Complete chloroplast genome sequence of Holoparasite Cistanche Deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from Its host Haloxylon Ammodendron (Chenopodiaceae)

The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. The authors report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae

The Mitochondrial Genome of the Legume Vigna radiata and the Analysis of Recombination across Short Mitochondrial Repeats

The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean), and show that despite its unexceptional size (401,262 nt), the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38–297 nt) repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes

Mosaic Origins of a Complex Chimeric Mitochondrial Gene in Silene vulgaris

Chimeric genes are significant sources of evolutionary innovation that are normally created when portions of two or more protein coding regions fuse to form a new open reading frame. In plant mitochondria astonishingly high numbers of different novel chimeric genes have been reported, where they are generated through processes of rearrangement and recombination. Nonetheless, because most studies do not find or report nucleotide variation within the same chimeric gene, evolution after the origination of these chimeric genes remains unstudied. Here we identify two alleles of a complex chimera in Silene vulgaris that are divergent in nucleotide sequence, genomic position relative to other mitochondrial genes, and expression patterns. Structural patterns suggest a history partially influenced by gene conversion between the chimeric gene and functional copies of subunit 1 of the mitochondrial ATP synthase gene (atp1). We identified small repeat structures within the chimeras that are likely recombination sites allowing generation of the chimera. These results establish the potential for chimeric gene divergence in different plant mitochondrial lineages within the same species. This result contrasts with the absence of diversity within mitochondrial chimeras found in crop species

Noniterative density functional response approach: application to nonlinear optical properties of p-nitroaniline and its methyl-substituted derivatives

We report the effect of substitution, position of the substituent, and the symmetry on the nonlinear optical properties of p-nitroanline (PNA) and its derivatives using our implementation of the noniterative approximation of couple-perturbed Kohn-Sham (CPKS) equation in the deMon2k. Dipole moment, static polarizability, and first hyperpolarizability of these p-conjugated donor-acceptor organic derivatives of PNA and its methyl-substituted analogs are calculated using our method at different exchange correlation functionals, namely, BP86, BPW91, and BLYP, using 6-31++G∗∗ basis set. A comparison of results obtained by our method with those obtained by MP2 (finite-field perturbation) method is presented in this paper. The effect of optical gap on charge transfer and subsequently on polarizabilities has been illustrated

Comparison of the auxiliary density perturbation theory and the noniterative approximation to the coupled perturbed Kohn-Sham method: case study of the polarizabilities of disubstituted azoarene molecules

We present a theoretical study of the polarizabilities of free and disubstituted azoarenes employing auxiliary density perturbation theory (ADPT) and the noniterative approximation to the coupled perturbed Kohn-Sham (NIA-CPKS) method. Both methods are noniterative but use different approaches to obtain the perturbed density matrix. NIA-CPKS is different from the conventional CPKS approach in that the perturbed Kohn-Sham matrix is obtained numerically, thereby yielding a single-step solution to CPKS. ADPT is an alternative approach to the analytical CPKS method in the framework of the auxiliary density functional theory. It is shown that the polarizabilities obtained using these two methods are in good agreement with each other. Comparisons are made for disubstituted azoarenes, which give support to the push-pull mechanism. Both methods reproduce the same trend for polarizabilities because of the substitution pattern of the azoarene moiety. Our results are consistent with the standard organic chemistry "activating/deactivating"sequence. We present the polarizabilities of the above molecules calculated with three different exchange-correlation functionals and two different auxiliary function sets. The computational advantages of both methods are also discussed