monotypic Heterogaura). Clarkia epilobioides, another diploid species in the section, was previously shown to be one parent of the allotetraploid C. delicata, the other parent being C. unguiculata from sect. Phaeostoma. Lewis and Lewis (1955) interpreted the parentage of C. delicata and other evidence of intersectional hybridization to mean that the diploid sections of the genus, though highly diverse, were closely related and should be maintained in the single genus Clarkia. Here we assess phylogenetic relationships among the species of sect. Sympherica and related species by analyzing the nucleotide sequences of PgiC1 and PgiC2, a pair of paralogous genes that encode the cytosolic isozyme of phosphoglucose isomerase (EC 5.3.1.9). The major results were the following: (1) C. unguiculata and both genomes of C. delicata are within a well-defined "Sympherica" clade; thus, C. delicata should not be considered an intersectional hybrid; (2) C. heterandra belongs in the clade and is closely related to C. unguiculata; and (3) on the evidence of PgiC1, C. dudleyana is not in the clade and is not closely related to C. heterandra.

The 5' leader of plant PgiC has an intron: the leader shows both the loss and maintenance of constraints compared with introns and exons in the coding region

PgiC, a complex gene with 23 coding exons and 22 intervening introns, encodes the cytosolic isozyme of phosphoglucose isomerase (EC 5.3.1.9) in higher plants. Here, we report RNA ligase-mediated rapid amplification of cDNA ends experiments that showed that PgiC in Clarkia (Onagraceae) and Arabidopsis thaliana has an intron in the 5' leader. Comparison of the EMBL accessions of the cDNA and genomic sequences showed that this is also the case in rice (Oryza sativa), suggesting that a leader intron is generally present in higher plant PgiC. The intron is bounded by consensus 5'-GT and AG-3' splice sites but showed alternative splicing in Clarkia, resulting in mature transcripts that differ by 8-19 nt in length. The intron is located 18 or 10 nt upstream of the start codon in Clarkia, 2 nt upstream in Arabidopsis, and 9 nt in rice. PgiC in Clarkia was duplicated before the divergence of the extant species, many of which have two expressed genes PgiC1 and PgiC2. Full-length transcripts of both genes identified the transcription start and made it possible to identify the leader intron and leader exon (between the transcription start and leader intron) from previously obtained genomic sequences of both genes in other Clarkia species. These data permit the comparison of evolution in the leader exon and intron with the exons and introns of the coding region, a topic that has not been studied previously. Both the leader exon and the leader intron resemble introns of the coding region in base substitution rate and accumulation of gaps. But the leader intron splice junctions are not strictly conserved in position as are those of the coding region introns. Also, in base composition, the leader intron resembles the other introns, whereas the leader exon more nearly resembles the coding exons. A difference in base composition between coding exons and flanking introns is known to be important for the recognition of splice sites. Thus, the marked difference in base composition between the leader exon and leader intron is probably maintained by selection despite a high rate of sequence divergence.

Characterization of duplicated two cytosolic phosphoglucose isomerase (PgiC) loci in Arabidopsis halleri ssp. gemmifera

Arabidopsis halleri ssp. gemmifera has two cytosolic phosphoglucose isomerase (PgiC) loci. A 48-bp deletion was observed in the junction of exon 17 and intron 17 for a locus (PgiC2). PCR-RFLP analysis using cDNA template did not detect the PgiC2 locus. Another locus (PgiC1) has common structure with A. thaliana and expressed normally. A phylogenetic tree of PgiC sequences revealed that duplication of the two loci in A. gemmifera occurred after species splitting of A. thaliana and A. gemmifera. More than 12 kb region encompassing PgiC was sequenced for both loci. In both PgiC1 and PgiC2, sequence homologous to A. thaliana PgiC 5' upstream region was not detected. A gene located on chromosome 4 of A. thaliana was detected in the 5' upstream of PgiC2. This result suggested that the microsyntheny around the PgiC region between A. thaliana and A. gemmifera is not established.

Speciation through homoploid hybridization between allotetraploids in peonies (Paeonia)

Phylogenies of Adh1 and Adh2 genes suggest that a widespread Mediterranean peony, Paeonia officinalis, is a homoploid hybrid species between two allotetraploid species, Paeonia peregrina and a member of the Paeonia arietina species group. Three phylogenetically distinct types of Adh sequences have been identified from both accessions of P. officinalis, of which two types are most closely related to the two homoeologous Adh loci of the P. arietina group and the remaining type came from one of the two Adh homoeologs of P. peregrina. The other Adh homoeolog of P. peregrina was apparently lost from the hybrid genome, possibly through backcrossing with the P. arietina group. This is a documentation of homoploid hybrid speciation between allotetraploid species in nature. This study suggests that hybrid speciation between allotetraploids can occur without an intermediate stage of genome diploidization or a further doubling of genome size.