PubMed Health⌕ Search

Biomedical subjects

T Sang

Publications and source records attributed to T Sang.

13 recordsLinked to original sources
PubMed2001

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.

Biological Evolution↗
PubMed2001

Phylogenetic utility of the glycerol-3-phosphate acyltransferase gene: evolution and implications in Paeonia (Paeoniaceae).

The nuclear-encoded chloroplast-expressed glycerol-3-phosphate acyltransferase (GPAT) gene has been found to be single-copy in a number of angiosperm families. In this study we investigated the phylogenetic utility of the GPAT gene at the interspecific level using the genus Paeonia (Paeoniaceae) as an example. An approximately 2.3- to 2.6-kb fragment of the GPAT gene, containing a large intron of more than 2 kb, was amplified, cloned, and sequenced from 19 accessions representing 13 Paeonia species. The GPAT gene phylogeny inferred by parsimony analysis supported interspecific relationships that were previously unresolved, suggesting that large introns of low-copy nuclear genes are particularly informative in the resolution of close relationships at low taxonomic levels. Whereas the GPAT phylogeny is largely congruent with the previous phylogenetic hypothesis of Paeonia, it shows a significant discordance involving the paraphyly of section Paeonia. Given evidence of an ancient duplication and the subsequent silencing of one GPAT locus in P. anomala, this discordance is most likely the result of paralogy. Two distinct genomic clones containing partial GPAT genes were isolated from P. anomala. The GPAT sequence from one clone corresponded to the functional copy of the gene, and the second genomic clone was determined to contain a GPAT pseudogene. The insertion of a retrotransposon in an intron of this pseudogene may have been responsible for the silencing of this GPAT locus in P. anomala. This study suggests that, although it is unlikely that universal nuclear gene markers free from paralogy are usually available, low-copy nuclear genes can be very useful in plant phylogenetic reconstruction, especially at low taxonomic levels, as long as the evolutionary dynamics of the genes are carefully examined.

DNA, Plant↗
PubMed2001

Rapid and reliable identification of rice genomes by RFLP analysis of PCR-amplified Adh genes.

The rice genus (Oryza L.) consists of 24 species with 10 recognized genome types. With the realization of many useful genes in species of wild rice, continuous efforts have been made to understand their genomic composition and relationships. However, the identification of rice genomes has often been difficult owing to complex morphological variation and formation of allotetraploids. Here we propose a rapid and reliable method for identifying rice genomes based on the restriction sites of PCR-amplified Adh genes. The experimental procedure was as follows: (i) amplify a portion of Adh1 and Adh2 genes with the locus-specific PCR primers; (ii) digest PCR products with restriction enzymes that distinguish different genomes; and (iii) run the digested products on 1.4% agarose gel, and photograph. Using various combinations of restriction digestion of the two Adh genes, all of the rice genomes can be identified.

Genome, Plant↗
PubMed2000

Testing hybridization hypotheses based on incongruent gene trees.

Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence between gene trees. The incongruence, in turn, offers an opportunity to detect hybrid speciation. Here we characterized certain distinctions between hybridization and other biological processes, including lineage sorting, paralogy, and lateral gene transfer, that are responsible for topological incongruence between gene trees. Consider two incongruent gene trees with three taxa, A, B, and C, where B is a sister group of A on gene tree 1 but a sister group of C on gene tree 2. With a theoretical model based on the molecular clock, we demonstrate that time of divergence of each gene between taxa A and C is nearly equal in the case of hybridization (B is a hybrid) or lateral gene transfer, but differs significantly in the case of lineage sorting or paralogy. After developing a bootstrap test to test these alternative hypotheses, we extended the model and test to account for incongruent gene trees with numerous taxa. Computer simulation studies supported the validity of the theoretical model and bootstrap test when each gene evolved at a constant rate. The computer simulation also suggested that the model remained valid as long as the rate heterogeneity was occurring proportionally in the same taxa for both genes. Although the model could not test hypotheses of hybridization versus lateral gene transfer as the cause of incongruence, these two processes may be distinguished by comparing phylogenies of multiple unlinked genes.

Biological Evolution↗
PubMed2000

Phylogeny and divergence times in Pinaceae: evidence from three genomes.

In Pinaceae, the chloroplast, mitochondrial, and nuclear genomes are paternally, maternally, and biparentally inherited, respectively. Examining congruence and incongruence of gene phylogenies among the three genomes should provide insights into phylogenetic relationships within the family. Here we studied intergeneric relationships of Pinaceae using sequences of the chloroplast matK gene, the mitochondrial nad5 gene, and the low-copy nuclear gene 4CL. The 4CL gene may exist as a single copy in some species of Pinaceae, but it constitutes a small gene family with two or three members in others. Duplication and deletion of the 4CL gene occurred at a tempo such that paralogous loci are maintained within but not between genera. Exons of the 4CL gene have diverged approximately twice as fast as the matK gene and five times more rapidly than the nad5 gene. The partition-homogeneity test indicates that the three data sets are homogeneous. A combined analysis of the three gene sequences generated a well-resolved and strongly supported phylogeny. The combined phylogeny, which is topologically congruent with the three individual gene trees based on the Templeton test, is likely to represent the organismal phylogeny of Pinaceae. This phylogeny agrees to a certain extent with previous phylogenetic hypotheses based on morphological, anatomical, and immunological data. Disagreement between the previous hypotheses and the three-genome phylogeny suggests that morphology of both vegetative and reproductive organs has undergone convergent evolution within the pine family. The strongly supported monophyly of Nothotsuga longibracteata, Tsuga mertensiana, and Tsuga canadensis on all three gene phylogenies provides evidence against previous hypotheses of intergeneric hybrid origins of N. longibracteata and T. mertensiana. Divergence times of the genera were estimated based on sequence divergence of the matK gene, and they correspond well with the fossil record.

Cell Nucleus↗
PubMed2000

[Determination of protocatechuic acid in Blumea riparia (Bl.) DC. by RP-HPLC].

OBJECTIVE: To determine the content of protocatechuic acid in Blumea riparia by RP-HPLC. METHOD: mu-Bondapak C18 column was used, mobile phase consisted of methanol-water-glacial acetic acid(19:80:1) and detection was performed at UV 260 nm. RESULT: The standard curve was linear in the range of 3.31-41.8 micrograms.ml-1. The correlation coefficient was 0.9999. The average recovery rate and RSD were 98.05% and 1.94% (n = 6) respectively. CONCLUSION: The method provides scientific indexes for quality control of riparia.

Asteraceae↗
PubMed1999

Phylogeny of rice genomes with emphasis on origins of allotetraploid species.

The rice genus, Oryza, which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germ plasm. By generating and comparing two nuclear gene (Adh1 and Adh2) trees and a chloroplast gene (matK) tree of all rice species, phylogenetic relationships among the rice genomes were inferred. Origins of the allotetraploid species, which constitute more than one-third of rice species diversity, were reconstructed based on the Adh gene phylogenies. Genome types of the maternal parents of allotetraploid species were determined based on the matK gene tree. The phylogenetic reconstruction largely supports the previous recognition of rice genomes. It further revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome. Three species of the CCDD genome may have originated through a single hybridization event, and their maternal parent had the CC genome. The BBCC genome species had different origins, and their maternal parents had either a BB or CC genome. An additional genome type, HHKK, was recognized for Oryza schlechteri and Porteresia coarctata, suggesting that P. coarctata is an Oryza species. The AA genome lineage, which contains cultivated rice, is a recently diverged and rapidly radiated lineage within the rice genus.

Alcohol Dehydrogenase↗
PubMed1999

Physical mapping of ribosomal RNA genes in peonies (Paeonia, Paeoniaceae) by fluorescent in situ hybridization: implications for phylogeny and concerted evolution.

Physical maps of the 18S-5.8S-26S ribosomal RNA genes (rDNA) were generated by fluorescent in situ hybridization for five diploid Paeonia species, P. delavayi and P. rockii of section Moutan, and P. emodi, P. tenuifolia, and P. veitchii of section Paeonia. Of five pairs of mitotic chromosomes, rDNA loci were mapped near the telomeres of chromosomes 3, 4, and 5 of P. rockii and P. tenuifolia, chromosomes 2, 3, 4, and 5 of P. delavayi, and all five pairs of chromosomes of P. emodi and P. veitchii. Combining this information with the previously obtained rDNA maps of P. brownii and P. californica of section Oneapia, we hypothesized that the most recent common ancestor of extant peony species had three rDNA loci located on chromosomes 3, 4, and 5. Increase in number of rDNA loci occurred later in each of the three sections, and the increase from three to four loci represents a parallel gain of an rDNA locus on chromosome 2 in P. delavayi of section Moutan and P. brownii of section Oneapia. The increase in number of rDNA loci likely resulted from the translocation of rDNA repeats from chromosomes bearing rDNA loci to chromosomes without them; such translocation is probably facilitated by the telomeric location of rDNA loci. For allotetraploid peony species lacking polymorphism in sequences of the internal transcribed spacers (ITS) of rDNA, the rDNAs derived from divergent diploid parents may have been homogenized through concerted evolution among at least six rDNA loci in the allotetraploids. Chromosomal location of rDNA loci has a more substantial impact on the tempo of concerted evolution than the number of loci.

Journal Article↗
PubMed1998

Chromosomal structural rearrangement of Paeonia brownii and P. californica revealed by fluorescence in situ hybridization.

Chromosomal structural rearrangement in Paeonia brownii and P. californica (2n = 10) was studied by in situ hybridization using 18S rDNA probes. Six major rDNA sites were detected in mitotic cells of P. californica; six major and two minor rDNA sites were found in P. brownii. Two cytotypes (A and B), with different chromosomal morphology and (or) rDNA locations, were observed in the population of P. californica. Cytotype A, with rDNA sites only on the short arms of chromosomes, was considered to be the normal cytotype. Both translocation and pericentric inversion may have occurred to give rise to cytotype B, in which one homolog of chromosome 4 has rDNA sites on both arms while its homolog has no rDNA sites: one homolog of chromosome 3 has a rDNA site on the long arm. Two rearranged cytotypes, C and D, were observed in the population of P. brownii. Given that the normal cytotype of P. brownii is most likely to have six major rDNA sites on the short arms of chromosomes 3, 4, and 5, and two minor sites on the short arms of chromosome 2, cytotype C may have resulted from a translocation between the short arm of one homolog of chromosome 2 and the long arm of one homolog of chromosome 4, and cytotype D may have resulted from a translocation between the short arm of one homolog of chromosome 3 and the long arm of one homolog of chromosome 4. These results supported previous observations, based on meiotic configurations, that chromosomal structural rearrangement occurred frequently in P. brownii and P. californica.

Chromosome Mapping↗
PubMed1997

Evolution of alcohol dehydrogenase genes in peonies (Paeonia): phylogenetic relationships of putative nonhybrid species.

Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequenced from 11 putative nonhybrid species of the angiosperm genus Paeonia. Sequences of five exons and six intron regions of the Adh gene were used to reconstruct the phylogeny of these species. Two paralogous genes, Adh1A, and Adh2, were found; an additional gene, Adh1B, is also present in section Moutan. Phylogenetic analyses of exon sequences of the Adh genes of Paeonia and a variety of other angiosperms imply that duplication of Adh1 and Adh2 occurred prior to the divergence of Paeonia species and was followed by a duplication resulting in Adh1A and Adh1B. Concerted evolution appears to be absent between these paralogous loci. Phylogenetic analysis of only the Paeonia Adh exon sequences, positioning the root of the tree between the paralogous genes Adh1 and Adh2, suggests that the first evolutionary split within the genus occurred between the shrubby section Moutan and the other two herbaceous sections Oneapia and Paeonia. Restriction of Adh1B genes to section Moutan may have resulted from deletion of Adh1B from the common ancestor of sections Oneapia and Paeonia. A relative-rate test was designed to compare rates of molecular change among lineages based on the divergence of paralogous genes, and the results indicate a slower rate of evolution within the shrubby section Moutan than in section Oneapia. This may be responsible for the relatively long branch length of section Oneapia and the short branch length between section Moutan and the other two sections found on the Adh, ITS (nrDNA), and matK (cpDNA) phylogenies of the genus. Adh1 and Adh2 intron sequences cannot be aligned, and we therefore carried out separate analyses of Adh1A and Adh2 genes using exon and intron sequences together. The Templeton test suggested that there is not significant incongruence among Adh1A, ITS, and matK data sets, but that these three data sets conflict significantly with Adh2 sequence data. A combined analysis of Adh1A, ITS, and matK sequences produced a tree that is better resolved than that of any individual gene, and congruent with morphology and the results of artificial hybridization. It is therefore considered to be the current best estimate of the species phylogeny. Paraphyly of section Paeonia in the Adh2 gene tree may be caused by longer coalescence times and random sorting of ancestral alleles.

Alcohol Dehydrogenase↗
PubMed1995

Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution.

The internal transcribed spacers (ITS) of nuclear ribosomal DNA of 33 species of genus Paeonia (Paeoniaceae) were sequenced. In section Paeonia, different patterns of nucleotide additivity were detected in 14 diploid and tetraploid species at sites that are variable in the other 12 species of the section, suggesting that reticulate evolution has occurred. Phylogenetic relationships of species that do not show additivity, and thus ostensibly were not derived through hybridization, were reconstructed by parsimony analysis. The taxa presumably derived through reticulate evolution were then added to the phylogenetic tree according to additivity from putative parents. The study provides an example of successfully using ITS sequences to reconstruct reticulate evolution in plants and further demonstrates that the sequence data could be highly informative and accurate for detecting hybridization. Maintenance of parental sequences in the species of hybrid origin is likely due to slowing of concerted evolution caused by the long generation time of peonies. The partial and uneven homogenization of parental sequences displayed in nine species of putative hybrid origin may have resulted from gradients of gene conversion. The documented hybridizations may have occurred since the Pleistocene glaciations. The species of hybrid origin and their putative parents are now distantly allopatric. Reconstruction of reticulate evolution with sequence data, therefore, provides gene records for distributional histories of some of the parental species.

Asia↗