Molecular cloning, characterization and evolutionary analysis of phytoene desaturase (PDS) gene from Haematococcus pluvialis

Phytoene desaturase is one of the most important enzymes necessary for the biosynthesis of carotenoids in some cyanobacteria, green algae and plants. In this study, genomic DNA and cDNA of pds were cloned from unicellular green alga Haematococcus pluvialis strain323 using PCR and RT-PCR methods. The cDNA was cloned into plasmid pET-28a and efficiently expressed in Escherichia coli BL21. The complete genomic PDS gene of H. pluvialis, 3.3 kb in size, included eight exons and seven introns. To locate transcriptional regulation elements, an approximate 1 kb of 5'-flanking region was isolated by genome-walking method. Results of bioinformatic analysis showed several putative cis-elements e.g. the ABRE motif (abscisic acid responsive element), the C-repeat/DRE (dehydration responsive element) motif and the GCN4 motif were located in 5'-flanking region of pds. Results of phylogenetic analyses reveal that different sources of PDS genes form a separate clade, respectively, with 100% bootstrap support. Moreover, a maximum likelihood approach was employed to detect evidence of positive selection in the evolution of PDS genes. Results of branch-site model analysis suggest that 7.9% of sites along the green algal branch are under positive selection, and the PDS gene in green algae exhibits a different evolutionary pattern from its counterparts in cyanobacteria and plants.

Chromosomal rearrangement in Pectinidae revealed by rRNA loci and implications for bivalve evolution

Karyotype and chromosomal localization of major (18-5.8-28S) and minor (5S) ribosomal RNA genes were studied in two species of Pectinidae, zhikong (Chlamys farreri) and bay (Argopecten irradians irradians) scallops. using fluorescence in situ hybridization (FISH). C. farreri had a haploid number of 19 with a karyotype of 3m + 4sm + 7sm-st + 4st + 1st-t, and A. i. irradians had a haploid number of 16 with a karyotype of 5st + 11t. In C. farreri, the major and minor rRNA genes had one locus each and were mapped to the same chromosome-Chromosome 5. In A. i. irradians, the major rRNA genes had two loci, located on Chromosomes 4 and 8, and the 5S rRNA gene was found at a third chromosome-Chromosome 10. Results of this and other studies indicate that karyotype of A. i. irradians (n = 16, 21 arms) is secondary and derived from an ancestral karyotype similar to that of C. farreri (n = 19, 38 arms) through considerable chromosomal loss and rearrangements. The ability to tolerate significant chromosomal loss suggests that the modal karyotype of Pectinidae and possibly other bivalves with a haploid number of 19 is likely tetraploid; i.e., at least one genome duplication has occurred during the evolution of Bivalvia.

Molecular phylogeny of some genera of Pamphagidae (Acridoidea, Orthoptera) from China based on mitochondrial 16S rDNA sequences

Based on the mitochondrial 16S ribosomal DNA partial sequences (473 bp) of 9 species of Pamphagidae (Acridoidea, Orthoptera) from China and of 4 species of Pamphagidae and 2 species of Pyrgomorphidae and Acrididae (as outgroups) retrieved from GenBank, we constructed the molecular phylogeny using the Neighbor Joining (NJ) and Minimum Evolution ( ME) methods based on the nucleotide Kimura 2-parameter model. The results of our study shown that: 1) the ranges of the 16S rDNA nucleotide divergence between two species of a genus were 0.21%, among genera of a subfamily were 0.42-3.38%, and among subfamilies of Pamphagidae were 1.90-8.88%, respectively. The phylogenetic tree shows that: 1) all Pamphagidae taxa form a monophyletic clade, and are well separated from the outgroup; 2) the African taxa Porthetinae (Lobosceliana brevicornis) and Akicerinae (Batrachotetrix sp.) are distinctly separated from the Chinese taxa Prionotropisinae; 3) Haplotropis bruneriana and Glauia terrea of Pamphaginae are nested in the middle of the tree, but their phylogenetic status is uncertain in this study; 4) 8 genera of Asiotmethis, Beybienkia, Mongolotmethis, Sinotmethis, Rhinotmethis, Filchnerella, Eotmethis and Pseudotmethis from China are all grouped into the subfamily Prionotropisinae, but their phylogenetic relationships are not clearly resolved.

Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae)

All taxa endemic to the Qinghai-Tibet Plateau are hypothesized to have originated in situ or from immediately adjacent areas because of the relatively recent formation of the plateau since the Pliocene, followed by the large-scaled biota extinction and recession caused by the Quaternary ice sheet. However, identification of specific progenitors remains difficult for some endemics, especially some endemic genera. Nannoglottis, with about eight species endemic to this region, is one such genus. Past taxonomic treatments have suggested its relationships with four different tribes of Asteraceae. We intend to identify the closest relatives of Nannoglottis by evaluating the level of monophyly, tribal delimitation, and systematic position of the genus by using molecular data from ndhF gene, trnL-F, and ITS region sequences. We find that all sampled species of Nannoglottis are a well-defined monophyly. This supports all recent taxonomic treatments of Nannoglottis, in which all sampled species were placed in one broadly re-circumscribed genus. Nannoglottis is most closely related to the Astereae, but stands as an isolated genus as the first diverging lineage of the tribe, without close relatives. A tentative relationship was suggested for Nannoglottis and the next lineage of the tribe was based on the ITS topology, the "basal group," which consists of seven genera from the Southern Hemisphere. Such a relationship is supported by some commonly shared plesiomorphic morphological characters. Despite the very early divergence of Nannoglottis in the Astereae, the tribe must be regarded to have its origin in Southern Hemisphere rather than in Asia, because based on all morphological, molecular, biogeographical, and fossil data, the Asteraceae and its major lineages (tribes) are supposed to have originated in the former area. Long-distance dispersal using Southeast Asia as a steppingstone from Southern Hemisphere to the Qinghai-Tibet Plateau is the most likely explanation for this unusual biogeographic link of Nannoglottis. The 23-32-million-year divergence time between Nannoglottis and the other Astereae estimated by DNA sequences predated the formation of the plateau. This estimation is further favored by the fossil record of the Asteraceae and the possible time of origin of the Astereae. Nannoglottis seems to have reached the Qinghai-Tibet area in the Oligocene-Eocene and then re-diversified with the uplift of the plateau. The molecular infragenetic phylogeny of the genus identifies two distinct clades, which reject the earlier infrageneric classification based on the arrangement of the involucral bracts and the length of the ligules, but agree well with the habits and ecological preferences of its current species. The "alpine shrub" vs. "coniferous forest" divergence within Nannoglottis was estimated at about 3.4 million years ago when the plateau began its first large-scale uplifting and the coniferous vegetation began to appear. Most of the current species at the "coniferous forest" clade of the genus are estimated to have originated from 1.02 to 1.94 million years ago, when the second and third uprisings of the plateau occurred, the climate oscillated and the habitats were strongly changed. The assumed evolution, speciation diversity, and radiation of Nannoglottis based on molecular phylogeny and divergence times agree well with the known geological and paleobotanical histories of the Qinghai-Tibet Plateau. (C) 2002 Elsevier Science (USA). All rights reserved.

Molecular evidence for the sister relationship of the eastern Asia-North American intercontinental species pair in the Podophyllum group (Berberidaceae)

The presumed pair relationships of intercontinental vicariad species in the Podophyllum group (Sinopodophyllum hexandrum vs. Podophyllum pelatum and Diphylleia grayi vs. D. cymosa) were recently, considered to be paraphyletic. In the present paper, the trnL-F and ITS gene sequences of the representatives were used to examine the sister relationships of these two vicariad species. A heuristic parsimony analysis based on the trnLF data identified Diphylleia as the basal clade of the other three genera, but provided poor resolution of their inter-relationships. High sequence divergence was found in the ITS data. ITS1 region, more variable but parsimonyuninformative. has no phylogenetic value, Sequence divergence of the ITS2 region provided abundant, phylogenetically informative variable characters. Analysis of ITS2 sequences confirmeda sister relationship between the presumable vicariad species, in spite of a low bootstrap support for Sinopodophyllum hexandrum vs. Podophyllum pelatum. The combined ITS2 and trnL-F data enforced a sister relationship between Sinopodophyllum hexandrum and Podophyllum pelatum with an elevated bootstrap support of 100%. Based on molecular phylogeny, the morphological evolution of this group was discussed. The self-pollination might have evolved from cross-fertilization two times in this group. The different pollination and seed dispersal systems of Sinopodophyllum hexandrum and Podophlyllum pelatum resulted from their adaptations to different ecological habitats. The divergence time of Sinopodophyllum hexandrum-Podophyllum pelatum is estimated to be 6.52+/-1.89 myr based on the ITS divergence. The divergence of this species pair predated or co-occurred with the recent uplift of the Himalayas 4-3 myr during the late Miocene and the formation of the alpine habitats. Sinopodophyllum hexandrum developed a host of specialized characters in its subsequent adaptation to the arid alpine surroundings. The present study confirmed the different patterns of species relationship between Asian-North American disjuncts. The isolation of plant elements between North America and eastern Asia must have been a gradual process, resulting in the different phylogenetic patterns and divergence times of the disjuncts.

Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences

The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e., represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau, On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister tars of one steppe? dweller and one shrub dweller is very low. These findings support the hypothesis that pikes have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution. (C) 2000 Academic Press.

Time-dependent wavepacket approach to the influence of intense fields on the population of molecular excited states

The influence of laser-field parameters, such as intensity and pulse width, on the population of molecular excited state is investigated by using the time-dependent wavepacket method. For a two-state system in intense laser fields, the populations in the upper and lower states are given by the wavefunctions obtained by solving the Schrodinger equation through split-operator scheme. The calculation shows that both the laser intensity and the pulse width have a strong effect on the population in molecular excited state, and that as the common feature of light-matter interaction (LMI), the periodic changing of the population with the evolution time in each state can be interpreted by Rabi oscillation and area-theorem. The results illustrate that by controlling these two parameters, the needed population in excited state of interest can be obtained, which provides the foundation of light manipulation of molecular processes. (C) 2005 Elsevier B.V. All rights reserved.